Start: 2024-03-28 00:20:14 GMT [testing] Package: r-bioc-hdf5array Version: 1.26.0-1 Installed-Size: 9027 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-delayedarray (>= 0.15.16), r-bioc-rhdf5 (>= 2.31.6), r-cran-matrix, r-bioc-rhdf5filters, r-bioc-biocgenerics (>= 0.31.5), r-bioc-s4vectors (>= 0.27.13), r-bioc-iranges, r-bioc-rhdf5lib, libc6 (>= 2.14), libhdf5-103-1, libhdf5-hl-100 Suggests: r-bioc-biocparallel, r-bioc-genomicranges, r-bioc-summarizedexperiment (>= 1.15.1), r-bioc-experimenthub, r-bioc-genomicfeatures, r-cran-runit, r-bioc-singlecellexperiment Description: HDF5 backend for DelayedArray objects Homepage: https://bioconductor.org/packages/HDF5Array/ Description-md5: 75935fc5e97c3a902de41900a4e583c7 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-hdf5array/r-bioc-hdf5array_1.26.0-1_amd64.deb Size: 8748140 MD5sum: ff56a7ec0da6489352a574a6bf979b3e SHA256: 7804052a22bfef2fd71ed88b24094d93530d90d8475357481fbed14cab7d4915 [sid] Package: r-bioc-hdf5array Source: r-bioc-hdf5array (1.30.1-1) Version: 1.30.1-1+b1 Installed-Size: 9041 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-delayedarray (>= 0.27.2), r-bioc-rhdf5 (>= 2.31.6), r-cran-matrix, r-bioc-rhdf5filters, r-bioc-biocgenerics (>= 0.31.5), r-bioc-s4vectors (>= 0.27.13), r-bioc-iranges, r-bioc-s4arrays (>= 1.1.1), r-bioc-rhdf5lib, libc6 (>= 2.14), libhdf5-103-1t64, libhdf5-hl-100t64 Suggests: r-bioc-biocparallel, r-bioc-genomicranges, r-bioc-summarizedexperiment (>= 1.15.1), r-bioc-experimenthub, r-bioc-genomicfeatures, r-cran-runit, r-bioc-singlecellexperiment, r-bioc-delayedmatrixstats, r-bioc-genefilter Description: HDF5 backend for DelayedArray objects Homepage: https://bioconductor.org/packages/HDF5Array/ Description-md5: 75935fc5e97c3a902de41900a4e583c7 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-hdf5array/r-bioc-hdf5array_1.30.1-1+b1_amd64.deb Size: 8764408 MD5sum: a4810de98a065082dbbe2b56aefc7004 SHA256: 800996585c7ab38460303800a534dc6b3ca27b7e94c32916f3e3df947a0289bb 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/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-hdf5array=1.30.1-1+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 1.4.1~202403190841~1.4-4-g85045c69 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/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-hdf5array=1.30.1-1+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/tmprjb_x4so 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmprjb_x4so 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmprjb_x4so/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'update'] 0m1.9s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-yf', 'dist-upgrade'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s INFO: Running scripts post_setup 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_dummy_users'] 0m4.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_dummy_users'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.22-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 0m4.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 0m4.6s INFO: Running scripts is_testable 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s INFO: Running scripts pre_test 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_test_root_password'] 0m4.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_test_root_password'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-hdf5array'] 0m4.9s DUMP: Package: r-bioc-hdf5array Version: 1.26.0-1 Installed-Size: 9027 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-api-bioc-3.16, r-bioc-delayedarray (>= 0.15.16), r-bioc-rhdf5 (>= 2.31.6), r-cran-matrix, r-bioc-rhdf5filters, r-bioc-biocgenerics (>= 0.31.5), r-bioc-s4vectors (>= 0.27.13), r-bioc-iranges, r-bioc-rhdf5lib, libc6 (>= 2.14), libhdf5-103-1, libhdf5-hl-100 Suggests: r-bioc-biocparallel, r-bioc-genomicranges, r-bioc-summarizedexperiment (>= 1.15.1), r-bioc-experimenthub, r-bioc-genomicfeatures, r-cran-runit, r-bioc-singlecellexperiment Description-en: HDF5 backend for DelayedArray objects Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed. Description-md5: 75935fc5e97c3a902de41900a4e583c7 Homepage: https://bioconductor.org/packages/HDF5Array/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-hdf5array/r-bioc-hdf5array_1.26.0-1_amd64.deb Size: 8748140 MD5sum: ff56a7ec0da6489352a574a6bf979b3e SHA256: 7804052a22bfef2fd71ed88b24094d93530d90d8475357481fbed14cab7d4915 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-hdf5array'] 0m4.9s INFO: apt-cache knows about the following packages: r-bioc-hdf5array 0m4.9s INFO: Running scripts pre_install 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 0m5.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 0m5.0s DUMP: r-bioc-hdf5array: Installed: (none) Candidate: 1.26.0-1 Version table: 1.26.0-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array'] 0m25.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core hdf5-helpers libaec-dev libaec0 libblas3 libblosc1 libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libcurl4-openssl-dev libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice6 libicu72 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libnsl-dev libnsl2 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 libsnappy1v5 libssh2-1 libssl-dev libssl3 libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev openssl r-base-core r-bioc-biocgenerics r-bioc-delayedarray r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-s4vectors r-cran-lattice r-cran-matrix r-cran-matrixstats readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: glibc-doc manpages-dev libcurl4-doc libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config low-memory-monitor krb5-doc krb5-user libhdf5-doc libssl-doc tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-genomicranges r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit r-bioc-biocparallel r-bioc-genefilter r-bioc-summarizedexperiment r-cran-lobstr r-bioc-delayedmatrixstats r-cran-knitr r-cran-rmarkdown r-bioc-biocstyle r-bioc-experimenthub r-bioc-genomicfeatures r-bioc-singlecellexperiment r-bioc-xvector r-bioc-genomicalignments r-bioc-sparsematrixstats r-cran-testthat r-cran-bit64 r-cran-dplyr r-cran-ggplot2 r-cran-mockery r-cran-tinytest r-bioc-shortread r-bioc-graph r-cran-data.table r-cran-base64enc r-cran-markdown r-cran-r.devices r-cran-r.rsp readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-cran-knitr r-cran-rmarkdown r-bioc-biocstyle r-cran-runit 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 hdf5-helpers libaec-dev libaec0 libblas3 libblosc1 libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libcurl4-openssl-dev libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice6 libicu72 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libnsl-dev libnsl2 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 libsnappy1v5 libssh2-1 libssl-dev libssl3 libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev openssl r-base-core r-bioc-biocgenerics r-bioc-delayedarray r-bioc-hdf5array r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-s4vectors r-cran-lattice r-cran-matrix r-cran-matrixstats readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 93.8 MB of archives. After this operation, 229 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:18 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libblosc1 amd64 1.21.3+ds-1 [49.3 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u4 [45.4 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.76-1 [1930 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:29 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u4 [1897 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u5 [390 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-10+deb12u5 [491 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.11-1~deb12u2 [2430 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:92 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:105 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5lib amd64 1.20.0+dfsg-1 [102 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5filters amd64 1.10.0+dfsg-1 [120 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhdf5 amd64 2.42.0+dfsg-1 [792 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 r-bioc-hdf5array amd64 1.26.0-1 [8748 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.8 MB in 1s (81.0 MB/s) Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6102 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libssl3:amd64. 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Preparing to unpack .../099-libxt6_1%3a1.2.1-1.1_amd64.deb ... Unpacking libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package zip. Preparing to unpack .../100-zip_3.0-13_amd64.deb ... Unpacking zip (3.0-13) ... Selecting previously unselected package unzip. Preparing to unpack .../101-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../102-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../103-r-base-core_4.2.2.20221110-2_amd64.deb ... Unpacking r-base-core (4.2.2.20221110-2) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../104-r-bioc-biocgenerics_0.44.0-2_all.deb ... Unpacking r-bioc-biocgenerics (0.44.0-2) ... Selecting previously unselected package r-cran-lattice. Preparing to unpack .../105-r-cran-lattice_0.20-45-3_amd64.deb ... Unpacking r-cran-lattice (0.20-45-3) ... Selecting previously unselected package r-cran-matrix. Preparing to unpack .../106-r-cran-matrix_1.5-3-1_amd64.deb ... Unpacking r-cran-matrix (1.5-3-1) ... Selecting previously unselected package r-cran-matrixstats. Preparing to unpack .../107-r-cran-matrixstats_0.63.0-1_amd64.deb ... Unpacking r-cran-matrixstats (0.63.0-1) ... Selecting previously unselected package r-bioc-matrixgenerics. Preparing to unpack .../108-r-bioc-matrixgenerics_1.10.0-1_all.deb ... Unpacking r-bioc-matrixgenerics (1.10.0-1) ... Selecting previously unselected package r-bioc-s4vectors. Preparing to unpack .../109-r-bioc-s4vectors_0.36.1-1_amd64.deb ... Unpacking r-bioc-s4vectors (0.36.1-1) ... Selecting previously unselected package r-bioc-iranges. Preparing to unpack .../110-r-bioc-iranges_2.32.0-1_amd64.deb ... Unpacking r-bioc-iranges (2.32.0-1) ... Selecting previously unselected package r-bioc-delayedarray. Preparing to unpack .../111-r-bioc-delayedarray_0.24.0+dfsg-1_amd64.deb ... Unpacking r-bioc-delayedarray (0.24.0+dfsg-1) ... Selecting previously unselected package r-bioc-rhdf5lib. Preparing to unpack .../112-r-bioc-rhdf5lib_1.20.0+dfsg-1_amd64.deb ... Unpacking r-bioc-rhdf5lib (1.20.0+dfsg-1) ... Selecting previously unselected package r-bioc-rhdf5filters. Preparing to unpack .../113-r-bioc-rhdf5filters_1.10.0+dfsg-1_amd64.deb ... Unpacking r-bioc-rhdf5filters (1.10.0+dfsg-1) ... Selecting previously unselected package r-bioc-rhdf5. Preparing to unpack .../114-r-bioc-rhdf5_2.42.0+dfsg-1_amd64.deb ... Unpacking r-bioc-rhdf5 (2.42.0+dfsg-1) ... Selecting previously unselected package r-bioc-hdf5array. Preparing to unpack .../115-r-bioc-hdf5array_1.26.0-1_amd64.deb ... Unpacking r-bioc-hdf5array (1.26.0-1) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up linux-libc-dev:amd64 (6.1.76-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up libsnappy1v5:amd64 (1.1.9-3) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up zip (3.0-13) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libssl-dev:amd64 (3.0.11-1~deb12u2) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libblosc1:amd64 (1.21.3+ds-1) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libc-dev-bin (2.36-9+deb12u4) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libaec-dev:amd64 (1.0.6-1+b1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up ucf (3.0043+nmu1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u5) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up libcurl4-openssl-dev:amd64 (7.88.1-10+deb12u5) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up libhdf5-fortran-102:amd64 (1.10.8+repack1-1) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1) ... Setting up libc6-dev:amd64 (2.36-9+deb12u4) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up r-cran-matrixstats (0.63.0-1) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up r-bioc-rhdf5lib (1.20.0+dfsg-1) ... Setting up r-bioc-rhdf5filters (1.10.0+dfsg-1) ... Setting up r-bioc-rhdf5 (2.42.0+dfsg-1) ... Setting up r-bioc-hdf5array (1.26.0-1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array'] 0m25.0s INFO: Running scripts post_install 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 0m25.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 0m25.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 0m25.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmprjb_x4so to sid 0m25.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m25.5s INFO: Running scripts pre_distupgrade 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'update'] 0m30.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9941 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7210 kB] Fetched 17.3 MB in 3s (4979 kB/s) Reading package lists... 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'update'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-yf', 'dist-upgrade'] 1m6.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libglib2.0-0 libnsl-dev libnsl2 libquadmath0 libtirpc-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libcurl4 libdb5.3 libext2fs2 libgnutls30 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhogweed6 libnettle8 libpng16-16 libpsl5 libreadline8 libssh2-1 libssl3 libtirpc3 libxt6 The following NEW packages will be installed: fonts-dejavu-mono gcc-14-base libapt-pkg6.0t64 libcurl4t64 libdb5.3t64 libext2fs2t64 libglib2.0-0t64 libgnutls30t64 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libhogweed6t64 libnettle8t64 libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libssh2-1t64 libssl3t64 libtirpc3t64 libunistring5 libxt6t64 r-bioc-s4arrays r-bioc-sparsearray r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-crayon 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-12-base gpgv grep gzip hdf5-helpers hostname init-system-helpers libacl1 libaec-dev libaec0 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libblosc1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcom-err2 libcrypt-dev libcrypt1 libcurl4-openssl-dev libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgfortran5 libglib2.0-0 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-dev libicu72 libidn2-0 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 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 libpcre2-8-0 libpixman-1-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsnappy1v5 libss2 libssl-dev libstdc++6 libsystemd0 libsz2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libudev1 libuuid1 libwebp7 libx11-6 libx11-data libxft2 libxxhash0 libzstd1 linux-libc-dev login logsave mawk mount ncurses-base ncurses-bin openssl passwd perl-base r-base-core r-bioc-biocgenerics r-bioc-delayedarray r-bioc-hdf5array r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-s4vectors r-cran-lattice r-cran-matrix r-cran-matrixstats readline-common sed sensible-utils sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra zlib1g zlib1g-dev 165 upgraded, 31 newly installed, 20 to remove and 0 not upgraded. Need to get 130 MB of archives. After this operation, 17.6 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 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-11 [97.4 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3+b1 [67.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.2 [10.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.2 [189 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libcurl4-openssl-dev amd64 8.6.0-4 [534 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libssl-dev amd64 3.1.5-1.1 [2474 kB] Get:14 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.6.0-4 [430 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libhdf5-dev amd64 1.10.10+repack-3.2 [2642 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.2 [1244 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.2 [63.2 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get:23 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:24 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:25 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240315-1 [42.9 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240315-1 [72.2 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240315-1 [836 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.2 [89.6 kB] Get:29 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:30 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:32 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:33 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:34 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.6-5-1 [3789 kB] Get:35 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2062 kB] Get:36 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.36.0-1 [2258 kB] Get:37 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [504 kB] Get:38 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.2.0-1 [484 kB] Get:39 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get:40 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get:41 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.42.0-1 [622 kB] Get:42 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1196 kB] Get:43 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1794 kB] Get:44 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5lib amd64 1.24.2+dfsg-1+b1 [103 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240315-1 [713 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.1.10-1+b1 [27.6 kB] Get:48 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libblosc1 amd64 1.21.5+ds-1+b1 [49.6 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:51 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5filters amd64 1.14.1+dfsg-3 [139 kB] Get:52 http://deb.debian.org/debian sid/main amd64 r-bioc-rhdf5 amd64 2.46.1+dfsg-1+b1 [843 kB] Get:53 http://deb.debian.org/debian sid/main amd64 r-bioc-hdf5array amd64 1.30.1-1+b1 [8764 kB] Get:54 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.2 [40.5 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.2 [131 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.2 [21.3 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2+b2 [290 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libjpeg-dev amd64 1:2.1.5-2+b2 [72.1 kB] Get:61 http://deb.debian.org/debian sid/main amd64 hdf5-helpers amd64 1.10.10+repack-3.2 [23.4 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:72 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.9.1-2.2 [296 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 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1+b1 [1426 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.14 [986 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:81 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1+b1 [364 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1+b1 [126 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b3 [10.2 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2+b1 [75.0 kB] Get:89 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:94 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3.2 [1643 kB] Get:95 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:96 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:98 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b3 [90.3 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:102 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:103 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:104 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-3 [649 kB] Get:105 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:107 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.14 [1370 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1+b1 [74.1 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.4-6 [275 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-11 [160 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-11 [191 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-6 [1222 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b2 [438 kB] Get:120 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:121 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:122 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3 [530 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-3 [278 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:131 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:134 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240315-1 [136 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [35.1 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [216 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [48.3 kB] Get:141 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:143 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:146 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:152 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:156 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:157 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.3.3-3+b1 [26.8 MB] Get:158 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.2 [82.6 kB] Get:159 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b1 [40.4 kB] Get:160 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.7.9-2 [2255 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:163 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:164 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:165 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.6 [1510 kB] Get:166 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:167 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:168 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:169 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:170 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:171 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:172 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:173 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:174 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-11 [117 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-11 [30.2 kB] Get:177 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-11 [155 kB] Get:178 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-11 [1231 kB] Get:179 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] Get:180 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:181 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:182 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:183 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.4 [20.1 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.4 [206 kB] Get:185 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.4 [571 kB] Get:186 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-11 [143 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:191 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:192 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240315-1 [147 kB] Get:194 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-15 [41.8 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2.4 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 130 MB in 1s (112 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12202 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (12.4+deb12u5) ... Setting up base-files (13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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Unpacking openssl (3.1.5-1.1) over (3.0.11-1~deb12u2) ... dpkg: libcurl4:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libcurl4 (>= 7.28.0). libhdf5-103-1:amd64 depends on libcurl4 (>= 7.16.2). (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 ... 12204 files and directories currently installed.) Removing libcurl4:amd64 (7.88.1-10+deb12u5) ... Selecting previously unselected package libcurl4t64:amd64. (Reading database ... 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Unpacking libhdf5-dev (1.10.10+repack-3.2) over (1.10.8+repack1-1) ... dpkg: libhdf5-103-1:amd64: dependency problems, but removing anyway as you requested: r-bioc-rhdf5lib depends on libhdf5-103-1. r-bioc-rhdf5 depends on libhdf5-103-1. r-bioc-hdf5array depends on libhdf5-103-1. libhdf5-hl-100:amd64 depends on libhdf5-103-1. libhdf5-fortran-102:amd64 depends on libhdf5-103-1. libhdf5-cpp-103-1:amd64 depends on libhdf5-103-1. (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 ... 12183 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14-20240315-1_amd64.deb ... Unpacking gcc-14-base:amd64 (14-20240315-1) ... Setting up gcc-14-base:amd64 (14-20240315-1) ... (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 ... 12406 files and directories currently installed.) Preparing to unpack .../libsnappy1v5_1.1.10-1+b1_amd64.deb ... Unpacking libsnappy1v5:amd64 (1.1.10-1+b1) over (1.1.9-3) ... Preparing to unpack .../liblz4-1_1.9.4-1+b2_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1+b2) over (1.9.4-1) ... Setting up liblz4-1:amd64 (1.9.4-1+b2) ... (Reading database ... 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Preparing to unpack .../r-bioc-biocgenerics_0.48.1-2_all.deb ... Unpacking r-bioc-biocgenerics (0.48.1-2) over (0.44.0-2) ... (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 ... 12424 files and directories currently installed.) Removing libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-fortran-100t64:amd64. (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 ... 12416 files and directories currently installed.) Preparing to unpack .../0-libhdf5-cpp-103-1t64_1.10.10+repack-3.2_amd64.deb ... Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.2) ... Selecting previously unselected package libhdf5-hl-cpp-100t64:amd64. Preparing to unpack .../1-libhdf5-hl-cpp-100t64_1.10.10+repack-3.2_amd64.deb ... Unpacking libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.2) ... Preparing to unpack .../2-libjpeg62-turbo-dev_1%3a2.1.5-2+b2_amd64.deb ... Unpacking libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) over (1:2.1.5-2) ... Preparing to unpack .../3-libjpeg62-turbo_1%3a2.1.5-2+b2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2+b2) over (1:2.1.5-2) ... Preparing to unpack .../4-libjpeg-dev_1%3a2.1.5-2+b2_amd64.deb ... Unpacking libjpeg-dev:amd64 (1:2.1.5-2+b2) over (1:2.1.5-2) ... Preparing to unpack .../5-hdf5-helpers_1.10.10+repack-3.2_amd64.deb ... Unpacking hdf5-helpers (1.10.10+repack-3.2) over (1.10.8+repack1-1) ... (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 ... 12431 files and directories currently installed.) Preparing to unpack .../00-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../01-libssh2-1t64_1.11.0-4.1+b1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Preparing to unpack .../02-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) over (1.0.9-2+b6) ... Preparing to unpack .../03-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) over (1.20.1-2+deb12u1) ... Preparing to unpack .../04-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) over (1.20.1-2+deb12u1) ... Preparing to unpack .../05-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) over (1.20.1-2+deb12u1) ... Preparing to unpack .../06-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) over (1.20.1-2+deb12u1) ... Preparing to unpack .../07-libcom-err2_1.47.0-2.4_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2.4) over (1.47.0-2) ... Preparing to unpack .../08-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.3-2) ... Preparing to unpack .../09-librtmp1_2.4+20151223.gitfa8646d.1-2+b3_amd64.deb ... 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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 ... 12450 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... Setting up libhogweed6t64:amd64 (3.9.1-2.2) ... (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 ... 12409 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.14) ... Setting up libapt-pkg6.0t64:amd64 (2.7.14) ... (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 ... 12459 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.3-2) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.10.3-2) ... (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 ... 12459 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.0-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.6.0-0.2) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.6.0-0.2) ... (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 ... 12459 files and directories currently installed.) Preparing to unpack .../libsystemd0_255.4-1+b1_amd64.deb ... Unpacking libsystemd0:amd64 (255.4-1+b1) over (252.22-1~deb12u1) ... Setting up libsystemd0: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 ... 12460 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1+b1_amd64.deb ... Unpacking libudev1:amd64 (255.4-1+b1) over (252.22-1~deb12u1) ... 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 ... 12461 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 (0.8.1-1) ... 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 ... 12462 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271+b3_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.271+b3) over (0.270) ... Setting up libdebconfclient0:amd64 (0.271+b3) ... (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 ... 12463 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4+b1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4+b1) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4+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 ... 12464 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2+b1_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2+b1) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2+b1) ... (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 ... 12450 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) over (3.4.4-1) ... 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 ... 12451 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... 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 ... 12445 files and directories currently installed.) Preparing to unpack .../0-libdb5.3t64_5.3.28+dfsg2-6_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Preparing to unpack .../1-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../2-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) over (2.1.28+dfsg-10) ... Preparing to unpack .../3-libldap-2.5-0_2.5.16+dfsg-2_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.16+dfsg-2) over (2.5.13+dfsg-5) ... Preparing to unpack .../4-libnghttp2-14_1.59.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.59.0-1+b1) over (1.52.0-1+deb12u1) ... Preparing to unpack .../5-libglib2.0-0_2.78.4-6_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.78.4-6) over (2.74.6-2) ... Preparing to unpack .../6-libblkid1_2.39.3-11_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-11) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-11) ... (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 ... 12429 files and directories currently installed.) Preparing to unpack .../00-libglib2.0-0t64_2.78.4-6_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.78.4-6) ... Preparing to unpack .../01-libfreetype6_2.13.2+dfsg-1+b2_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.2+dfsg-1+b2) over (2.12.1+dfsg-5) ... Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) over (2.37-6) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../03-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Preparing to unpack .../04-fontconfig-config_2.15.0-1.1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1) over (2.14.1-4) ... Preparing to unpack .../05-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) over (2.5.0-1) ... Preparing to unpack .../06-libfontconfig1_2.15.0-1.1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1) over (2.14.1-4) ... Preparing to unpack .../07-libpixman-1-0_0.42.2-1+b1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1+b1) over (0.42.2-1) ... Preparing to unpack .../08-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) over (2:1.8.4-2+deb12u2) ... Preparing to unpack .../09-libx11-6_2%3a1.8.7-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.7-1) over (2:1.8.4-2+deb12u2) ... Preparing to unpack .../10-libcairo2_1.18.0-3_amd64.deb ... Unpacking libcairo2:amd64 (1.18.0-3) over (1.16.0-7) ... dpkg: libpng16-16:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libpng16-16 (>= 1.6.2-1). (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 ... 12468 files and directories currently installed.) Removing libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libpng16-16t64: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 ... 12457 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-3_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-3) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libreadline8 (>= 6.0). (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 ... 12469 files and directories currently installed.) Removing libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libreadline8t64: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 ... 12456 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) over (8.2-1.3) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.4-4) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... dpkg: libxt6:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libxt6. (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 ... 12477 files and directories currently installed.) Removing libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package libxt6t64:amd64. (Reading database ... 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Unpacking libthai-data (0.1.29-2) over (0.1.29-1) ... Preparing to unpack .../11-libdatrie1_0.2.13-3_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3) over (0.2.13-2+b1) ... Preparing to unpack .../12-libthai0_0.1.29-2_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-2) over (0.1.29-1) ... Preparing to unpack .../13-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) over (2024a-0+deb12u1) ... Preparing to unpack .../14-libtcl8.6_8.6.14+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1) over (8.6.13+dfsg-2) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../15-libsharpyuv0_1.3.2-0.4+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Preparing to unpack .../16-libwebp7_1.3.2-0.4+b1_amd64.deb ... Unpacking libwebp7:amd64 (1.3.2-0.4+b1) over (1.2.4-0.2+deb12u1) ... Preparing to unpack .../17-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) over (1.14-1) ... 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(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 ... 11728 files and directories currently installed.) Removing libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:amd64. (Reading database ... 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Preparing to unpack .../libnsl2_1.3.0-3+b1_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b1) over (1.3.0-2) ... Preparing to unpack .../linux-libc-dev_6.7.9-2_all.deb ... Unpacking linux-libc-dev (6.7.9-2) over (6.1.76-1) ... Preparing to unpack .../libc6_2.37-15.1_amd64.deb ... Unpacking libc6:amd64 (2.37-15.1) over (2.36-9+deb12u4) ... Setting up libc6:amd64 (2.37-15.1) ... (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 ... 13390 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-15.1_amd64.deb ... Unpacking libc-bin (2.37-15.1) over (2.36-9+deb12u4) ... Setting up libc-bin (2.37-15.1) ... (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 ... 13390 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3.1_amd64.deb ... Unpacking coreutils (9.4-3.1) over (9.1-1) ... 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 ... 13384 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6_amd64.deb ... Unpacking dash (0.5.12-6) over (0.5.12-2) ... Setting up dash (0.5.12-6) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (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 ... 13382 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_amd64.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (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 ... 13384 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.9.0-4) ... 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 ... 13384 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1.1_amd64.deb ... Unpacking gzip (1.12-1.1) over (1.12-1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1.1) ... (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 ... 13384 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu2_amd64.deb ... Unpacking hostname (3.23+nmu2) over (3.23+nmu1) ... Setting up hostname (3.23+nmu2) ... (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 ... 13383 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-bin (6.4+20240113-1) ... (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 ... 13383 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-2_amd64.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (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 ... 13383 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-11_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.3-11) over (2.38.1-5+b1) ... Setting up libsmartcols1:amd64 (2.39.3-11) ... (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 ... 13382 files and directories currently installed.) Preparing to unpack .../libuuid1_2.39.3-11_amd64.deb ... Unpacking libuuid1:amd64 (2.39.3-11) over (2.38.1-5+b1) ... Setting up libuuid1:amd64 (2.39.3-11) ... (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 ... 13381 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.3-11_amd64.deb ... Unpacking util-linux-extra (2.39.3-11) over (2.38.1-5+b1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty Setting up util-linux-extra (2.39.3-11) ... (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 ... 13386 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-11_amd64.deb ... Unpacking util-linux (2.39.3-11) over (2.38.1-5+b1) ... Setting up util-linux (2.39.3-11) ... (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 ... 13388 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (37~deb12u1) ... Setting up usr-is-merged (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 ... 13388 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.65.2) ... 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 ... 13388 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1_all.deb ... Unpacking ncurses-base (6.4+20240113-1) over (6.4-4) ... Setting up ncurses-base (6.4+20240113-1) ... (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 ... 13386 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_amd64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... (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 ... 13386 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4_amd64.deb ... Unpacking logsave (1.47.0-2.4) over (1.47.0-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2). (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 ... 13386 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2) ... Selecting previously unselected package libext2fs2t64: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 ... 13379 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4_amd64.deb ... 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 (1.47.0-2) ... 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 .../mount_2.39.3-11_amd64.deb ... Unpacking mount (2.39.3-11) over (2.38.1-5+b1) ... Preparing to unpack .../libpam-runtime_1.5.3-6_all.deb ... Unpacking libpam-runtime (1.5.3-6) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-6) ... (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 ... 13391 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-1_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-1) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-1) ... (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 ... 13391 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-2) ... (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 ... 13391 files and directories currently installed.) Preparing to unpack .../0-mawk_1.3.4.20240123-1_amd64.deb ... Unpacking mawk (1.3.4.20240123-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../1-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) over (0.0.17+nmu1) ... Preparing to unpack .../2-libquadmath0_14-20240315-1_amd64.deb ... Unpacking libquadmath0:amd64 (14-20240315-1) over (12.2.0-14) ... Preparing to unpack .../3-gcc-12-base_12.3.0-15_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-15) over (12.2.0-14) ... Preparing to unpack .../4-libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) over (0.11.7-2) ... Preparing to unpack .../5-libss2_1.47.0-2.4_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2.4) over (1.47.0-2) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up hdf5-helpers (1.10.10+repack-3.2) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libtirpc-common (1.3.4+ds-1.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.59.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up linux-libc-dev (6.7.9-2) ... Setting up libgomp1:amd64 (14-20240315-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libsnappy1v5:amd64 (1.1.10-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up gcc-12-base:amd64 (12.3.0-15) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 28 00:21:13 UTC 2024. Universal Time is now: Thu Mar 28 00:21:13 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libglib2.0-0t64:amd64 (2.78.4-6) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libquadmath0:amd64 (14-20240315-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:amd64 (3.1.5-1.1) ... Setting up libpng16-16t64:amd64 (1.6.43-3) ... Setting up libss2:amd64 (1.47.0-2.4) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-lgc-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/57-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/58-dejavu-lgc-sans-mono.conf ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up logsave (1.47.0-2.4) ... Setting up libgfortran5:amd64 (14-20240315-1) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Setting up mount (2.39.3-11) ... Setting up sensible-utils (0.0.22) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up libblosc1:amd64 (1.21.5+ds-1+b1) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libthai-data (0.1.29-2) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Setting up libc-dev-bin (2.37-15.1) ... Setting up openssl (3.1.5-1.1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libglib2.0-0:amd64 (2.78.4-6) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libaec-dev:amd64 (1.1.3-1) ... Setting up e2fsprogs (1.47.0-2.4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 8 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libc6-dev:amd64 (2.37-15.1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.2) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libcairo2:amd64 (1.18.0-3) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.2) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up libnsl2:amd64 (1.3.0-3+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libcurl4t64:amd64 (8.6.0-4) ... Setting up libjpeg-dev:amd64 (1:2.1.5-2+b2) ... Setting up libcurl4-openssl-dev:amd64 (8.6.0-4) ... Setting up r-base-core (4.3.3-3+b1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up libnsl-dev:amd64 (1.3.0-3+b1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.2) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.2) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up r-cran-matrixstats (1.2.0-1) ... Setting up r-bioc-matrixgenerics (1.14.0-1) ... Setting up r-cran-abind (1.4-5-2) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.2) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.2) ... Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ... Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-bioc-iranges (2.36.0-1) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.2) ... Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.2) ... Setting up libhdf5-dev (1.10.10+repack-3.2) ... Setting up r-bioc-xvector (0.42.0-1) ... Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ... Setting up r-bioc-rhdf5lib (1.24.2+dfsg-1+b1) ... Setting up r-bioc-rhdf5filters (1.14.1+dfsg-3) ... Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ... Setting up r-bioc-rhdf5 (2.46.1+dfsg-1+b1) ... Setting up r-bioc-hdf5array (1.30.1-1+b1) ... 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. 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-yf', 'dist-upgrade'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m8.2s DUMP: 03fe75764183fb310f7b56942e7e3b94 - 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-hdf5array'] 1m8.5s DUMP: Package: r-bioc-hdf5array Source: r-bioc-hdf5array (1.30.1-1) Version: 1.30.1-1+b1 Installed-Size: 9041 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.18, r-bioc-delayedarray (>= 0.27.2), r-bioc-rhdf5 (>= 2.31.6), r-cran-matrix, r-bioc-rhdf5filters, r-bioc-biocgenerics (>= 0.31.5), r-bioc-s4vectors (>= 0.27.13), r-bioc-iranges, r-bioc-s4arrays (>= 1.1.1), r-bioc-rhdf5lib, libc6 (>= 2.14), libhdf5-103-1t64, libhdf5-hl-100t64 Suggests: r-bioc-biocparallel, r-bioc-genomicranges, r-bioc-summarizedexperiment (>= 1.15.1), r-bioc-experimenthub, r-bioc-genomicfeatures, r-cran-runit, r-bioc-singlecellexperiment, r-bioc-delayedmatrixstats, r-bioc-genefilter Description-en: HDF5 backend for DelayedArray objects Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed. Description-md5: 75935fc5e97c3a902de41900a4e583c7 Homepage: https://bioconductor.org/packages/HDF5Array/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-hdf5array/r-bioc-hdf5array_1.30.1-1+b1_amd64.deb Size: 8764408 MD5sum: a4810de98a065082dbbe2b56aefc7004 SHA256: 800996585c7ab38460303800a534dc6b3ca27b7e94c32916f3e3df947a0289bb 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-hdf5array'] 1m8.5s INFO: apt-cache knows about the following packages: r-bioc-hdf5array 1m8.5s INFO: Running scripts pre_install 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 1m8.6s 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: 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 1m8.6s DUMP: r-bioc-hdf5array: Installed: 1.30.1-1+b1 Candidate: 1.30.1-1+b1 Version table: *** 1.30.1-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 1m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array'] 1m9.4s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-hdf5array is already the newest version (1.30.1-1+b1). The following packages were automatically installed and are no longer required: libglib2.0-0 libnsl-dev libnsl2 libquadmath0 libtirpc-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array'] 1m9.4s INFO: Running scripts post_install 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 1m9.4s INFO: Running scripts post_distupgrade 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_exceptions'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_exceptions'] 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_zz_backports'] 1m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_distupgrade_zz_backports'] 1m9.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m9.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m9.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m10.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m10.4s INFO: Running scripts pre_install 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_database-server'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_exceptions'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_extras'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m10.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 1m10.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy'] 1m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 1m10.6s DUMP: r-bioc-hdf5array: Installed: 1.30.1-1+b1 Candidate: 1.30.1-1+b1 Version table: *** 1.30.1-1+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-cache', 'policy', 'r-bioc-hdf5array'] 1m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array=1.30.1-1+b1'] 1m11.2s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-hdf5array is already the newest version (1.30.1-1+b1). The following packages were automatically installed and are no longer required: libglib2.0-0 libnsl-dev libnsl2 libquadmath0 libtirpc-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', 'install', 'r-bioc-hdf5array=1.30.1-1+b1'] 1m11.2s INFO: Running scripts post_install 1m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 1m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_install_exceptions'] 1m11.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m11.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m11.9s INFO: /bin converted to /usr/bin by /usr merge 1m11.9s INFO: /lib converted to /usr/lib by /usr merge 1m11.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m11.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m11.9s INFO: /sbin converted to /usr/sbin by /usr merge 1m12.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', '-ac', '--ignore-obsolete'] 1m14.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', '-ac', '--ignore-obsolete'] 1m14.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m14.3s DUMP: 0.15.6 1m14.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m14.3s INFO: Running adequate version 0.15.6 now. 1m14.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'r-bioc-hdf5array'] 1m14.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'r-bioc-hdf5array'] 1m14.4s INFO: Running scripts pre_remove 1m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_exceptions'] 1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/pre_remove_exceptions'] 1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m18.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.14 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 1:2.39.3-11 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-12-base:amd64 gcc-12-base 12.3.0-15 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240315-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hdf5-helpers hdf5-helpers 1.10.10+repack-3.2 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 libaec-dev:amd64 libaec-dev 1.1.3-1 install ok installed libaec0:amd64 libaec0 1.1.3-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 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 2.39.3-11 install ok installed libblosc1:amd64 libblosc1 1.21.5+ds-1+b1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 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 1.18.0-3 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 libcurl4-openssl-dev:amd64 libcurl4-openssl-dev 8.6.0-4 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+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 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-s1:amd64 libgcc-s1 14-20240315-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgfortran5:amd64 libgfortran5 14-20240315-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.4-6 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1+b1 install ok installed libgomp1:amd64 libgomp1 14-20240315-1 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+b1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-3.2 install ok installed libhdf5-cpp-103-1t64:amd64 libhdf5-cpp-103-1t64 1.10.10+repack-3.2 install ok installed libhdf5-dev libhdf5-dev 1.10.10+repack-3.2 install ok installed libhdf5-fortran-102t64:amd64 libhdf5-fortran-102t64 1.10.10+repack-3.2 install ok installed libhdf5-hl-100t64:amd64 libhdf5-hl-100t64 1.10.10+repack-3.2 install ok installed libhdf5-hl-cpp-100t64:amd64 libhdf5-hl-cpp-100t64 1.10.10+repack-3.2 install ok installed libhdf5-hl-fortran-100t64:amd64 libhdf5-hl-fortran-100t64 1.10.10+repack-3.2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libice6:amd64 libice6 2:1.0.10-1 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 libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg-dev:amd64 libjpeg-dev 1:2.1.5-2+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjpeg62-turbo-dev:amd64 libjpeg62-turbo-dev 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 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 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 2.39.3-11 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+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b1 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 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 14-20240315-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 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 2.39.3-11 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.10-1+b1 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 libssl-dev:amd64 libssl-dev 3.1.5-1.1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240315-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libsz2:amd64 libsz2 1.1.3-1 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 libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.2 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.2 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.2 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-11 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 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 login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-11 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 openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed r-base-core r-base-core 4.3.3-3+b1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.48.1-2 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.28.0+dfsg-1 install ok installed r-bioc-hdf5array r-bioc-hdf5array 1.30.1-1+b1 install ok installed r-bioc-iranges r-bioc-iranges 2.36.0-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.14.0-1 install ok installed r-bioc-rhdf5 r-bioc-rhdf5 2.46.1+dfsg-1+b1 install ok installed r-bioc-rhdf5filters r-bioc-rhdf5filters 1.14.1+dfsg-3 install ok installed r-bioc-rhdf5lib r-bioc-rhdf5lib 1.24.2+dfsg-1+b1 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-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-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 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 readline-common readline-common 8.2-4 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 usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-11 install ok installed util-linux-extra util-linux-extra 2.39.3-11 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 1m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'hdf5-helpers-', 'libaec-dev:amd64-', 'libaec0:amd64-', 'libblas3:amd64-', 'libblosc1:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4-openssl-dev:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-cpp-103-1t64:amd64-', 'libhdf5-dev-', 'libhdf5-fortran-102t64:amd64-', 'libhdf5-hl-100t64:amd64-', 'libhdf5-hl-cpp-100t64:amd64-', 'libhdf5-hl-fortran-100t64:amd64-', 'libice6:amd64-', 'libicu72:amd64-', 'libjbig0:amd64-', 'libjpeg-dev:amd64-', 'libjpeg62-turbo:amd64-', 'libjpeg62-turbo-dev:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'liblapack3:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'libnghttp2-14:amd64-', 'libnsl-dev:amd64-', 'libnsl2: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-', 'libsnappy1v5:amd64-', 'libssh2-1t64:amd64-', 'libssl-dev:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'openssl-', 'r-base-core-', 'r-bioc-biocgenerics-', 'r-bioc-delayedarray-', 'r-bioc-iranges-', 'r-bioc-matrixgenerics-', 'r-bioc-rhdf5-', 'r-bioc-rhdf5filters-', 'r-bioc-rhdf5lib-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-crayon-', 'r-cran-lattice-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-hdf5array-'] 1m21.3s 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 hdf5-helpers libaec-dev libaec0 libblas3 libblosc1 libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4-openssl-dev libcurl4t64 libdatrie1 libdb5.3t64 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libice6 libicu72 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libnsl-dev libnsl2 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 libsnappy1v5 libssh2-1t64 libssl-dev libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl r-base-core r-bioc-biocgenerics r-bioc-delayedarray r-bioc-hdf5array r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhdf5 r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-crayon r-cran-lattice r-cran-matrix r-cran-matrixstats readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev The following NEW packages will be installed: libdb5.3 0 upgraded, 1 newly installed, 125 to remove and 0 not upgraded. Need to get 697 kB of archives. After this operation, 236 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 697 kB in 0s (9765 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 ... 13394 files and directories currently installed.) Removing r-bioc-hdf5array (1.30.1-1+b1) ... 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-crayon (1.5.2-1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-cran-matrix (1.6-5-1) ... Removing r-bioc-rhdf5 (2.46.1+dfsg-1+b1) ... Removing r-bioc-rhdf5filters (1.14.1+dfsg-3) ... Removing r-bioc-rhdf5lib (1.24.2+dfsg-1+b1) ... Removing libhdf5-dev (1.10.10+repack-3.2) ... Removing hdf5-helpers (1.10.10+repack-3.2) ... Removing libaec-dev:amd64 (1.1.3-1) ... Removing libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.2) ... Removing libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.2) ... Removing libhdf5-hl-100t64:amd64 (1.10.10+repack-3.2) ... Removing libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.2) ... Removing libblosc1:amd64 (1.21.5+ds-1+b1) ... Removing libcurl4-openssl-dev:amd64 (8.6.0-4) ... Removing r-bioc-xvector (0.42.0-1) ... Removing r-bioc-zlibbioc (1.48.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libjpeg-dev:amd64 (1:2.1.5-2+b2) ... Removing libjpeg62-turbo-dev:amd64 (1:2.1.5-2+b2) ... 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) ... Removing libglib2.0-0:amd64 (2.78.4-6) ... Removing libnsl-dev:amd64 (1.3.0-3+b1) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.2) ... Removing libnsl2:amd64 (1.3.0-3+b1) ... Removing libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.2) ... Removing libquadmath0:amd64 (14-20240315-1) ... Removing libsnappy1v5:amd64 (1.1.10-1+b1) ... Removing libssl-dev:amd64 (3.1.5-1.1) ... Removing linux-libc-dev (6.7.9-2) ... Removing r-bioc-iranges (2.36.0-1) ... 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-cran-lattice (0.22-6-1) ... Removing r-cran-matrixstats (1.2.0-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-base-core (4.3.3-3+b1) ... 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 (1.18.0-3) ... 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 libhdf5-103-1t64:amd64 (1.10.10+repack-3.2) ... Removing libsz2:amd64 (1.1.3-1) ... Removing libaec0:amd64 (1.1.3-1) ... 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) ... 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) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libgfortran5:amd64 (14-20240315-1) ... Removing libglib2.0-0t64:amd64 (2.78.4-6) ... Removing libgomp1:amd64 (14-20240315-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.2) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libkrb5-3:amd64 (1.20.1-6+b1) ... Removing libk5crypto3:amd64 (1.20.1-6+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6+b1) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.59.0-1+b1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpng16-16t64:amd64 (1.6.43-3) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... 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-common (1.3.4+ds-1.2) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing openssl (3.1.5-1.1) ... Removing readline-common (8.2-4) ... 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 libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.12.2-1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libdb5.3: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 ... 5381 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 1m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'ca-certificates-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'hdf5-helpers-', 'libaec-dev:amd64-', 'libaec0:amd64-', 'libblas3:amd64-', 'libblosc1:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo2:amd64-', 'libcrypt-dev:amd64-', 'libcurl4-openssl-dev:amd64-', 'libcurl4t64:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdeflate0:amd64-', 'libexpat1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgfortran5:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libgomp1:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-cpp-103-1t64:amd64-', 'libhdf5-dev-', 'libhdf5-fortran-102t64:amd64-', 'libhdf5-hl-100t64:amd64-', 'libhdf5-hl-cpp-100t64:amd64-', 'libhdf5-hl-fortran-100t64:amd64-', 'libice6:amd64-', 'libicu72:amd64-', 'libjbig0:amd64-', 'libjpeg-dev:amd64-', 'libjpeg62-turbo:amd64-', 'libjpeg62-turbo-dev:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'liblapack3:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'libnghttp2-14:amd64-', 'libnsl-dev:amd64-', 'libnsl2: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-', 'libsnappy1v5:amd64-', 'libssh2-1t64:amd64-', 'libssl-dev:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', 'libtirpc3t64:amd64-', 'libtk8.6:amd64-', 'libwebp7:amd64-', 'libx11-6:amd64-', 'libx11-data-', 'libxau6:amd64-', 'libxcb-render0:amd64-', 'libxcb-shm0:amd64-', 'libxcb1:amd64-', 'libxdmcp6:amd64-', 'libxext6:amd64-', 'libxft2:amd64-', 'libxrender1:amd64-', 'libxss1:amd64-', 'libxt6t64:amd64-', 'linux-libc-dev-', 'openssl-', 'r-base-core-', 'r-bioc-biocgenerics-', 'r-bioc-delayedarray-', 'r-bioc-iranges-', 'r-bioc-matrixgenerics-', 'r-bioc-rhdf5-', 'r-bioc-rhdf5filters-', 'r-bioc-rhdf5lib-', 'r-bioc-s4arrays-', 'r-bioc-s4vectors-', 'r-bioc-sparsearray-', 'r-bioc-xvector-', 'r-bioc-zlibbioc-', 'r-cran-abind-', 'r-cran-crayon-', 'r-cran-lattice-', 'r-cran-matrix-', 'r-cran-matrixstats-', 'readline-common-', 'rpcsvc-proto-', 'sensible-utils-', 'ucf-', 'unzip-', 'x11-common-', 'xdg-utils-', 'zip-', 'zlib1g-dev:amd64-', 'r-bioc-hdf5array-'] 1m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 1m22.6s 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, 1 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/697 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 ... 5388 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1'] 1m22.6s INFO: Running scripts post_remove 1m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_remove_exceptions'] 1m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_remove_exceptions'] 1m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4-openssl-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-dev', 'libhdf5-fortran-102t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhdf5-hl-cpp-100t64:amd64', 'libhdf5-hl-fortran-100t64:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2: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', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libssl-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-delayedarray', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhdf5', 'r-bioc-rhdf5filters', 'r-bioc-rhdf5lib', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-crayon', 'r-cran-lattice', 'r-cran-matrix', 'r-cran-matrixstats', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m23.3s DUMP: (Reading database ... 5388 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 '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove hdf5-helpers which isn't installed dpkg: warning: ignoring request to remove libaec-dev which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libblosc1 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 libcurl4-openssl-dev which isn't installed 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 libdb5.3t64 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 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 (2.78.4-6) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-dev which isn't installed dpkg: warning: ignoring request to remove libhdf5-fortran-102t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-cpp-100t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-fortran-100t64 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg-dev which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo-dev which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove 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 libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 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 (8.2-4) ... 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 libsnappy1v5 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libssl-dev which isn't installed dpkg: warning: ignoring request to remove libsz2 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 libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.2) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.2) ... dpkg: warning: ignoring request to remove libtk8.6 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 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 Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for r-base-core (4.3.3-3+b1) ... dpkg: warning: ignoring request to remove r-bioc-biocgenerics 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-iranges 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-rhdf5 which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhdf5filters which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhdf5lib 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-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-crayon 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-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed Purging configuration files for readline-common (8.2-4) ... 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 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'hdf5-helpers', 'libaec-dev:amd64', 'libaec0:amd64', 'libblas3:amd64', 'libblosc1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4-openssl-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-dev', 'libhdf5-fortran-102t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhdf5-hl-cpp-100t64:amd64', 'libhdf5-hl-fortran-100t64:amd64', 'libice6:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg-dev:amd64', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2: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', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libssl-dev:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-delayedarray', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhdf5', 'r-bioc-rhdf5filters', 'r-bioc-rhdf5lib', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-crayon', 'r-cran-lattice', 'r-cran-matrix', 'r-cran-matrixstats', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', 'r-bioc-hdf5array'] 1m23.3s DUMP: dpkg: warning: ignoring request to remove r-bioc-hdf5array which isn't installed 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', 'r-bioc-hdf5array'] 1m23.3s INFO: Running scripts post_purge 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_purge_exceptions'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_purge_exceptions'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', '--pending'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--purge', '--pending'] 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--remove', '--pending'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg', '--remove', '--pending'] 1m23.3s INFO: Running scripts post_test 1m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_test_exceptions'] 1m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'tmp/scripts/post_test_exceptions'] 1m23.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m23.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-divert', '--list'] 1m23.6s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /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 1m23.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'dpkg-divert', '--list'] 1m23.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'clean'] 1m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprjb_x4so', 'apt-get', 'clean'] 1m23.7s DEBUG: Recording chroot state 1m24.3s 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 1m24.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/shm'] 1m24.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/shm'] 1m24.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/console'] 1m24.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/console'] 1m24.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/ptmx'] 1m24.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/ptmx'] 1m24.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts'] 1m24.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/dev/pts'] 1m24.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/proc'] 1m24.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprjb_x4so/proc'] 1m24.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m24.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprjb_x4so'] 1m24.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmprjb_x4so 1m24.8s INFO: PASS: Upgrading between Debian distributions. 1m24.8s INFO: PASS: All tests. 1m24.8s INFO: piuparts run ends. ret=0 End: 2024-03-28 00:21:40 GMT