Start: 2024-08-23 14:27:24 GMT [stable] Package: r-bioc-tximeta Version: 1.16.1+dfsg-1 Installed-Size: 308 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.2.2.20221110-2), r-api-4.0, r-api-bioc-3.16, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-jsonlite, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomicranges, r-bioc-annotationdbi, r-bioc-genomicfeatures, r-bioc-ensembldb, r-bioc-biocfilecache, r-bioc-annotationhub, r-bioc-biostrings, r-cran-tibble, r-bioc-genomeinfodb, r-cran-matrix Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat, r-bioc-tximportdata, r-bioc-deseq2, r-bioc-fishpond, r-bioc-edger, r-bioc-limma, r-cran-devtools Description: Transcript Quantification Import with Automatic Metadata Homepage: https://bioconductor.org/packages/tximeta/ Description-md5: 75f999d7edd35b8ba0d462a84ab80b38 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tximeta/r-bioc-tximeta_1.16.1+dfsg-1_all.deb Size: 142440 MD5sum: f87fd51f4cd14098111f93a5399bebea SHA256: 64388f905acd27986f486e928c13b8d9a9c77cee764d4ca28d1051cc8d766da7 [testing] [sid] Package: r-bioc-tximeta Version: 1.22.1+dfsg-1 Installed-Size: 728 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-tximport (>= 1.32.0), r-cran-jsonlite, r-bioc-s4vectors (>= 0.42.1), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-annotationdbi (>= 1.66.0), r-bioc-genomicfeatures (>= 1.56.0), r-bioc-txdbmaker, r-bioc-ensembldb (>= 2.28.0), r-bioc-biocfilecache (>= 2.12.0), r-bioc-annotationhub (>= 3.12.0), r-bioc-biostrings (>= 2.72.1), r-cran-tibble, r-bioc-genomeinfodb (>= 1.40.1), r-cran-matrix Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat, r-bioc-tximportdata (>= 1.32.0), r-bioc-deseq2 (>= 1.44.0), r-bioc-fishpond (>= 2.10.0), r-bioc-edger (>= 4.2.0), r-bioc-limma (>= 3.60.3), r-cran-devtools Description: Transcript Quantification Import with Automatic Metadata Homepage: https://bioconductor.org/packages/tximeta/ Description-md5: 75f999d7edd35b8ba0d462a84ab80b38 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tximeta/r-bioc-tximeta_1.22.1+dfsg-1_all.deb Size: 538420 MD5sum: 34d1631861379f3246c65246fdfe3d9f SHA256: 2f819c1e8e7de846e860c316bcb4bd63c0e70a5d25d44e23d51d2d435945763c 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 stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt r-bioc-tximeta=1.22.1+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 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 stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt r-bioc-tximeta=1.22.1+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpt0_pwphj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpt0_pwphj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpt0_pwphj/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 0m1.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.8s INFO: Running scripts post_setup 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_dummy_users'] 0m2.7s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_dummy_users'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_forbid_home'] 0m2.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_forbid_home'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_minimize'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_setup_zz_backports'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s 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+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 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+deb12u1 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+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 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+deb12u3 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+deb12u1 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+deb12u1 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+deb12u1 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 252.26-1~deb12u2 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 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 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+deb12u1 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+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 0m3.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 0m3.3s INFO: Running scripts is_testable 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 0m3.7s DUMP: Package: r-bioc-tximeta Version: 1.16.1+dfsg-1 Installed-Size: 308 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.2.2.20221110-2), r-api-4.0, r-api-bioc-3.16, r-bioc-summarizedexperiment, r-bioc-tximport, r-cran-jsonlite, r-bioc-s4vectors, r-bioc-iranges, r-bioc-genomicranges, r-bioc-annotationdbi, r-bioc-genomicfeatures, r-bioc-ensembldb, r-bioc-biocfilecache, r-bioc-annotationhub, r-bioc-biostrings, r-cran-tibble, r-bioc-genomeinfodb, r-cran-matrix Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat, r-bioc-tximportdata, r-bioc-deseq2, r-bioc-fishpond, r-bioc-edger, r-bioc-limma, r-cran-devtools Description-en: Transcript Quantification Import with Automatic Metadata Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility. Description-md5: 75f999d7edd35b8ba0d462a84ab80b38 Homepage: https://bioconductor.org/packages/tximeta/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tximeta/r-bioc-tximeta_1.16.1+dfsg-1_all.deb Size: 142440 MD5sum: f87fd51f4cd14098111f93a5399bebea SHA256: 64388f905acd27986f486e928c13b8d9a9c77cee764d4ca28d1051cc8d766da7 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 0m3.7s INFO: apt-cache knows about the following packages: r-bioc-tximeta 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 0m3.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 0m3.9s DUMP: r-bioc-tximeta: Installed: (none) Candidate: 1.16.1+dfsg-1 Version table: 1.16.1+dfsg-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta'] 0m39.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax javascript-common libasan8 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 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 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libuv1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data r-base-core r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-interactivedisplaybase r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: apache2 | lighttpd | httpd libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc manpages-dev low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc libstdc++-12-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php perl python ruby libjs-katex citation-style-language-styles elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-go.db r-cran-runit r-bioc-org.hs.eg.db r-bioc-graph r-bioc-biocstyle r-cran-testthat r-bioc-variantannotation r-bioc-experimenthub r-bioc-all r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-shortread r-cran-batchtools r-cran-data.table r-cran-mockery r-cran-webmockr r-bioc-bsgenome r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-ggbio r-bioc-gviz r-bioc-edger r-cran-markdown r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-limma r-bioc-rhdf5 r-bioc-tximportdata r-bioc-fishpond r-cran-devtools r-cran-readr r-cran-covr r-cran-remotes r-cran-roxygen2 r-cran-ff r-cran-callr r-cran-processx r-cran-ps r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-bench r-cran-desc r-cran-ggplot2 r-cran-scales r-cran-spelling r-cran-rmysql r-cran-future r-cran-testit r-cran-unitizer r-cran-forcats r-cran-r.utils r-cran-waldo r-cran-lubridate r-cran-cairo r-cran-ragg r-cran-jpeg r-cran-r.rsp r-cran-sf r-cran-rgl r-cran-webshot r-cran-reticulate r-cran-magick r-cran-gridsvg r-cran-lintr r-cran-tidyverse r-cran-getopt r-cran-r.devices r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline r-cran-usethis r-cran-downlit r-cran-gert r-cran-gh r-cran-rvest r-cran-rlecuyer r-cran-brio r-cran-pkgbuild r-cran-pkgload r-cran-tidyr r-cran-pkgdown r-cran-zeallot r-cran-plm r-cran-zoo readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs node-jquery krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-thematic r-cran-mockery r-cran-decor r-cran-brio r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-bench r-cran-broom r-cran-callr r-cran-covr r-cran-ggplot2 r-cran-lobstr r-cran-rsvg r-cran-testit r-cran-survival r-cran-pkgload r-cran-markdown r-cran-sp r-cran-tikzdevice node-highlight.js r-cran-runit r-cran-sodium r-cran-lubridate r-cran-future r-cran-tufte r-cran-dygraphs r-cran-rsconnect r-cran-dbitest r-cran-data.table r-cran-mockr r-cran-formattable r-cran-waldo libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax javascript-common libasan8 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 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 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libuv1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data r-base-core r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-interactivedisplaybase r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximeta r-bioc-tximport r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded. Need to get 230 MB of archives. After this operation, 798 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 3.0.13-1~deb12u1 [2022 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 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+deb12u3 [398 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 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 javascript-common all 11+nmu1 [6260 B] Get:19 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:21 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u7 [45.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.94-1 [1994 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:35 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u7 [1899 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:47 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u6 [390 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:90 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libjs-modernizr all 2.6.2+ds1-5 [47.1 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 liblua5.3-0 amd64 5.3.6-2 [123 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:107 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1+deb12u1 [136 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:123 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 pandoc-data all 2.17.1.1-2~deb12u1 [418 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 pandoc amd64 2.17.1.1-2~deb12u1 [21.3 MB] Get:130 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:162 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:166 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:169 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationfilter all 1.22.0+dfsg-1 [234 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 r-cran-biocmanager all 1.30.20+dfsg-1 [126 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocversion all 3.16.0-1 [10.6 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 r-cran-later amd64 1.3.0+dfsg-1+b1 [117 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 r-cran-promises amd64 1.2.0.1+dfsg-1 [274 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 r-cran-httpuv amd64 1.6.9+dfsg-1 [478 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmltools amd64 0.5.4-1 [364 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 r-cran-fontawesome all 0.5.0-1 [1304 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 r-cran-commonmark amd64 1.8.1-1 [117 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 r-cran-fs amd64 1.6.1+dfsg-1 [226 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 r-cran-sass amd64 0.4.5+dfsg-1 [942 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 r-cran-bslib all 0.4.2+dfsg-1 [3773 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 r-cran-shiny all 1.7.4+dfsg-2+deb12u1 [2751 kB] Get:207 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 r-cran-evaluate all 0.20-1 [85.9 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 r-cran-xfun amd64 0.37+dfsg-1 [394 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 r-cran-highr all 0.10+dfsg-1 [38.1 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 r-cran-knitr all 1.42+dfsg-1 [901 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 r-cran-tinytex all 0.44-1 [138 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 r-cran-rmarkdown all 2.20+dfsg-1 [2265 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 r-cran-htmlwidgets all 1.6.1+dfsg-1 [120 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 r-cran-crosstalk all 1.2.0+dfsg-1 [171 kB] Get:218 http://deb.debian.org/debian bookworm/main amd64 r-cran-dt all 0.27+dfsg-1 [236 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 r-bioc-interactivedisplaybase all 1.36.0+dfsg-1 [30.0 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationhub all 3.6.0+dfsg-1 [435 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:229 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:237 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 r-bioc-protgenerics all 1.30.0-1 [215 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 r-bioc-ensembldb all 2.22.0+dfsg-1 [1484 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 r-bioc-tximport all 1.26.1+dfsg-1 [87.9 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 r-bioc-tximeta all 1.16.1+dfsg-1 [142 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 230 MB in 1s (201 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 ... 6093 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. Preparing to unpack .../002-libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.13-1~deb12u1_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../006-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../008-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-libfreetype6_2.12.1+dfsg-5+deb12u3_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.14.1-4_amd64.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../014-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../015-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../016-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package javascript-common. Preparing to unpack .../017-javascript-common_11+nmu1_all.deb ... Unpacking javascript-common (11+nmu1) ... Selecting previously unselected package libasan8:amd64. Preparing to unpack .../018-libasan8_12.2.0-14_amd64.deb ... Unpacking libasan8:amd64 (12.2.0-14) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../019-libatomic1_12.2.0-14_amd64.deb ... Unpacking libatomic1:amd64 (12.2.0-14) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../020-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../021-libgomp1_12.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (12.2.0-14) ... Selecting previously unselected package libitm1:amd64. Preparing to unpack .../022-libitm1_12.2.0-14_amd64.deb ... Unpacking libitm1:amd64 (12.2.0-14) ... Selecting previously unselected package liblsan0:amd64. Preparing to unpack .../023-liblsan0_12.2.0-14_amd64.deb ... Unpacking liblsan0:amd64 (12.2.0-14) ... Selecting previously unselected package libtsan2:amd64. Preparing to unpack .../024-libtsan2_12.2.0-14_amd64.deb ... Unpacking libtsan2:amd64 (12.2.0-14) ... Selecting previously unselected package libubsan1:amd64. Preparing to unpack .../025-libubsan1_12.2.0-14_amd64.deb ... Unpacking libubsan1:amd64 (12.2.0-14) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../026-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgcc-12-dev:amd64. Preparing to unpack .../027-libgcc-12-dev_12.2.0-14_amd64.deb ... Unpacking libgcc-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package libc-dev-bin. Preparing to unpack .../028-libc-dev-bin_2.36-9+deb12u7_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u7) ... Selecting previously unselected package linux-libc-dev:amd64. Preparing to unpack .../029-linux-libc-dev_6.1.94-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.94-1) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../030-libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../031-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../032-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../033-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../034-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../035-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../036-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3:amd64. Preparing to unpack .../037-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../038-libnsl2_1.3.0-2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../039-libtirpc-dev_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../040-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package rpcsvc-proto. Preparing to unpack .../041-rpcsvc-proto_1.4.3-1_amd64.deb ... Unpacking rpcsvc-proto (1.4.3-1) ... Selecting previously unselected package libc6-dev:amd64. Preparing to unpack .../042-libc6-dev_2.36-9+deb12u7_amd64.deb ... Unpacking libc6-dev:amd64 (2.36-9+deb12u7) ... Selecting previously unselected package libstdc++-12-dev:amd64. Preparing to unpack .../043-libstdc++-12-dev_12.2.0-14_amd64.deb ... Unpacking libstdc++-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../044-libboost1.74-dev_1.74.0+ds1-21_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../045-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../046-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../047-libpixman-1-0_0.42.2-1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.42.2-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../048-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../049-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../050-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../051-libx11-data_2%3a1.8.4-2+deb12u2_all.deb ... Unpacking libx11-data (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../052-libx11-6_2%3a1.8.4-2+deb12u2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libxcb-render0:amd64. Preparing to unpack .../053-libxcb-render0_1.15-1_amd64.deb ... Unpacking libxcb-render0:amd64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:amd64. Preparing to unpack .../054-libxcb-shm0_1.15-1_amd64.deb ... Unpacking libxcb-shm0:amd64 (1.15-1) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../055-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../056-libxrender1_1%3a0.9.10-1.1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../057-libcairo2_1.16.0-7_amd64.deb ... Unpacking libcairo2:amd64 (1.16.0-7) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../058-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../059-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../060-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../061-libnghttp2-14_1.52.0-1+deb12u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../062-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../063-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../064-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. 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Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Setting up libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... 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 libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 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 libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-2~deb12u1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libgcc-12-dev:amd64 (12.2.0-14) ... 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+deb12u6) ... 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 libxt6:amd64 (1:1.2.1-1.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... 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 libxft2:amd64 (2.3.6-1) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-sourcetools (0.1.7-1-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-45-3) ... Setting up r-cran-formatr (1.14-1) ... Setting up r-cran-xml (3.99-0.13-1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u7) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up r-cran-commonmark (1.8.1-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-cran-filelock (1.0.2-2) ... Setting up r-bioc-genomeinfodbdata (1.2.9-1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up r-cran-fs (1.6.1+dfsg-1) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up r-cran-curl (5.0.0+dfsg-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up r-cran-matrixstats (0.63.0-1) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.17-1) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up r-cran-xfun (0.37+dfsg-1) ... Setting up r-cran-sys (3.4.1-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-mime (0.12-1+b1) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-base64enc (0.1-3-3) ... Setting up r-cran-digest (0.6.31-1) ... Setting up r-cran-yaml (2.3.7-1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-xml2 (1.3.3-1+b1) ... Setting up r-bioc-protgenerics (1.30.0-1) ... Setting up r-cran-evaluate (0.20-1) ... Setting up r-cran-dbi (1.1.3-1) ... Setting up r-cran-highr (0.10+dfsg-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.0-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-bitops (1.0-7-1) ... Setting up r-bioc-biocversion (3.16.0-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-cran-biocmanager (1.30.20+dfsg-1) ... Setting up r-cran-askpass (1.1-2) ... Setting up r-cran-fastmap (1.1.1-1) ... Setting up r-cran-png (0.1-8-1) ... Setting up r-bioc-biobase (2.58.0-2) ... Setting up r-cran-jsonlite (1.8.4+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-stringi (1.7.12-1) ... Setting up r-cran-cpp11 (0.4.3-1) ... Setting up r-bioc-s4vectors (0.36.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-later (1.3.0+dfsg-1+b1) ... Setting up r-cran-matrix (1.5-3-1) ... Setting up r-cran-tinytex (0.44-1) ... Setting up r-bioc-tximport (1.26.1+dfsg-1) ... Setting up r-cran-knitr (1.42+dfsg-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up r-cran-cachem (1.0.7-1) ... Setting up r-bioc-iranges (2.32.0-1) ... Setting up r-cran-rjson (0.2.21-1) ... Setting up r-cran-rcurl (1.98-1.10+dfsg-1) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-vctrs (0.5.2-1) ... Setting up r-bioc-delayedarray (0.24.0+dfsg-1) ... Setting up r-cran-pillar (1.8.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.2-2) ... Setting up r-cran-openssl (2.0.5+dfsg-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up r-cran-stringr (1.5.0-1) ... Setting up r-cran-tibble (3.1.8+dfsg-1) ... Setting up r-bioc-biocio (1.8.0+dfsg-1) ... Setting up r-bioc-zlibbioc (1.44.0+dfsg-1) ... Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-promises (1.2.0.1+dfsg-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-blob (1.2.3-1) ... Setting up r-cran-htmltools (0.5.4-1) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up r-cran-sass (0.4.5+dfsg-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up r-cran-dbplyr (2.3.0+dfsg-1) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-cran-bh (1.74.0-2) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up r-bioc-biocfilecache (2.6.1+dfsg-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-cran-httpuv (1.6.9+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-bioc-annotationfilter (1.22.0+dfsg-1) ... Setting up r-cran-fontawesome (0.5.0-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up r-cran-bslib (0.4.2+dfsg-1) ... Setting up r-bioc-rsamtools (2.14.0-1) ... Setting up r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Setting up r-bioc-keggrest (1.38.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.60.0-1) ... Setting up r-cran-shiny (1.7.4+dfsg-2+deb12u1) ... Setting up r-cran-rmarkdown (2.20+dfsg-1) ... Setting up r-bioc-biomart (2.54.0+dfsg-1) ... Setting up r-bioc-genomicalignments (1.34.0-1) ... Setting up r-cran-crosstalk (1.2.0+dfsg-1) ... Setting up r-bioc-rtracklayer (1.58.0-1) ... Setting up r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Setting up r-cran-htmlwidgets (1.6.1+dfsg-1) ... Setting up r-bioc-ensembldb (2.22.0+dfsg-1) ... Setting up r-cran-dt (0.27+dfsg-1) ... Setting up r-bioc-interactivedisplaybase (1.36.0+dfsg-1) ... Setting up r-bioc-annotationhub (3.6.0+dfsg-1) ... Setting up r-bioc-tximeta (1.16.1+dfsg-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... 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. 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta'] 0m39.0s INFO: Running scripts post_install 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 0m39.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 0m41.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 0m41.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt0_pwphj to testing 0m41.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m41.3s INFO: Running scripts pre_distupgrade 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m41.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 0m44.2s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [169 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9260 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6169 kB] Fetched 15.6 MB in 2s (8211 kB/s) Reading package lists... 0m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 0m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 1m32.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax javascript-common libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-14-dev libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 liblua5.4-0 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 libssh2-1t64 libstdc++-12-dev libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libyaml-0-2 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data r-base-core r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biocversion r-bioc-genomeinfodbdata r-bioc-interactivedisplaybase r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-tximport r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto ucf unzip x11-common xdg-utils zip zlib1g-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost1.74-dev libcurl4 libdb5.3 libext2fs2 libglib2.0-0 libgnutls30 libhogweed6 libnettle8 libpng16-16 libpsl5 libreadline8 libssh2-1 libssl3 libtirpc3 libuv1 libxt6 r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biocio r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-tximeta r-bioc-xvector r-cran-restfulr The following NEW packages will be installed: fonts-dejavu-mono gcc-14-base libapt-pkg6.0t64 libboost1.83-dev libcurl4t64 libdb5.3t64 libext2fs2t64 libgcc-14-dev libglib2.0-0t64 libgnutls30t64 libhogweed6t64 libhwasan0 liblua5.4-0 libnettle8t64 libpng16-16t64 libpsl5t64 libreadline8t64 libsharpyuv0 libssh2-1t64 libssl3t64 libstdc++-14-dev libtirpc3t64 libunistring5 libuv1t64 libxt6t64 r-cran-tidyr 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 hostname init-system-helpers libacl1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libboost-dev libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcap-ng0 libcap2 libcom-err2 libcrypt-dev libcrypt1 libdatrie1 libdebconfclient0 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libjs-modernizr libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 liblz4-1 liblzma5 libmd0 libmount1 libnghttp2-14 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-8-0 libpixman-1-0 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsm6 libsmartcols1 libss2 libstdc++-12-dev libstdc++6 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan2 libubsan1 libudev1 libuuid1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxft2 libxml2 libxrender1 libxss1 libxxhash0 libyaml-0-2 libzstd1 linux-libc-dev littler login logsave mawk mount ncurses-base ncurses-bin openssl pandoc pandoc-data passwd perl-base r-base-core r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biocversion r-bioc-genomeinfodbdata r-bioc-interactivedisplaybase r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-tximport r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-biocmanager r-cran-blob r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-evaluate r-cran-fansi r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jsonlite r-cran-knitr r-cran-later r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgkitten r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-yaml readline-common sed sensible-utils sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra x11-common zip zlib1g zlib1g-dev 249 upgraded, 26 newly installed, 38 to remove and 0 not upgraded. Need to get 218 MB of archives. After this operation, 49.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.5 [72.8 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libnsl-dev amd64 1.3.0-3+b2 [67.2 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.39-7 [1925 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.39-7 [51.6 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [189 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.1+dfsg-1 [178 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1+b1 [787 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1 [87.9 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9344 B] Get:14 http://deb.debian.org/debian trixie/main amd64 r-bioc-tximport all 1.30.0+dfsg-1 [89.9 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 r-bioc-protgenerics all 1.34.0-1 [224 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.3.0-1 [502 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-1 [45.7 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-1 [72.8 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.39-7 [2791 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.39-7 [610 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-1 [713 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-5 [148 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.3-1 [26.7 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1 [2082 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [443 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.36-1 [206 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.0+dfsg-1 [240 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.0.8-1 [72.0 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.2-1 [1325 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 r-cran-shiny all 1.8.1.1+dfsg-1 [2894 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.45+dfsg-1 [519 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 0.24.0-1 [93.7 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.8-2 [107 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.47+dfsg-1 [912 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 r-cran-tinytex all 0.51-1 [146 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.3+ds-3 [24.3 MB] Get:55 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.3-2 [445 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.6-3+b1 [147 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 r-cran-rmarkdown all 2.27+dfsg-1 [1473 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 r-cran-crosstalk all 1.2.1+dfsg-1 [175 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 r-cran-dt all 0.33+dfsg-1 [248 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 r-bioc-interactivedisplaybase all 1.40.0+dfsg-1 [30.1 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocversion all 3.18.1-1 [10.7 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-1 [137 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-1 [25.9 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-1 [9280 B] Get:70 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-1 [2727 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-1 [1205 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-1 [1075 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libstdc++-12-dev amd64 12.4.0-2 [2081 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-1 [145 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-1 [837 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libgcc-12-dev amd64 12.4.0-2 [2431 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-1 [2461 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 gcc-12-base amd64 12.4.0-2 [42.9 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-1 [1489 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-1 [2673 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-1 [2341 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:83 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.1 [10.6 MB] Get:84 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:85 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.4.7-1 [219 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.36.0-1 [1337 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 r-cran-dplyr amd64 1.1.4-1 [1524 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.3-1 [861 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1188 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 r-cran-filelock amd64 1.0.3-1 [27.3 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libzstd1 amd64 1.5.6+dfsg-1 [303 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.9.1-2 [463 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.2-1 [2246 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.2-1 [43.7 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.0-1 [24.0 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [301 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.62.0-1 [2119 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3 [1285 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [38.0 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 liblzma5 amd64 5.6.2-2 [254 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:128 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.50-3 [81.5 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-6 [843 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10-1 [303 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10-1 [334 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-2 [424 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.6-2 [1444 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.8 [1045 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.9.4-3 [59.4 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.5-1 [381 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.5-1 [144 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.272 [10.0 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.5-2+b4 [75.1 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 base-passwd amd64 3.6.4 [50.9 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-7 [19.6 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [697 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:3.1.2-4 [11.5 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-2 [17.2 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:3.1.2-4+b1 [49.0 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libcrypt1 amd64 1:4.4.36-5 [89.8 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.38.2-5 [1643 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 debconf all 1.5.87 [119 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.5.3-7 [67.7 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.5.3-7 [54.4 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.5.3-7 [265 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.5.3-7 [140 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.15.3-2 [564 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libacl1 amd64 2.3.2-2 [32.4 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:163 http://deb.debian.org/debian trixie/main amd64 libsepol2 amd64 3.7-1 [293 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.5-1+b4 [90.1 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.15.3-2 [973 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.43-8 [216 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.5.5-1+b1 [47.3 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.8 [1410 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-7 [57.2 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-2 [186 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.62.1-2 [74.9 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-1 [166 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-1 [198 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get:186 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-1 [48.0 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-1 [219 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-1 [35.0 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.81.1-3 [1496 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5-2 [344 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.20 [89.5 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.11 [1531 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 sysvinit-utils amd64 3.10-1 [32.7 kB] Get:214 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-1 [34.9 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get:221 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.1-1 [28.3 MB] Get:237 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.10.4-1 [2369 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.21-2.1+b1 [1498 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-1 [104 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-9 [93.2 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 findutils amd64 4.10.0-3 [700 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 grep amd64 3.11-4 [431 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5-2 [433 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 sed amd64 4.9-2 [329 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-1 [138 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-1 [1214 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 util-linux-extra amd64 2.40.2-1 [263 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 usr-is-merged all 39 [5572 B] Get:255 http://deb.debian.org/debian trixie/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5-2 [270 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 logsave amd64 1.47.1-1 [22.7 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 libext2fs2t64 amd64 1.47.1-1 [210 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 e2fsprogs amd64 1.47.1-1 [583 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-1 [154 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 mawk amd64 1.3.4.20240622-2 [136 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 liblua5.3-0 amd64 5.3.6-2+b2 [129 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 libss2 amd64 1.47.1-1 [27.6 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.12-1 [12.6 MB] Get:267 http://deb.debian.org/debian trixie/main amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [126 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:270 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-0-3 [4127 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.17-1 [1761 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 218 MB in 2s (104 MB/s) (Reading database ... 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Preparing to unpack .../10-libgpg-error0_1.50-3_amd64.deb ... Unpacking libgpg-error0:amd64 (1.50-3) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.50-3) ... (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 ... 46261 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.11.0-6_amd64.deb ... Unpacking libgcrypt20:amd64 (1.11.0-6) over (1.10.1-3) ... Setting up libgcrypt20:amd64 (1.11.0-6) ... dpkg: libnettle8:amd64: dependency problems, but removing anyway as you requested: libhogweed6:amd64 depends on libnettle8. libgnutls30:amd64 depends on libnettle8 (>= 3.7~). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46261 files and directories currently installed.) Removing libnettle8:amd64 (3.8.1-2) ... Selecting previously unselected package libnettle8t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46253 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10-1) ... Setting up libnettle8t64:amd64 (3.10-1) ... dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (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 ... 46263 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u3) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46234 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.6-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.6-2) ... Setting up libgnutls30t64:amd64 (3.8.6-2) ... dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 2.6.1). (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 ... 46263 files and directories currently installed.) Removing libapt-pkg6.0:amd64 (2.6.1) ... Selecting previously unselected package libapt-pkg6.0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46214 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.8_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.8) ... Setting up libapt-pkg6.0t64:amd64 (2.9.8) ... (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 ... 46265 files and directories currently installed.) Preparing to unpack .../libsystemd0_256.5-1_amd64.deb ... Unpacking libsystemd0:amd64 (256.5-1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (256.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46265 files and directories currently installed.) Preparing to unpack .../libudev1_256.5-1_amd64.deb ... Unpacking libudev1:amd64 (256.5-1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (256.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46265 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.272_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.272) over (0.270) ... Setting up libdebconfclient0:amd64 (0.272) ... (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 ... 46265 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 ... 46266 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2+b4_amd64.deb ... Unpacking libselinux1:amd64 (3.5-2+b4) over (3.4-1+b6) ... Setting up libselinux1:amd64 (3.5-2+b4) ... (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 ... 46267 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.4_amd64.deb ... Unpacking base-passwd (3.6.4) over (3.6.1) ... Setting up base-passwd (3.6.4) ... (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 ... 46266 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 ... 46260 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... (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 ... 46266 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-4_all.deb ... Unpacking libaudit-common (1:3.1.2-4) over (1:3.0.9-1) ... Setting up libaudit-common (1:3.1.2-4) ... (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 ... 46266 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.5-2) ... (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 ... 46265 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-4+b1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-4+b1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-4+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 ... 46266 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-5) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-5) ... (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 ... 46266 files and directories currently installed.) Preparing to unpack .../perl-base_5.38.2-5_amd64.deb ... Unpacking perl-base (5.38.2-5) over (5.36.0-7+deb12u1) ... Setting up perl-base (5.38.2-5) ... (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 ... 46270 files and directories currently installed.) Preparing to unpack .../debconf_1.5.87_all.deb ... Unpacking debconf (1.5.87) over (1.5.82) ... Setting up debconf (1.5.87) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46269 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-7_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam0g:amd64 (1.5.3-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46268 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46267 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-7) ... Installing new version of config file /etc/security/namespace.init ... (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 ... 46267 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-7_all.deb ... Unpacking libpam-runtime (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-runtime (1.5.3-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46266 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 ... 46266 files and directories currently installed.) Preparing to unpack .../libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) over (0.11.7-2) ... Setting up libbsd0:amd64 (0.12.2-1) ... (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 ... 46266 files and directories currently installed.) Preparing to unpack .../login_1%3a4.15.3-2_amd64.deb ... Unpacking login (1:4.15.3-2) over (1:4.13+dfsg1-1+b1) ... Setting up login (1:4.15.3-2) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (Reading database ... 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Selecting previously unselected package libglib2.0-0t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 46216 files and directories currently installed.) Preparing to unpack .../libglib2.0-0t64_2.81.1-3_amd64.deb ... libglib2.0-0t64.preinst: Removing /var/lib/dpkg/info/libglib2.0-0:amd64.postrm to avoid loss of /usr/share/glib-2.0/schemas/gschemas.compiled... removed '/var/lib/dpkg/info/libglib2.0-0:amd64.postrm' Unpacking libglib2.0-0t64:amd64 (2.81.1-3) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libreadline8 (>= 6.0). (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... 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_6.5-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.5-2) over (6.4-4) ... Setting up libtinfo6:amd64 (6.5-2) ... dpkg: libxt6:amd64: dependency problems, but removing anyway as you requested: r-base-core depends on libxt6. (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 ... 46243 files and directories currently installed.) Preparing to unpack .../libxt6t64_1%3a1.2.1-1.2_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ... Preparing to unpack .../debianutils_5.20_amd64.deb ... Unpacking debianutils (5.20) over (5.7-0.5~deb12u1) ... Setting up debianutils (5.20) ... (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 ... 46237 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.10-1_amd64.deb ... Unpacking sysvinit-utils (3.10-1) 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 (3.10-1) ... (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 ... 46237 files and directories currently installed.) Preparing to unpack .../x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) over (1:7.7+23) ... Preparing to unpack .../libice6_2%3a1.0.10-1+b1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1+b1) over (2:1.0.10-1) ... Preparing to unpack .../libuuid1_2.40.2-1_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-1) over (2.38.1-5+deb12u1) ... Setting up libuuid1:amd64 (2.40.2-1) ... (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 ... 46238 files and directories currently installed.) Preparing to unpack .../00-libsm6_2%3a1.2.3-1+b1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1+b1) over (2:1.2.3-1) ... Preparing to unpack .../01-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) over (3.0-13) ... Preparing to unpack .../02-libpaper1_1.1.29+b1_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29+b1) over (1.1.29) ... Preparing to unpack .../03-libpaper-utils_1.1.29+b1_amd64.deb ... Unpacking libpaper-utils (1.1.29+b1) over (1.1.29) ... Preparing to unpack .../04-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) over (3.11.0-2) ... Preparing to unpack .../05-libdeflate0_1.21-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.21-1) over (1.14-1) ... Preparing to unpack .../06-libjpeg62-turbo_1%3a2.1.5-3_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3) over (1:2.1.5-2) ... Preparing to unpack .../07-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) over (3.11.0-2) ... Preparing to unpack .../08-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) over (2024a-0+deb12u1) ... Preparing to unpack .../09-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 .../10-libsharpyuv0_1.4.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ... Preparing to unpack .../11-libwebp7_1.4.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1) over (1.2.4-0.2+deb12u1) ... Preparing to unpack .../12-libjbig0_2.1-6.1+b1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b1) over (2.1-6.1) ... Preparing to unpack .../13-liblerc4_4.0.0+ds-4+b1_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-4+b1) over (4.0.0+ds-2) ... Preparing to unpack .../14-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) over (4.5.0-6+deb12u1) ... Preparing to unpack .../15-libxft2_2.3.6-1+b1_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b1) over (2.3.6-1) ... Preparing to unpack .../16-libxss1_1%3a1.2.3-1+b1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b1) over (1:1.2.3-1) ... Preparing to unpack .../17-libtk8.6_8.6.14-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.14-1) over (8.6.13-2) ... Preparing to unpack .../18-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311) ... Preparing to unpack .../19-r-base-core_4.4.1-1_amd64.deb ... Unpacking r-base-core (4.4.1-1) over (4.2.2.20221110-2) ... dpkg: libtirpc3:amd64: dependency problems, but removing anyway as you requested: libnsl2:amd64 depends on libtirpc3 (>= 1.0.2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45650 files and directories currently installed.) Removing libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 45643 files and directories currently installed.) Preparing to unpack .../libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Preparing to unpack .../libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) over (1.3.0-2) ... Preparing to unpack .../linux-libc-dev_6.10.4-1_all.deb ... Unpacking linux-libc-dev (6.10.4-1) over (6.1.94-1) ... Preparing to unpack .../bash_5.2.21-2.1+b1_amd64.deb ... Unpacking bash (5.2.21-2.1+b1) over (5.2.15-2+b7) ... Setting up bash (5.2.21-2.1+b1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (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 ... 47335 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-1_amd64.deb ... Unpacking bsdutils (1:2.40.2-1) over (1:2.38.1-5+deb12u1) ... Setting up bsdutils (1:2.40.2-1) ... (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 ... 47336 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 ... (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 ... 47341 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-9_amd64.deb ... Unpacking dash (0.5.12-9) over (0.5.12-2) ... Setting up dash (0.5.12-9) ... 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 ... 47338 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 ... 47340 files and directories currently installed.) Preparing to unpack .../findutils_4.10.0-3_amd64.deb ... Unpacking findutils (4.10.0-3) over (4.9.0-4) ... Setting up findutils (4.10.0-3) ... (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 ... 47338 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_amd64.deb ... Unpacking grep (3.11-4) over (3.8-5) ... Setting up grep (3.11-4) ... (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 ... 47338 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 ... 47338 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 ... (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 ... 47338 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.5-2_amd64.deb ... Unpacking ncurses-bin (6.5-2) over (6.4-4) ... Setting up ncurses-bin (6.5-2) ... (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 ... 47338 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 ... 47338 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-1) over (2.38.1-5+deb12u1) ... Setting up libsmartcols1:amd64 (2.40.2-1) ... (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 ... 47339 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-1_amd64.deb ... Unpacking util-linux (2.40.2-1) over (2.38.1-5+deb12u1) ... Setting up util-linux (2.40.2-1) ... (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 ... 47313 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.40.2-1_amd64.deb ... Adding 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-1) over (2.38.1-5+deb12u1) ... 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 (2.40.2-1) ... (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 ... 47353 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 ... 47353 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 ... 47353 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5-2_all.deb ... Unpacking ncurses-base (6.5-2) over (6.4-4) ... Setting up ncurses-base (6.5-2) ... (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 ... 47351 files and directories currently installed.) Preparing to unpack .../logsave_1.47.1-1_amd64.deb ... Unpacking logsave (1.47.1-1) 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 ... 47351 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 ... 47344 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.1-1_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 (1.47.1-1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.1-1) ... (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 ... 47360 files and directories currently installed.) Preparing to unpack .../00-e2fsprogs_1.47.1-1_amd64.deb ... Unpacking e2fsprogs (1.47.1-1) 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 .../01-mount_2.40.2-1_amd64.deb ... Unpacking mount (2.40.2-1) over (2.38.1-5+deb12u1) ... Preparing to unpack .../02-mawk_1.3.4.20240622-2_amd64.deb ... Unpacking mawk (1.3.4.20240622-2) over (1.3.4.20200120-3.1) ... Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) over (0.0.17+nmu1) ... Preparing to unpack .../04-liblua5.3-0_5.3.6-2+b2_amd64.deb ... Unpacking liblua5.3-0:amd64 (5.3.6-2+b2) over (5.3.6-2) ... Preparing to unpack .../05-libss2_1.47.1-1_amd64.deb ... 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Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libxcb-render0:amd64 (1.17.0-2) ... Setting up libyaml-0-2:amd64 (0.2.5-1+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libuv1t64:amd64 (1.48.0-5) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up linux-libc-dev (6.10.4-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up libgomp1:amd64 (14.2.0-1) ... Setting up libjs-modernizr (3.13.0-0.1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up gcc-12-base:amd64 (12.4.0-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Aug 23 14:28:48 UTC 2024. Universal Time is now: Fri Aug 23 14:28:48 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up zip (3.0-14) ... Setting up libblas3:amd64 (3.12.0-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libquadmath0:amd64 (14.2.0-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libatomic1:amd64 (14.2.0-1) ... Setting up libss2:amd64 (1.47.1-1) ... 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 ... 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Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up pandoc-data (3.1.3-2) ... Setting up libtsan2:amd64 (14.2.0-1) ... Setting up libc-dev-bin (2.39-7) ... Setting up openssl (3.2.2-1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liblsan0:amd64 (14.2.0-1) ... Setting up libitm1:amd64 (14.2.0-1) ... Setting up libice6:amd64 (2:1.0.10-1+b1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up e2fsprogs (1.47.1-1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/mke2fs.conf ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-2) ... 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 libglib2.0-0t64:amd64 (2.81.1-3) ... No schema files found: doing nothing. Setting up pandoc (3.1.3+ds-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libgcc-12-dev:amd64 (12.4.0-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libc6-dev:amd64 (2.39-7) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libgcc-14-dev:amd64 (14.2.0-1) ... Setting up libstdc++-14-dev:amd64 (14.2.0-1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.1) ... Setting up libcurl4t64:amd64 (8.9.1-2) ... Setting up libstdc++-12-dev:amd64 (12.4.0-2) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-1) ... Setting up r-base-core (4.4.1-1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Replacing config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-xml (3.99-0.17-1) ... Setting up libnsl-dev:amd64 (1.3.0-3+b2) ... Setting up r-cran-commonmark (1.9.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Setting up r-cran-filelock (1.0.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.12-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-fs (1.6.4+dfsg-1) ... Setting up r-cran-rcpp (1.0.13-1) ... Setting up r-cran-curl (5.2.1+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.3.0-1) ... Setting up littler (0.3.20-1) ... Setting up r-bioc-matrixgenerics (1.14.0-1) ... Setting up r-cran-xfun (0.45+dfsg-1) ... Setting up r-cran-sys (3.4.2-1) ... Setting up r-cran-withr (3.0.0+dfsg-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-digest (0.6.36-1) ... Setting up r-cran-yaml (2.3.8-2) ... Setting up r-bioc-protgenerics (1.34.0-1) ... Setting up r-cran-evaluate (0.24.0-1) ... Setting up r-cran-dbi (1.2.3-1) ... Setting up r-cran-highr (0.11+dfsg-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-cli (3.6.2-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-bioc-biocversion (3.18.1-1) ... Setting up r-cran-biocmanager (1.30.22+dfsg-2) ... Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ... Setting up r-cran-askpass (1.2.0-1) ... Setting up r-cran-png (0.1-8-1+b1) ... Setting up r-bioc-biobase (2.62.0-1) ... Setting up r-cran-jsonlite (1.8.8+dfsg-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.3-1) ... Setting up r-cran-cpp11 (0.4.7-1) ... Setting up r-cran-later (1.3.2+dfsg-1) ... Setting up r-cran-matrix (1.7-0-3) ... Setting up r-cran-htmltools (0.5.8.1-1) ... Setting up r-cran-tinytex (0.51-1) ... Setting up r-bioc-tximport (1.30.0+dfsg-1) ... Setting up r-cran-knitr (1.47+dfsg-1) ... Setting up r-cran-cachem (1.0.8-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biocparallel (1.36.0-1) ... Setting up r-bioc-rhtslib (2.4.1+dfsg-3) ... Setting up r-cran-xml2 (1.3.6-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-promises (1.3.0+dfsg-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-cran-dplyr (1.1.4-1) ... Setting up r-cran-rsqlite (2.3.7-2) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-cran-shiny (1.8.1.1+dfsg-1) ... Setting up r-cran-rmarkdown (2.27+dfsg-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-cran-dbplyr (2.4.0+dfsg-1) ... Setting up r-cran-crosstalk (1.2.1+dfsg-1) ... Setting up r-bioc-biocfilecache (2.10.1+dfsg-1) ... Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... Setting up r-cran-dt (0.33+dfsg-1) ... Setting up r-bioc-interactivedisplaybase (1.40.0+dfsg-1) ... Processing triggers for libc-bin (2.39-7) ... Processing triggers for debianutils (5.20) ... 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. 1m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 1m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m33.9s DUMP: 2c4d716416de6232ea90313ae1b7703f - 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 1m34.0s DUMP: E: No packages found 1m34.0s DEBUG: Command failed (status=100), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 1m34.0s INFO: apt-cache does not know about any of the requested packages 1m34.0s INFO: Running scripts post_distupgrade 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_exceptions'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_exceptions'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_zz_backports'] 1m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_zz_backports'] 1m34.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 1m36.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 1m36.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt0_pwphj to sid 1m36.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m36.1s INFO: Running scripts pre_distupgrade 1m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_exceptions'] 1m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_exceptions'] 1m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 1m39.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9953 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7304 kB] Fetched 17.5 MB in 3s (6749 kB/s) Reading package lists... 1m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'update'] 1m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 1m47.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax javascript-common libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-14-dev libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 liblua5.4-0 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 libssh2-1t64 libstdc++-12-dev libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libyaml-0-2 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data r-base-core r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biocversion r-bioc-genomeinfodbdata r-bioc-interactivedisplaybase r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-tximport r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto ucf unzip x11-common xdg-utils zip zlib1g-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: login.defs openssl-provider-legacy The following packages will be upgraded: bash bsdutils gcc-14-base libasan8 libatomic1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libgcc-14-dev libgcc-s1 libgfortran5 libglib2.0-0t64 libgomp1 libharfbuzz0b libhwasan0 libitm1 libldap-2.5-0 liblsan0 libmount1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libquadmath0 libreadline8t64 libselinux1 libsmartcols1 libssl3t64 libstdc++-14-dev libstdc++6 libtsan2 libubsan1 libuuid1 libxml2 linux-libc-dev login mawk mount openssl passwd r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biocversion r-bioc-interactivedisplaybase r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-tximport r-bioc-zlibbioc r-cran-digest readline-common util-linux util-linux-extra 55 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 38.0 MB of archives. After this operation, 584 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.32-1 [1499 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-7 [105 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.40.2-7 [265 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-7 [35.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-7 [167 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-7 [199 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-7 [139 kB] Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-7 [1217 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-7 [154 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.7-1+b1 [76.6 kB] Get:13 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-4 [185 kB] Get:14 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-7 [57.7 kB] Get:15 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-4 [1232 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-3 [2728 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-3 [1075 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-3 [137 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-3 [25.9 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-3 [9288 B] Get:21 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-3 [1205 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-3 [1488 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-3 [145 kB] Get:24 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-3 [46.2 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-3 [713 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-3 [2365 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-3 [2671 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-3 [2461 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-3 [72.8 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Get:32 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.3.1-7 [298 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.3.1-7 [2269 kB] Get:34 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240819-2 [138 kB] Get:35 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.81.2-1 [1497 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 9.0.0-1 [474 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-2 [35.2 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-2 [54.4 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-2 [223 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:44 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.10.6-1 [2376 kB] Get:45 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.1-7 [1381 kB] Get:46 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-1 [9652 B] Get:47 http://deb.debian.org/debian sid/main amd64 r-bioc-tximport all 1.32.0+dfsg-1 [91.2 kB] Get:48 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.0.0+dfsg-1 [1334 kB] Get:49 http://deb.debian.org/debian sid/main amd64 r-bioc-protgenerics all 1.36.0-1 [237 kB] Get:50 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.16.0-1 [423 kB] Get:51 http://deb.debian.org/debian sid/main amd64 r-bioc-interactivedisplaybase all 1.42.0+dfsg-1 [30.6 kB] Get:52 http://deb.debian.org/debian sid/main amd64 r-bioc-biocversion all 3.19.1-1 [10.9 kB] Get:53 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:54 http://deb.debian.org/debian sid/main amd64 r-bioc-biocfilecache all 2.12.0+dfsg-1 [301 kB] Get:55 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.64.0-2 [2132 kB] Get:56 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.50.0-1 [606 kB] Get:57 http://deb.debian.org/debian sid/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.0 MB in 0s (118 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 ... 47444 files and directories currently installed.) Preparing to unpack .../bash_5.2.32-1_amd64.deb ... Unpacking bash (5.2.32-1) over (5.2.21-2.1+b1) ... Setting up bash (5.2.32-1) ... Installing new version of config file /etc/bash.bashrc ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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Leaving 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-7) over (2.40.2-1) ... Preparing to unpack .../libuuid1_2.40.2-7_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-7) over (2.40.2-1) ... Setting up libuuid1:amd64 (2.40.2-7) ... (Reading database ... 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Unpacking openssl-provider-legacy (3.3.1-7) ... Setting up libssl3t64:amd64 (3.3.1-7) ... Setting up openssl-provider-legacy (3.3.1-7) ... (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 ... 47404 files and directories currently installed.) Preparing to unpack .../00-mawk_1.3.4.20240819-2_amd64.deb ... Unpacking mawk (1.3.4.20240819-2) over (1.3.4.20240622-2) ... Preparing to unpack .../01-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) over (8.2-4) ... 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Leaving 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Leaving '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' Leaving 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Leaving '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 (8.2-5) over (8.2-4) ... Preparing to unpack .../09-libxml2_2.12.7+dfsg-3+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-3+b1) over (2.9.14+dfsg-1.3+b3) ... Preparing to unpack .../10-linux-libc-dev_6.10.6-1_all.deb ... Unpacking linux-libc-dev (6.10.6-1) over (6.10.4-1) ... Preparing to unpack .../11-openssl_3.3.1-7_amd64.deb ... Unpacking openssl (3.3.1-7) over (3.2.2-1) ... 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Setting up linux-libc-dev (6.10.6-1) ... Setting up libgomp1:amd64 (14.2.0-3) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up r-bioc-biocversion (3.19.1-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-1) ... Setting up r-bioc-biobase (2.64.0-2) ... Setting up libquadmath0:amd64 (14.2.0-3) ... Setting up libatomic1:amd64 (14.2.0-3) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up r-bioc-tximport (1.32.0+dfsg-1) ... Setting up libubsan1:amd64 (14.2.0-3) ... Setting up mount (2.40.2-7) ... Setting up libhwasan0:amd64 (14.2.0-3) ... Setting up libasan8:amd64 (14.2.0-3) ... Setting up mawk (1.3.4.20240819-2) ... Setting up libtsan2:amd64 (14.2.0-3) ... Setting up openssl (3.3.1-7) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up liblsan0:amd64 (14.2.0-3) ... Setting up libitm1:amd64 (14.2.0-3) ... Setting up util-linux-extra (2.40.2-7) ... Setting up login (1:4.16.0-2+really2.40.2-7) ... Setting up r-bioc-rhtslib (3.0.0+dfsg-1) ... Setting up libglib2.0-0t64:amd64 (2.81.2-1) ... No schema files found: doing nothing. Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libharfbuzz0b:amd64 (9.0.0-1) ... Setting up libgcc-14-dev:amd64 (14.2.0-3) ... Setting up libstdc++-14-dev:amd64 (14.2.0-3) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Processing triggers for debianutils (5.20) ... Processing triggers for libc-bin (2.39-7) ... 1m47.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-yf', 'dist-upgrade'] 1m47.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m47.6s DUMP: c6b4bcc6dd80aeeda6f3d4a51151beb7 - 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 1m47.9s DUMP: Package: r-bioc-tximeta Version: 1.22.1+dfsg-1 Installed-Size: 728 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-summarizedexperiment (>= 1.34.0), r-bioc-tximport (>= 1.32.0), r-cran-jsonlite, r-bioc-s4vectors (>= 0.42.1), r-bioc-iranges (>= 2.38.1), r-bioc-genomicranges (>= 1.56.1), r-bioc-annotationdbi (>= 1.66.0), r-bioc-genomicfeatures (>= 1.56.0), r-bioc-txdbmaker, r-bioc-ensembldb (>= 2.28.0), r-bioc-biocfilecache (>= 2.12.0), r-bioc-annotationhub (>= 3.12.0), r-bioc-biostrings (>= 2.72.1), r-cran-tibble, r-bioc-genomeinfodb (>= 1.40.1), r-cran-matrix Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat, r-bioc-tximportdata (>= 1.32.0), r-bioc-deseq2 (>= 1.44.0), r-bioc-fishpond (>= 2.10.0), r-bioc-edger (>= 4.2.0), r-bioc-limma (>= 3.60.3), r-cran-devtools Description-en: Transcript Quantification Import with Automatic Metadata Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility. Description-md5: 75f999d7edd35b8ba0d462a84ab80b38 Homepage: https://bioconductor.org/packages/tximeta/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-tximeta/r-bioc-tximeta_1.22.1+dfsg-1_all.deb Size: 538420 MD5sum: 34d1631861379f3246c65246fdfe3d9f SHA256: 2f819c1e8e7de846e860c316bcb4bd63c0e70a5d25d44e23d51d2d435945763c 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-tximeta'] 1m47.9s INFO: apt-cache knows about the following packages: r-bioc-tximeta 1m47.9s INFO: Running scripts pre_install 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m47.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m47.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 1m48.0s 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: 1m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 1m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 1m48.0s DUMP: r-bioc-tximeta: Installed: (none) Candidate: 1.22.1+dfsg-1 Version table: 1.22.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 1m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 1m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta'] 2m30.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgcc-12-dev liblua5.3-0 libnsl-dev libnsl2 libstdc++-12-dev libtirpc-dev r-bioc-interactivedisplaybase r-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: fonts-lmodern libbibtex-parser-perl libgdbm-compat4t64 libgdbm6t64 libio-string-perl libjs-lunr libkpathsea6 liblatex-tounicode-perl libmpfi0 libmpfr6 libperl5.38t64 libpotrace0 libptexenc1 libsynctex2 libteckit0 libtexlua53-5 libxaw7 libxi6 libxmu6 libxpm4 libzzip-0-13t64 perl perl-modules-5.38 r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biocio r-bioc-biocstyle r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-ucsc.utils r-bioc-xvector r-cran-abind r-cran-bookdown r-cran-httr2 r-cran-restfulr t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base Suggested packages: gdbm-l10n libmpfi-doc perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl r-bioc-go.db r-cran-runit r-bioc-org.hs.eg.db r-bioc-graph r-cran-testthat r-bioc-variantannotation r-bioc-experimenthub r-cran-mockery r-cran-httptest2 r-bioc-pwalign r-bioc-bsgenome r-bioc-affy r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-ggbio r-bioc-gviz r-cran-r.utils r-cran-data.table r-bioc-shortread r-bioc-deseq2 r-bioc-edger r-cran-markdown r-bioc-annotate r-bioc-dexseq r-bioc-limma r-bioc-rhdf5 r-cran-rmariadb r-bioc-tximportdata r-bioc-fishpond r-cran-devtools debhelper ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc wp2latex Recommended packages: netbase r-cran-downlit r-cran-rstudioapi r-cran-miniui r-cran-rsconnect r-cran-testit r-cran-tufte r-cran-webshot r-cran-testthat r-cran-bench r-cran-clipr r-cran-covr r-cran-docopt r-cran-webfakes r-cran-runit lmodern dvisvgm The following NEW packages will be installed: fonts-lmodern libbibtex-parser-perl libgdbm-compat4t64 libgdbm6t64 libio-string-perl libjs-lunr libkpathsea6 liblatex-tounicode-perl libmpfi0 libmpfr6 libperl5.38t64 libpotrace0 libptexenc1 libsynctex2 libteckit0 libtexlua53-5 libxaw7 libxi6 libxmu6 libxpm4 libzzip-0-13t64 perl perl-modules-5.38 r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biocio r-bioc-biocstyle r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-tximeta r-bioc-ucsc.utils r-bioc-xvector r-cran-abind r-cran-bookdown r-cran-httr2 r-cran-restfulr t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 178 MB/178 MB of archives. After this operation, 400 MB of additional disk space will be used. 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2:1.8.1-1 [79.0 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:24 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-1 [1894 kB] Get:25 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:26 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:27 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:28 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:29 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:30 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:31 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:32 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.56.1+dfsg-1 [1842 kB] Get:33 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationfilter all 1.28.0+dfsg-1 [245 kB] Get:34 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationhub all 3.12.0+dfsg-1 [445 kB] Get:35 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.14.0+dfsg-1 [210 kB] Get:36 http://deb.debian.org/debian sid/main amd64 r-cran-bookdown all 0.40+dfsg-1 [1404 kB] Get:37 http://deb.debian.org/debian sid/main amd64 tex-common all 6.18 [32.5 kB] Get:38 http://deb.debian.org/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:39 http://deb.debian.org/debian sid/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-4 [8493 kB] Get:40 http://deb.debian.org/debian sid/main amd64 texlive-base all 2024.20240706-1 [22.7 MB] Get:41 http://deb.debian.org/debian sid/main amd64 texlive-latex-base all 2024.20240706-1 [1274 kB] Get:42 http://deb.debian.org/debian sid/main amd64 texlive-bibtex-extra all 2024.20240706-2 [79.1 MB] Get:43 http://deb.debian.org/debian sid/main amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [453 kB] Get:44 http://deb.debian.org/debian sid/main amd64 r-cran-httr2 all 1.0.2-1 [582 kB] Get:45 http://deb.debian.org/debian sid/main amd64 r-bioc-biomart all 2.60.1+dfsg-1 [452 kB] Get:46 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-5-2 [64.6 kB] Get:47 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.4.1+dfsg-1 [524 kB] Get:48 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.4.8+dfsg-1 [1254 kB] Get:49 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.30.1+dfsg-1 [1847 kB] Get:50 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.20.0+dfsg-1 [3600 kB] Get:51 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.34.0+dfsg-1 [1102 kB] Get:52 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.40.0-1 [2160 kB] Get:53 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.64.0-1 [5061 kB] Get:54 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.56.0+dfsg-1 [918 kB] Get:55 http://deb.debian.org/debian sid/main amd64 r-bioc-ensembldb all 2.28.0+dfsg-1 [1508 kB] Get:56 http://deb.debian.org/debian sid/main amd64 r-bioc-txdbmaker all 1.0.1+ds-1 [739 kB] Get:57 http://deb.debian.org/debian sid/main amd64 r-bioc-tximeta all 1.22.1+dfsg-1 [538 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 178 MB in 1s (127 MB/s) Selecting previously unselected package perl-modules-5.38. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 47412 files and directories currently installed.) Preparing to unpack .../00-perl-modules-5.38_5.38.2-5_all.deb ... Unpacking perl-modules-5.38 (5.38.2-5) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../01-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../02-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../03-libperl5.38t64_5.38.2-5_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-5) ... Selecting previously unselected package perl. Preparing to unpack .../04-perl_5.38.2-5_amd64.deb ... Unpacking perl (5.38.2-5) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../05-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../06-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package liblatex-tounicode-perl. Preparing to unpack .../07-liblatex-tounicode-perl_0.54-2_all.deb ... Unpacking liblatex-tounicode-perl (0.54-2) ... Selecting previously unselected package libbibtex-parser-perl. 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Unpacking r-bioc-annotationdbi (1.66.0-1) ... Selecting previously unselected package r-bioc-genomicranges. Preparing to unpack .../31-r-bioc-genomicranges_1.56.1+dfsg-1_amd64.deb ... Unpacking r-bioc-genomicranges (1.56.1+dfsg-1) ... Selecting previously unselected package r-bioc-annotationfilter. Preparing to unpack .../32-r-bioc-annotationfilter_1.28.0+dfsg-1_all.deb ... Unpacking r-bioc-annotationfilter (1.28.0+dfsg-1) ... Selecting previously unselected package r-bioc-annotationhub. Preparing to unpack .../33-r-bioc-annotationhub_3.12.0+dfsg-1_all.deb ... Unpacking r-bioc-annotationhub (3.12.0+dfsg-1) ... Selecting previously unselected package r-bioc-biocio. Preparing to unpack .../34-r-bioc-biocio_1.14.0+dfsg-1_all.deb ... Unpacking r-bioc-biocio (1.14.0+dfsg-1) ... Selecting previously unselected package r-cran-bookdown. Preparing to unpack .../35-r-cran-bookdown_0.40+dfsg-1_all.deb ... Unpacking r-cran-bookdown (0.40+dfsg-1) ... Selecting previously unselected package tex-common. Preparing to unpack .../36-tex-common_6.18_all.deb ... Unpacking tex-common (6.18) ... Selecting previously unselected package t1utils. Preparing to unpack .../37-t1utils_1.41-4_amd64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package texlive-binaries. Preparing to unpack .../38-texlive-binaries_2024.20240313.70630+ds-4_amd64.deb ... Unpacking texlive-binaries (2024.20240313.70630+ds-4) ... Selecting previously unselected package texlive-base. Preparing to unpack .../39-texlive-base_2024.20240706-1_all.deb ... Unpacking texlive-base (2024.20240706-1) ... Selecting previously unselected package texlive-latex-base. Preparing to unpack .../40-texlive-latex-base_2024.20240706-1_all.deb ... Unpacking texlive-latex-base (2024.20240706-1) ... Selecting previously unselected package texlive-bibtex-extra. Preparing to unpack .../41-texlive-bibtex-extra_2024.20240706-2_all.deb ... Unpacking texlive-bibtex-extra (2024.20240706-2) ... Selecting previously unselected package r-bioc-biocstyle. Preparing to unpack .../42-r-bioc-biocstyle_2.32.1+dfsg-1_all.deb ... Unpacking r-bioc-biocstyle (2.32.1+dfsg-1) ... Selecting previously unselected package r-cran-httr2. Preparing to unpack .../43-r-cran-httr2_1.0.2-1_all.deb ... Unpacking r-cran-httr2 (1.0.2-1) ... Selecting previously unselected package r-bioc-biomart. Preparing to unpack .../44-r-bioc-biomart_2.60.1+dfsg-1_all.deb ... Unpacking r-bioc-biomart (2.60.1+dfsg-1) ... Selecting previously unselected package r-cran-abind. Preparing to unpack .../45-r-cran-abind_1.4-5-2_all.deb ... Unpacking r-cran-abind (1.4-5-2) ... Selecting previously unselected package r-bioc-s4arrays. Preparing to unpack .../46-r-bioc-s4arrays_1.4.1+dfsg-1_amd64.deb ... Unpacking r-bioc-s4arrays (1.4.1+dfsg-1) ... Selecting previously unselected package r-bioc-sparsearray. Preparing to unpack .../47-r-bioc-sparsearray_1.4.8+dfsg-1_amd64.deb ... Unpacking r-bioc-sparsearray (1.4.8+dfsg-1) ... Selecting previously unselected package r-bioc-delayedarray. Preparing to unpack .../48-r-bioc-delayedarray_0.30.1+dfsg-1_amd64.deb ... Unpacking r-bioc-delayedarray (0.30.1+dfsg-1) ... Selecting previously unselected package r-bioc-rsamtools. Preparing to unpack .../49-r-bioc-rsamtools_2.20.0+dfsg-1_amd64.deb ... Unpacking r-bioc-rsamtools (2.20.0+dfsg-1) ... Selecting previously unselected package r-bioc-summarizedexperiment. Preparing to unpack .../50-r-bioc-summarizedexperiment_1.34.0+dfsg-1_all.deb ... Unpacking r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Selecting previously unselected package r-bioc-genomicalignments. Preparing to unpack .../51-r-bioc-genomicalignments_1.40.0-1_amd64.deb ... Unpacking r-bioc-genomicalignments (1.40.0-1) ... Selecting previously unselected package r-cran-restfulr. Preparing to unpack .../52-r-cran-restfulr_0.0.15-1_amd64.deb ... Unpacking r-cran-restfulr (0.0.15-1) ... Selecting previously unselected package r-bioc-rtracklayer. Preparing to unpack .../53-r-bioc-rtracklayer_1.64.0-1_amd64.deb ... Unpacking r-bioc-rtracklayer (1.64.0-1) ... Selecting previously unselected package r-bioc-genomicfeatures. Preparing to unpack .../54-r-bioc-genomicfeatures_1.56.0+dfsg-1_all.deb ... Unpacking r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Selecting previously unselected package r-bioc-ensembldb. Preparing to unpack .../55-r-bioc-ensembldb_2.28.0+dfsg-1_all.deb ... Unpacking r-bioc-ensembldb (2.28.0+dfsg-1) ... Selecting previously unselected package r-bioc-txdbmaker. Preparing to unpack .../56-r-bioc-txdbmaker_1.0.1+ds-1_all.deb ... Unpacking r-bioc-txdbmaker (1.0.1+ds-1) ... Selecting previously unselected package r-bioc-tximeta. Preparing to unpack .../57-r-bioc-tximeta_1.22.1+dfsg-1_all.deb ... Unpacking r-bioc-tximeta (1.22.1+dfsg-1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libgdbm6t64:amd64 (1.24-2) ... Setting up libxpm4:amd64 (1:3.5.17-1+b1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libgdbm-compat4t64:amd64 (1.24-2) ... Setting up r-cran-abind (1.4-5-2) ... Setting up libjs-lunr (2.3.9~dfsg-2) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up r-cran-httr2 (1.0.2-1) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up libmpfr6:amd64 (4.2.1-1+b1) ... Setting up libteckit0:amd64 (2.5.12+ds1-1) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-1) ... Setting up perl-modules-5.38 (5.38.2-5) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Setting up libmpfi0:amd64 (1.5.4+ds-3) ... Setting up libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Setting up fonts-lmodern (2.005-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up libperl5.38t64:amd64 (5.38.2-5) ... Setting up r-cran-restfulr (0.0.15-1) ... Setting up r-cran-bookdown (0.40+dfsg-1) ... Setting up libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Setting up libpotrace0:amd64 (1.16-2+b1) ... Setting up r-bioc-s4arrays (1.4.1+dfsg-1) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-biocio (1.14.0+dfsg-1) ... Setting up perl (5.38.2-5) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2024.20240706-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up r-bioc-sparsearray (1.4.8+dfsg-1) ... Setting up r-bioc-genomicranges (1.56.1+dfsg-1) ... Setting up liblatex-tounicode-perl (0.54-2) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-bioc-annotationfilter (1.28.0+dfsg-1) ... Setting up libio-string-perl (1.08-4) ... Setting up texlive-latex-base (2024.20240706-1) ... Setting up r-bioc-rsamtools (2.20.0+dfsg-1) ... Setting up r-bioc-delayedarray (0.30.1+dfsg-1) ... Setting up r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Setting up r-bioc-keggrest (1.44.1+dfsg-1) ... Setting up r-bioc-annotationdbi (1.66.0-1) ... Setting up libbibtex-parser-perl (1.04+dfsg-1) ... Setting up texlive-bibtex-extra (2024.20240706-2) ... Setting up r-bioc-annotationhub (3.12.0+dfsg-1) ... Setting up r-bioc-biomart (2.60.1+dfsg-1) ... Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ... Setting up r-bioc-genomicalignments (1.40.0-1) ... Setting up r-bioc-rtracklayer (1.64.0-1) ... Setting up r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Setting up r-bioc-txdbmaker (1.0.1+ds-1) ... Setting up r-bioc-ensembldb (2.28.0+dfsg-1) ... Setting up r-bioc-tximeta (1.22.1+dfsg-1) ... Processing triggers for libc-bin (2.39-7) ... Processing triggers for fontconfig (2.15.0-1.1) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta'] 2m30.8s INFO: Running scripts post_install 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 2m30.8s INFO: Running scripts post_distupgrade 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_exceptions'] 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_exceptions'] 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_zz_backports'] 2m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_distupgrade_zz_backports'] 2m30.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m33.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m36.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m36.1s INFO: Running scripts pre_install 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 2m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_database-server'] 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 2m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_exceptions'] 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 2m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_extras'] 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 2m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture'] 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 2m36.2s 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: 2m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy'] 2m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 2m36.2s DUMP: r-bioc-tximeta: Installed: 1.22.1+dfsg-1 Candidate: 1.22.1+dfsg-1 Version table: *** 1.22.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-cache', 'policy', 'r-bioc-tximeta'] 2m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta=1.22.1+dfsg-1'] 2m36.9s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-tximeta is already the newest version (1.22.1+dfsg-1). The following packages were automatically installed and are no longer required: libgcc-12-dev liblua5.3-0 libnsl-dev libnsl2 libstdc++-12-dev libtirpc-dev r-bioc-interactivedisplaybase r-cran-assertthat r-cran-ellipsis Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m36.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', '-y', 'install', 'r-bioc-tximeta=1.22.1+dfsg-1'] 2m36.9s INFO: Running scripts post_install 2m36.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 2m36.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_install_exceptions'] 2m37.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m39.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 2m44.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', '-ac', '--ignore-obsolete'] 2m49.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', '-ac', '--ignore-obsolete'] 2m49.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m49.9s DUMP: 0.15.6 2m49.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m49.9s INFO: Running adequate version 0.15.6 now. 2m49.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'r-bioc-tximeta'] 2m50.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'r-bioc-tximeta'] 2m50.1s INFO: Running scripts pre_remove 2m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_exceptions'] 2m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/pre_remove_exceptions'] 2m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m58.0s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 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 fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-glyphicons-halflings fonts-glyphicons-halflings 1.009~3.4.1+dfsg-3 install ok installed fonts-lmodern fonts-lmodern 2.005-1 install ok installed fonts-mathjax fonts-mathjax 2.7.9+dfsg-1 install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed javascript-common javascript-common 11+nmu1 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libasan8:amd64 libasan8 14.2.0-3 install ok installed libatomic1:amd64 libatomic1 14.2.0-3 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libbibtex-parser-perl libbibtex-parser-perl 1.04+dfsg-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-3.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.39-7 install ok installed libc-dev-bin libc-dev-bin 2.39-7 install ok installed libc6:amd64 libc6 2.39-7 install ok installed libc6-dev:amd64 libc6-dev 2.39-7 install ok installed libcairo2:amd64 libcairo2 1.18.0-3+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl4t64:amd64 libcurl4t64 8.9.1-2 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.21-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 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+b4 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.4.0-2 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-3 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.24-2 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.24-2 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-3 deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 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installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3 install ok installed libjs-bootstrap libjs-bootstrap 3.4.1+dfsg-3 install ok installed libjs-bootstrap4 libjs-bootstrap4 4.6.1+dfsg1-4 install ok installed libjs-d3 libjs-d3 3.5.17-4 install ok installed libjs-es5-shim libjs-es5-shim 4.6.7-2 install ok installed libjs-highlight.js libjs-highlight.js 9.18.5+dfsg1-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-datatables libjs-jquery-datatables 1.11.5+dfsg-2 install ok installed libjs-jquery-datatables-extensions libjs-jquery-datatables-extensions 0.0+git20150910.28fd64e+dfsg-5 install ok installed libjs-jquery-selectize.js libjs-jquery-selectize.js 0.12.6+dfsg-1.1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-json libjs-json 0~20221030+~1.0.8-1 install ok installed libjs-lunr libjs-lunr 2.3.9~dfsg-2 install ok installed libjs-mathjax libjs-mathjax 2.7.9+dfsg-1 install ok installed libjs-microplugin.js libjs-microplugin.js 0.0.3+dfsg-1.1 install ok installed libjs-modernizr libjs-modernizr 3.13.0-0.1 install ok installed libjs-popper.js libjs-popper.js 1.16.1+ds-6 install ok installed libjs-prettify libjs-prettify 2015.12.04+dfsg-1.1 install ok installed libjs-sifter.js libjs-sifter.js 0.6.0+dfsg-3 install ok installed libjs-twitter-bootstrap-datepicker libjs-twitter-bootstrap-datepicker 1.3.1+dfsg1-4.1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkpathsea6:amd64 libkpathsea6 2024.20240313.70630+ds-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblatex-tounicode-perl liblatex-tounicode-perl 0.54-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblsan0:amd64 liblsan0 14.2.0-3 install ok installed liblua5.3-0:amd64 liblua5.3-0 5.3.6-2+b2 install ok installed liblua5.4-0:amd64 liblua5.4-0 5.4.6-3+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libmpfi0:amd64 libmpfi0 1.5.4+ds-3 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.62.1-2 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3+b2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-2 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-2 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-2 install ok installed libpaper-utils libpaper-utils 1.1.29+b1 install ok installed libpaper1:amd64 libpaper1 1.1.29+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-5 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libpotrace0:amd64 libpotrace0 1.16-2+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libptexenc1:amd64 libptexenc1 2024.20240313.70630+ds-4 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-7 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-1+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl3t64:amd64 libssl3t64 3.3.1-7 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.4.0-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-3 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsynctex2:amd64 libsynctex2 2024.20240313.70630+ds-4 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 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 libteckit0:amd64 libteckit0 2.5.12+ds1-1 install ok installed libtexlua53-5:amd64 libtexlua53-5 2024.20240313.70630+ds-4 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-3 install ok installed libubsan1:amd64 libubsan1 14.2.0-3 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libuv1t64:amd64 libuv1t64 1.48.0-5 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1+b1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1+b1 install ok installed libxaw7:amd64 libxaw7 2:1.0.14-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2 install ok installed libxcb1:amd64 libxcb1 1.17.0-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3+b1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg-3+b1 install ok installed libxmu6:amd64 libxmu6 2:1.1.3-3+b2 install ok installed libxpm4:amd64 libxpm4 1:3.5.17-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b1 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed libzzip-0-13t64:amd64 libzzip-0-13t64 0.13.72+dfsg.1-1.3 install ok installed linux-libc-dev linux-libc-dev 6.10.6-1 install ok installed littler littler 0.3.20-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240819-2 install ok installed mount mount 2.40.2-7 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed node-bootstrap-sass node-bootstrap-sass 3.4.3-2 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed node-normalize.css node-normalize.css 8.0.1-5 install ok installed openssl openssl 3.3.1-7 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.1-7 install ok installed pandoc pandoc 3.1.3+ds-3 install ok installed pandoc-data pandoc-data 3.1.3-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl perl 5.38.2-5 install ok installed perl-base perl-base 5.38.2-5 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-5 install ok installed r-base-core r-base-core 4.4.1-1 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.66.0-1 install ok installed r-bioc-annotationfilter r-bioc-annotationfilter 1.28.0+dfsg-1 install ok installed r-bioc-annotationhub r-bioc-annotationhub 3.12.0+dfsg-1 install ok installed r-bioc-biobase r-bioc-biobase 2.64.0-2 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.12.0+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.50.0-1 install ok installed r-bioc-biocio r-bioc-biocio 1.14.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.38.0-2 install ok installed r-bioc-biocstyle r-bioc-biocstyle 2.32.1+dfsg-1 install ok installed r-bioc-biocversion r-bioc-biocversion 3.19.1-1 install ok installed r-bioc-biomart r-bioc-biomart 2.60.1+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.72.1+dfsg-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.30.1+dfsg-1 install ok installed r-bioc-ensembldb r-bioc-ensembldb 2.28.0+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.40.1+dfsg-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.12-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.40.0-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.56.0+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.56.1+dfsg-1 install ok installed r-bioc-interactivedisplaybase r-bioc-interactivedisplaybase 1.42.0+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.38.1-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.44.1+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.16.0-1 install ok installed r-bioc-protgenerics r-bioc-protgenerics 1.36.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 3.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.20.0+dfsg-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.64.0-1 install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.4.1+dfsg-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.42.1+dfsg-1 install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.4.8+dfsg-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.34.0+dfsg-1 install ok installed r-bioc-txdbmaker r-bioc-txdbmaker 1.0.1+ds-1 install ok installed r-bioc-tximeta r-bioc-tximeta 1.22.1+dfsg-1 install ok installed r-bioc-tximport r-bioc-tximport 1.32.0+dfsg-1 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.0.0+ds-2 install ok installed r-bioc-xvector r-bioc-xvector 0.44.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.50.0+dfsg-1 install ok installed r-cran-abind r-cran-abind 1.4-5-2 install ok installed r-cran-askpass r-cran-askpass 1.2.0-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-base64enc r-cran-base64enc 0.1-3-3 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-biocmanager r-cran-biocmanager 1.30.22+dfsg-2 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 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install ok installed r-cran-evaluate r-cran-evaluate 0.24.0-1 install ok installed r-cran-fansi r-cran-fansi 1.0.5-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-filelock r-cran-filelock 1.0.3-1 install ok installed r-cran-fontawesome r-cran-fontawesome 0.5.2-1 install ok installed r-cran-formatr r-cran-formatr 1.14-2 install ok installed r-cran-fs r-cran-fs 1.6.4+dfsg-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.7.0-1 install ok installed r-cran-highr r-cran-highr 0.11+dfsg-1 install ok installed r-cran-hms r-cran-hms 1.1.3-1 install ok installed r-cran-htmltools r-cran-htmltools 0.5.8.1-1 install ok installed r-cran-htmlwidgets r-cran-htmlwidgets 1.6.4+dfsg-1 install ok installed r-cran-httpuv r-cran-httpuv 1.6.15+dfsg-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-httr2 r-cran-httr2 1.0.2-1 install ok installed r-cran-jquerylib r-cran-jquerylib 0.1.4+dfsg-4 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.8+dfsg-1 install ok installed r-cran-knitr r-cran-knitr 1.47+dfsg-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-later r-cran-later 1.3.2+dfsg-1 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.2-1+b1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-matrix r-cran-matrix 1.7-0-3 install ok installed r-cran-matrixstats r-cran-matrixstats 1.3.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mime r-cran-mime 0.12-2 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.9.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.3-1 install ok installed r-cran-plogr r-cran-plogr 0.2.0-3 install ok installed r-cran-png r-cran-png 0.1-8-1+b1 install ok installed r-cran-prettyunits r-cran-prettyunits 1.2.0-1 install ok installed r-cran-progress r-cran-progress 1.2.3-1 install ok installed r-cran-promises r-cran-promises 1.3.0+dfsg-1 install ok installed r-cran-purrr r-cran-purrr 1.0.2-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.13-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.14+dfsg-1+b1 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rmarkdown r-cran-rmarkdown 2.27+dfsg-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.7-2 install ok installed r-cran-sass r-cran-sass 0.4.9+dfsg-1 install ok installed r-cran-shiny r-cran-shiny 1.8.1.1+dfsg-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-sourcetools r-cran-sourcetools 0.1.7-1-1 install ok installed r-cran-stringi r-cran-stringi 1.8.3-1 install ok installed r-cran-stringr r-cran-stringr 1.5.1-1 install ok installed r-cran-sys r-cran-sys 3.4.2-1 install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-2 install ok installed r-cran-tidyr r-cran-tidyr 1.3.1-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1 install ok installed r-cran-tinytex r-cran-tinytex 0.51-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-withr r-cran-withr 3.0.0+dfsg-1 install ok installed r-cran-xfun r-cran-xfun 0.45+dfsg-1 install ok installed r-cran-xml r-cran-xml 3.99-0.17-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.6-1 install ok installed r-cran-xtable r-cran-xtable 1:1.8-4-2 install ok installed r-cran-yaml r-cran-yaml 2.3.8-2 install ok installed readline-common readline-common 8.2-5 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.24 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed t1utils t1utils 1.41-4 install ok installed tar tar 1.35+dfsg-3 install ok installed tex-common tex-common 6.18 install ok installed texlive-base texlive-base 2024.20240706-1 install ok installed texlive-bibtex-extra texlive-bibtex-extra 2024.20240706-2 install ok installed texlive-binaries texlive-binaries 2024.20240313.70630+ds-4 install ok installed texlive-latex-base texlive-latex-base 2024.20240706-1 install ok installed tzdata tzdata 2024a-4 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-7 install ok installed util-linux-extra util-linux-extra 2.40.2-7 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1 2m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.38', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-annotationfilter', 'r-bioc-annotationhub', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-ensembldb', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-interactivedisplaybase', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-protgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-txdbmaker', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-tximeta'] 3m1.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Package 'libglib2.0-0' is not installed, so not removed The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libasan8 libatomic1 libbibtex-parser-perl libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libio-string-perl libitm1 libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblsan0 liblua5.3-0 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnsl-dev libnsl2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.38t64 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-12-dev libstdc++-14-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 linux-libc-dev littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.38 r-base-core r-bioc-annotationdbi r-bioc-annotationfilter r-bioc-annotationhub r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart r-bioc-biostrings r-bioc-delayedarray r-bioc-ensembldb r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-interactivedisplaybase r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-protgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-txdbmaker r-bioc-tximeta r-bioc-tximport r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-assertthat r-cran-base64enc r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark r-cran-cpp11 r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-highr r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr r-cran-httr2 r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite r-cran-sass r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml readline-common rpcsvc-proto sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 295 to remove and 0 not upgraded. After this operation, 1235 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61138 files and directories currently installed.) Removing r-bioc-tximeta (1.22.1+dfsg-1) ... Removing r-bioc-txdbmaker (1.0.1+ds-1) ... Removing r-bioc-ensembldb (2.28.0+dfsg-1) ... Removing r-bioc-interactivedisplaybase (1.42.0+dfsg-1) ... Removing r-cran-dt (0.33+dfsg-1) ... Removing r-cran-htmlwidgets (1.6.4+dfsg-1) ... Removing r-bioc-genomicfeatures (1.56.0+dfsg-1) ... Removing r-bioc-biocstyle (2.32.1+dfsg-1) ... Removing texlive-bibtex-extra (2024.20240706-2) ... Removing r-cran-bookdown (0.40+dfsg-1) ... Removing r-cran-crosstalk (1.2.1+dfsg-1) ... Removing texlive-latex-base (2024.20240706-1) ... Removing fonts-lmodern (2.005-1) ... Removing libstdc++-12-dev:amd64 (12.4.0-2) ... Removing libgcc-12-dev:amd64 (12.4.0-2) ... Removing texlive-base (2024.20240706-1) ... Removing libbibtex-parser-perl (1.04+dfsg-1) ... Removing r-bioc-biomart (2.60.1+dfsg-1) ... Removing r-cran-httr2 (1.0.2-1) ... Removing r-bioc-annotationhub (3.12.0+dfsg-1) ... Removing r-bioc-annotationdbi (1.66.0-1) ... Removing r-bioc-keggrest (1.44.1+dfsg-1) ... Removing r-bioc-annotationfilter (1.28.0+dfsg-1) ... Removing liblatex-tounicode-perl (0.54-2) ... Removing libio-string-perl (1.08-4) ... Removing libnsl-dev:amd64 (1.3.0-3+b2) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.3) ... Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing r-bioc-biocfilecache (2.12.0+dfsg-1) ... Removing r-cran-dbplyr (2.4.0+dfsg-1) ... Removing r-cran-tidyr (1.3.1-1) ... Removing r-cran-stringr (1.5.1-1) ... Removing r-cran-stringi (1.8.3-1) ... Removing r-cran-xml2 (1.3.6-1) ... Removing libjs-jquery-datatables-extensions (0.0+git20150910.28fd64e+dfsg-5) ... Removing libjs-lunr (2.3.9~dfsg-2) ... Removing liblua5.3-0:amd64 (5.3.6-2+b2) ... Removing r-cran-png (0.1-8-1+b1) ... Removing littler (0.3.20-1) ... Removing r-bioc-tximport (1.32.0+dfsg-1) ... Removing r-bioc-biocversion (3.19.1-1) ... Removing r-bioc-protgenerics (1.36.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-biocmanager (1.30.22+dfsg-2) ... Removing r-cran-rsqlite (2.3.7-2) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.4-1) ... Removing r-cran-dplyr (1.1.4-1) ... Removing r-cran-tidyselect (1.2.1+dfsg-1) ... Removing r-cran-tibble (3.2.1+dfsg-2) ... Removing r-cran-pillar (1.9.0+dfsg-1) ... Removing r-cran-progress (1.2.3-1) ... Removing r-cran-dbi (1.2.3-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-fansi (1.0.5-1) ... Removing r-cran-filelock (1.0.3-1) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-purrr (1.0.2-1) ... Removing r-cran-hms (1.1.3-1) ... Removing r-cran-lazyeval (0.2.2-1+b1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-prettyunits (1.2.0-1) ... Removing r-cran-utf8 (1.2.4-1) ... Removing r-bioc-rtracklayer (1.64.0-1) ... Removing r-bioc-genomicalignments (1.40.0-1) ... Removing r-bioc-summarizedexperiment (1.34.0+dfsg-1) ... Removing r-bioc-delayedarray (0.30.1+dfsg-1) ... Removing r-bioc-sparsearray (1.4.8+dfsg-1) ... Removing r-bioc-s4arrays (1.4.1+dfsg-1) ... Removing r-cran-abind (1.4-5-2) ... Removing r-bioc-rsamtools (2.20.0+dfsg-1) ... Removing r-bioc-biocparallel (1.38.0-2) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-rmarkdown (2.27+dfsg-1) ... Removing r-cran-shiny (1.8.1.1+dfsg-1) ... Removing texlive-binaries (2024.20240313.70630+ds-4) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing r-cran-knitr (1.47+dfsg-1) ... Removing libjs-mathjax (2.7.9+dfsg-1) ... Removing fonts-mathjax (2.7.9+dfsg-1) ... Removing r-cran-bslib (0.7.0+dfsg-1) ... Removing libjs-bootstrap4 (4.6.1+dfsg1-4) ... Removing libjs-popper.js (1.16.1+ds-6) ... Removing javascript-common (11+nmu1) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-3.1) ... Removing libstdc++-14-dev:amd64 (14.2.0-3) ... Removing libgcc-14-dev:amd64 (14.2.0-3) ... Removing libasan8:amd64 (14.2.0-3) ... Removing r-bioc-biostrings (2.72.1+dfsg-1) ... Removing r-bioc-genomicranges (1.56.1+dfsg-1) ... Removing r-bioc-xvector (0.44.0-1) ... Removing r-bioc-rhtslib (3.0.0+dfsg-1) ... Removing r-bioc-zlibbioc (1.50.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Removing libc6-dev:amd64 (2.39-7) ... Removing libc-dev-bin (2.39-7) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing perl (5.38.2-5) ... Removing libperl5.38t64:amd64 (5.38.2-5) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libhwasan0:amd64 (14.2.0-3) ... Removing libxaw7:amd64 (2:1.0.14-1+b2) ... Removing libxmu6:amd64 (2:1.1.3-3+b2) ... Removing libitm1:amd64 (14.2.0-3) ... Removing libjs-d3 (3.5.17-4) ... Removing libjs-es5-shim (4.6.7-2) ... Removing r-cran-highr (0.11+dfsg-1) ... Removing libjs-highlight.js (9.18.5+dfsg1-2) ... Removing r-cran-jquerylib (0.1.4+dfsg-4) ... Removing libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... Removing libjs-jquery-datatables (1.11.5+dfsg-2) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-json (0~20221030+~1.0.8-1) ... Removing libjs-microplugin.js (0.0.3+dfsg-1.1) ... Removing libjs-modernizr (3.13.0-0.1) ... Removing libjs-prettify (2015.12.04+dfsg-1.1) ... Removing libjs-sifter.js (0.6.0+dfsg-3) ... Removing libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... Removing libptexenc1:amd64 (2024.20240313.70630+ds-4) ... Removing libkpathsea6:amd64 (2024.20240313.70630+ds-4) ... Removing liblsan0:amd64 (14.2.0-3) ... Removing pandoc (3.1.3+ds-3) ... Removing liblua5.4-0:amd64 (5.4.6-3+b1) ... Removing libmpfi0:amd64 (1.5.4+ds-3) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libpotrace0:amd64 (1.16-2+b1) ... Removing libquadmath0:amd64 (14.2.0-3) ... Removing libsynctex2:amd64 (2024.20240313.70630+ds-4) ... Removing libteckit0:amd64 (2.5.12+ds1-1) ... Removing libtexlua53-5:amd64 (2024.20240313.70630+ds-4) ... Removing libtsan2:amd64 (14.2.0-3) ... Removing libubsan1:amd64 (14.2.0-3) ... Removing r-cran-httpuv (1.6.15+dfsg-1) ... Removing r-cran-sass (0.4.9+dfsg-1) ... Removing r-cran-fs (1.6.4+dfsg-1) ... Removing libuv1t64:amd64 (1.48.0-5) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxpm4:amd64 (1:3.5.17-1+b1) ... Removing libyaml-0-2:amd64 (0.2.5-1+b1) ... Removing libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Removing linux-libc-dev (6.10.6-1) ... Removing node-bootstrap-sass (3.4.3-2) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing node-normalize.css (8.0.1-5) ... Removing pandoc-data (3.1.3-2) ... Removing perl-modules-5.38 (5.38.2-5) ... Removing r-bioc-biobase (2.64.0-2) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Removing r-bioc-ucsc.utils (1.0.0+ds-2) ... Removing r-bioc-iranges (2.38.1-1) ... Removing r-bioc-biocio (1.14.0+dfsg-1) ... Removing r-bioc-genomeinfodbdata (1.2.12-1) ... Removing r-bioc-matrixgenerics (1.16.0-1) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... Removing r-cran-askpass (1.2.0-1) ... Removing r-cran-fontawesome (0.5.2-1) ... Removing r-cran-htmltools (0.5.8.1-1) ... Removing r-cran-base64enc (0.1-3-3) ... Removing r-cran-rcurl (1.98-1.14+dfsg-1+b1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.8-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-commonmark (1.9.1-1) ... Removing r-cran-cpp11 (0.4.7-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-digest (0.6.37-1) ... Removing r-cran-evaluate (0.24.0-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-2) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-glue (1.7.0-1) ... Removing r-cran-jsonlite (1.8.8+dfsg-1) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-matrixstats (1.3.0-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sourcetools (0.1.7-1-1) ... Removing r-cran-sys (3.4.2-1) ... Removing r-cran-tinytex (0.51-1) ... Removing r-cran-withr (3.0.0+dfsg-1) ... Removing r-cran-xfun (0.45+dfsg-1) ... Removing r-cran-xml (3.99-0.17-1) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-cran-yaml (2.3.8-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing tex-common (6.18) ... Removing t1utils (1.41-4) ... Removing r-cran-matrix (1.7-0-3) ... Removing r-cran-promises (1.3.0+dfsg-1) ... Removing libjs-bootstrap (3.4.1+dfsg-3) ... Removing fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Removing r-cran-curl (5.2.1+dfsg-1) ... Removing libxml2:amd64 (2.12.7+dfsg-3+b1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing r-bioc-s4vectors (0.42.1+dfsg-1) ... Removing r-bioc-biocgenerics (0.50.0-1) ... Removing r-cran-cli (3.6.2-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-later (1.3.2+dfsg-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-rcpp (1.0.13-1) ... Removing r-cran-littler (0.3.20-1) ... Removing r-cran-pkgkitten (0.2.3-1) ... Removing r-base-core (4.4.1-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-2) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-2) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-2) ... Removing fontconfig (2.15.0-1.1) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libharfbuzz0b:amd64 (9.0.0-1) ... Removing libglib2.0-0t64:amd64 (2.81.2-1) ... Removing libatomic1:amd64 (14.2.0-3) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libcairo2:amd64 (1.18.0-3+b1) ... Removing libcurl4t64:amd64 (8.9.1-2) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.21-1) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgfortran5:amd64 (14.2.0-3) ... Removing libgomp1:amd64 (14.2.0-3) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libxt6t64:amd64 (1:1.2.1-1.2) ... Removing libsm6:amd64 (2:1.2.3-1+b1) ... Removing libice6:amd64 (2:1.0.10-1+b1) ... Removing libicu72:amd64 (72.1-5) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing libnghttp2-14:amd64 (1.62.1-2) ... Removing libpaper-utils (1.1.29+b1) ... Removing libpaper1:amd64 (1.1.29+b1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-7) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-7) ... Removing libwebp7:amd64 (1.4.0-0.1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libxss1:amd64 (1:1.2.3-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2) ... Removing libxcb-render0:amd64 (1.17.0-2) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing openssl (3.3.1-7) ... Removing readline-common (8.2-5) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-14) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libx11-6:amd64 (2:1.8.7-1+b1) ... Removing libx11-data (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-2) ... Removing libxau6:amd64 (1:1.0.9-1+b1) ... Removing libxdmcp6:amd64 (1:1.1.2-3+b1) ... Processing triggers for libc-bin (2.39-7) ... 3m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.38', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-annotationfilter', 'r-bioc-annotationhub', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-ensembldb', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-interactivedisplaybase', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-protgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-txdbmaker', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-tximeta'] 3m1.9s INFO: Running scripts post_remove 3m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_remove_exceptions'] 3m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_remove_exceptions'] 3m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.38', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-annotationfilter', 'r-bioc-annotationhub', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-ensembldb', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-interactivedisplaybase', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-protgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-txdbmaker', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 3m2.4s DUMP: (Reading database ... 5352 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) ... Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-glyphicons-halflings which isn't installed Purging configuration files for fonts-lmodern (2.005-1) ... dpkg: warning: while removing fonts-lmodern, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove fonts-mathjax which isn't installed Purging configuration files for javascript-common (11+nmu1) ... dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbibtex-parser-perl which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.81.2-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-bootstrap which isn't installed Purging configuration files for libjs-bootstrap4 (4.6.1+dfsg1-4) ... dpkg: warning: ignoring request to remove libjs-d3 which isn't installed dpkg: warning: ignoring request to remove libjs-es5-shim which isn't installed dpkg: warning: ignoring request to remove libjs-highlight.js which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-datatables which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-datatables-extensions which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-selectize.js which isn't installed dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-json which isn't installed dpkg: warning: ignoring request to remove libjs-lunr which isn't installed dpkg: warning: ignoring request to remove libjs-mathjax which isn't installed dpkg: warning: ignoring request to remove libjs-microplugin.js which isn't installed dpkg: warning: ignoring request to remove libjs-modernizr which isn't installed Purging configuration files for libjs-popper.js (1.16.1+ds-6) ... dpkg: warning: ignoring request to remove libjs-prettify which isn't installed dpkg: warning: ignoring request to remove libjs-sifter.js which isn't installed dpkg: warning: ignoring request to remove libjs-twitter-bootstrap-datepicker which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkpathsea6 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblatex-tounicode-perl which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblua5.3-0 which isn't installed dpkg: warning: ignoring request to remove liblua5.4-0 which isn't installed dpkg: warning: ignoring request to remove libmpfi0 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove 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+b1) ... dpkg: warning: ignoring request to remove libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libpotrace0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libptexenc1 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libstdc++-14-dev which isn't installed dpkg: warning: ignoring request to remove libsynctex2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libteckit0 which isn't installed dpkg: warning: ignoring request to remove libtexlua53-5 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libuv1t64 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxaw7 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmu6 which isn't installed dpkg: warning: ignoring request to remove libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove libzzip-0-13t64 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove node-bootstrap-sass which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed dpkg: warning: ignoring request to remove node-normalize.css which isn't installed Purging configuration files for openssl (3.3.1-7) ... dpkg: warning: ignoring request to remove pandoc which isn't installed dpkg: warning: ignoring request to remove pandoc-data which isn't installed Purging configuration files for perl (5.38.2-5) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for r-base-core (4.4.1-1) ... dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-annotationfilter which isn't installed dpkg: warning: ignoring request to remove r-bioc-annotationhub which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocfilecache which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocstyle which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocversion which isn't installed dpkg: warning: ignoring request to remove r-bioc-biomart which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-ensembldb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicalignments which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicfeatures which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-interactivedisplaybase which isn't installed dpkg: warning: ignoring request to remove r-bioc-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-keggrest which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-protgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-txdbmaker which isn't installed dpkg: warning: ignoring request to remove r-bioc-tximport which isn't installed dpkg: warning: ignoring request to remove r-bioc-ucsc.utils which isn't installed dpkg: warning: ignoring request to remove r-bioc-xvector which isn't installed dpkg: warning: ignoring request to remove r-bioc-zlibbioc which isn't installed dpkg: warning: ignoring request to remove r-cran-abind which isn't installed dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-base64enc which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-biocmanager which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-bookdown which isn't installed dpkg: warning: ignoring request to remove r-cran-bslib which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-commonmark which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-crosstalk which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-dbplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-dt which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-filelock which isn't installed dpkg: warning: ignoring request to remove r-cran-fontawesome which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-fs which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-generics which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-highr which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-htmltools which isn't installed dpkg: warning: ignoring request to remove r-cran-htmlwidgets which isn't installed dpkg: warning: ignoring request to remove r-cran-httpuv which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-httr2 which isn't installed dpkg: warning: ignoring request to remove r-cran-jquerylib which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-knitr which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-later which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lazyeval which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-promises which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rmarkdown which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-sass which isn't installed dpkg: warning: ignoring request to remove r-cran-shiny which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-sourcetools which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyr which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-tinytex which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xfun which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 which isn't installed dpkg: warning: ignoring request to remove r-cran-xtable which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove t1utils which isn't installed Purging configuration files for tex-common (6.18) ... Purging configuration files for texlive-base (2024.20240706-1) ... Purging configuration files for texlive-bibtex-extra (2024.20240706-2) ... dpkg: warning: ignoring request to remove texlive-binaries which isn't installed Purging configuration files for texlive-latex-base (2024.20240706-1) ... Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: 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 3m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-glyphicons-halflings', 'fonts-lmodern', 'fonts-mathjax', 'javascript-common', 'libasan8:amd64', 'libatomic1:amd64', 'libbibtex-parser-perl', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-bootstrap', 'libjs-bootstrap4', 'libjs-d3', 'libjs-es5-shim', 'libjs-highlight.js', 'libjs-jquery', 'libjs-jquery-datatables', 'libjs-jquery-datatables-extensions', 'libjs-jquery-selectize.js', 'libjs-jquery-ui', 'libjs-json', 'libjs-lunr', 'libjs-mathjax', 'libjs-microplugin.js', 'libjs-modernizr', 'libjs-popper.js', 'libjs-prettify', 'libjs-sifter.js', 'libjs-twitter-bootstrap-datepicker', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkpathsea6:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblatex-tounicode-perl', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'liblua5.3-0:amd64', 'liblua5.4-0:amd64', 'libmpfi0:amd64', 'libmpfr6: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', 'libperl5.38t64:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpotrace0:amd64', 'libpsl5t64:amd64', 'libptexenc1:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-14-dev:amd64', 'libsynctex2:amd64', 'libtcl8.6:amd64', 'libteckit0:amd64', 'libtexlua53-5:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libuv1t64:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxpm4:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'libyaml-0-2:amd64', 'libzzip-0-13t64:amd64', 'linux-libc-dev', 'littler', 'node-bootstrap-sass', 'node-html5shiv', 'node-normalize.css', 'openssl', 'pandoc', 'pandoc-data', 'perl', 'perl-modules-5.38', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-annotationfilter', 'r-bioc-annotationhub', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biocstyle', 'r-bioc-biocversion', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-ensembldb', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-interactivedisplaybase', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-protgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-txdbmaker', 'r-bioc-tximport', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-base64enc', 'r-cran-bh', 'r-cran-biocmanager', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-bookdown', 'r-cran-bslib', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-commonmark', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-crosstalk', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-dt', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-fontawesome', 'r-cran-formatr', 'r-cran-fs', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-highr', 'r-cran-hms', 'r-cran-htmltools', 'r-cran-htmlwidgets', 'r-cran-httpuv', 'r-cran-httr', 'r-cran-httr2', 'r-cran-jquerylib', 'r-cran-jsonlite', 'r-cran-knitr', 'r-cran-lambda.r', 'r-cran-later', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-promises', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rmarkdown', 'r-cran-rsqlite', 'r-cran-sass', 'r-cran-shiny', 'r-cran-snow', 'r-cran-sourcetools', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-tinytex', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xfun', 'r-cran-xml', 'r-cran-xml2', 'r-cran-xtable', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 't1utils', 'tex-common', 'texlive-base', 'texlive-bibtex-extra', 'texlive-binaries', 'texlive-latex-base', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 3m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', 'r-bioc-tximeta'] 3m2.4s DUMP: dpkg: warning: ignoring request to remove r-bioc-tximeta which isn't installed 3m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', 'r-bioc-tximeta'] 3m2.4s INFO: Running scripts post_purge 3m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_purge_exceptions'] 3m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_purge_exceptions'] 3m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', '--pending'] 3m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--purge', '--pending'] 3m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--remove', '--pending'] 3m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg', '--remove', '--pending'] 3m2.5s INFO: Running scripts post_test 3m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_test_exceptions'] 3m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'tmp/scripts/post_test_exceptions'] 3m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 3m3.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 3m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-divert', '--list'] 3m3.0s DUMP: diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra 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 /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra 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 diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra 3m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'dpkg-divert', '--list'] 3m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'clean'] 3m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj', 'apt-get', 'clean'] 3m3.1s DEBUG: Recording chroot state 3m3.6s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fonts-lmodern, fontconfig-config, fonts-dejavu-mono, fonts-dejavu-core /etc/fonts/conf.d/ owned by: fonts-lmodern, 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 3m4.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/shm'] 3m4.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/shm'] 3m4.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/console'] 3m4.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/console'] 3m4.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/ptmx'] 3m4.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/ptmx'] 3m4.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts'] 3m4.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/dev/pts'] 3m4.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/proc'] 3m4.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj/proc'] 3m4.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 3m4.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt0_pwphj'] 3m4.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpt0_pwphj 3m4.2s INFO: PASS: Upgrading between Debian distributions. 3m4.2s INFO: PASS: All tests. 3m4.2s INFO: piuparts run ends. ret=0 End: 2024-08-23 14:30:29 GMT