Start: 2024-11-26 21:24:12 GMT [sid] Package: r-bioc-geoquery Version: 2.72.0+dfsg-1 Installed-Size: 13435 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biobase, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-bioc-limma, r-cran-curl, r-cran-r.utils Suggests: r-cran-knitr, r-cran-rmarkdown, r-bioc-biocgenerics, r-cran-testthat, r-cran-covr, r-cran-markdown Description: Get data from NCBI Gene Expression Omnibus (GEO) Homepage: https://bioconductor.org/packages/GEOquery/ Description-md5: 952355a18eb44e818e0bf24162ae78a1 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-geoquery/r-bioc-geoquery_2.72.0+dfsg-1_all.deb Size: 13670876 MD5sum: a870a3f4d7efc4c51b9f632b8afeadc9 SHA256: 16b6a6f3ccfb7a55dda41fccbef0b5bde18c532c0a5cd8762a368d6d3b6a0ba2 [experimental] Package: r-bioc-geoquery Version: 2.74.0+dfsg-1 Installed-Size: 13518 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-biobase, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-bioc-limma, r-cran-curl, r-cran-rentrez, r-cran-r.utils, r-cran-stringr, r-bioc-summarizedexperiment, r-bioc-s4vectors, r-cran-rvest, r-cran-httr2 Suggests: r-cran-knitr, r-cran-rmarkdown, r-bioc-biocgenerics, r-cran-testthat, r-cran-covr, r-cran-markdown Description: Get data from NCBI Gene Expression Omnibus (GEO) Homepage: https://bioconductor.org/packages/GEOquery/ Description-md5: 952355a18eb44e818e0bf24162ae78a1 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-geoquery/r-bioc-geoquery_2.74.0+dfsg-1_all.deb Size: 13734460 MD5sum: 8afd6567223e36589da190a5dc412007 SHA256: 5ce3fdaa1410972e653ec7f06097ffddfde192a0bf76bc019ab61ddcee6051fb Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt r-bioc-geoquery=2.74.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt r-bioc-geoquery=2.74.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmppp88712c 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppp88712c 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppp88712c', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppp88712c', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppp88712c/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppp88712c/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/tmppp88712c/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/tmppp88712c/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmppp88712c/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', 'update'] 0m2.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7344 kB] Fetched 17.6 MB in 2s (9841 kB/s) Reading package lists... 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', 'update'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libseccomp2 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 47.8 kB of archives. After this operation, 3072 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.8 kB in 0s (2989 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5150 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... Processing triggers for libc-bin (2.40-4) ... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 51ddbcd7e1fba113d75e06c3c4cfadf9 - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DUMP: install ok installed apt apt 2.9.14 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-4 install ok installed libc6:amd64 libc6 2.40-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m4.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m4.3s INFO: Running scripts is_testable 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s INFO: Running scripts pre_test 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-geoquery'] 0m4.4s DUMP: Package: r-bioc-geoquery Version: 2.72.0+dfsg-1 Installed-Size: 13435 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biobase, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-bioc-limma, r-cran-curl, r-cran-r.utils Suggests: r-cran-knitr, r-cran-rmarkdown, r-bioc-biocgenerics, r-cran-testthat, r-cran-covr, r-cran-markdown Description-en: Get data from NCBI Gene Expression Omnibus (GEO) The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. Description-md5: 952355a18eb44e818e0bf24162ae78a1 Homepage: https://bioconductor.org/packages/GEOquery/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-geoquery/r-bioc-geoquery_2.72.0+dfsg-1_all.deb Size: 13670876 MD5sum: a870a3f4d7efc4c51b9f632b8afeadc9 SHA256: 16b6a6f3ccfb7a55dda41fccbef0b5bde18c532c0a5cd8762a368d6d3b6a0ba2 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-geoquery'] 0m4.4s INFO: apt-cache knows about the following packages: r-bioc-geoquery 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy', 'r-bioc-geoquery'] 0m4.5s DUMP: r-bioc-geoquery: Installed: (none) Candidate: 2.72.0+dfsg-1 Version table: 2.72.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy', 'r-bioc-geoquery'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-y', 'install', 'r-bioc-geoquery'] 0m16.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libatomic1 libblas3 libbrotli1 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 littler node-html5shiv openssl r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-limma r-cran-bit r-cran-bit64 r-cran-cli r-cran-clipr r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dplyr r-cran-fansi r-cran-generics r-cran-glue r-cran-hms r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcpp r-cran-readr r-cran-rlang r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-vroom r-cran-withr r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip Suggested packages: low-memory-monitor krb5-doc krb5-user tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-golubesets r-bioc-biocstyle r-cran-knitr r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-rmarkdown r-cran-testthat r-cran-covr r-cran-markdown r-cran-biasedurn r-cran-ellipse r-cran-gplots r-cran-locfit r-cran-mass r-bioc-go.db r-bioc-org.hs.eg.db r-cran-roxygen2 r-cran-ff r-cran-rstudioapi r-cran-microbenchmark r-cran-lubridate r-cran-getopt r-cran-dbi r-cran-formattable r-cran-ggplot2 r-cran-nanotime r-cran-palmerpenguins r-cran-scales r-cran-survival r-cran-units r-cran-vdiffr r-cran-codetools r-cran-inline r-cran-bench r-cran-blob r-cran-brio r-cran-callr r-cran-evaluate r-cran-here r-cran-htmltools r-cran-pkgbuild r-cran-pkgload readline-doc Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-cran-callr r-cran-covr r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-testthat r-cran-whoami r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-ggplot2 r-cran-lobstr r-cran-scales r-cran-spelling r-cran-jsonlite r-cran-later r-cran-httpuv r-cran-webutils r-cran-xts r-cran-zoo r-cran-yaml r-cran-markdown r-cran-broom r-cran-dbi r-cran-dbplyr r-cran-rmysql r-cran-rpostgresql r-cran-rsqlite r-cran-unitizer r-cran-pkgload r-cran-waldo r-cran-lintr r-cran-tidyverse r-cran-lubridate r-cran-codetools r-cran-httr r-cran-fs r-cran-usethis r-cran-mockr r-cran-formattable r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libatomic1 libblas3 libbrotli1 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16t64 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 littler node-html5shiv openssl r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-geoquery r-bioc-limma r-cran-bit r-cran-bit64 r-cran-cli r-cran-clipr r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dplyr r-cran-fansi r-cran-generics r-cran-glue r-cran-hms r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rcpp r-cran-readr r-cran-rlang r-cran-statmod r-cran-stringi r-cran-stringr r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tzdb r-cran-utf8 r-cran-vctrs r-cran-vroom r-cran-withr r-cran-xml2 readline-common sensible-utils ucf unzip x11-common xdg-utils zip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 211 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:2 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:4 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:5 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:10 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:11 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:12 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:14 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:16 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:31 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:38 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:49 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:55 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:56 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:64 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:77 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB] Get:78 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:79 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:80 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:81 http://deb.debian.org/debian sid/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:82 http://deb.debian.org/debian sid/main amd64 littler all 0.3.20-1 [16.0 kB] Get:83 http://deb.debian.org/debian sid/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:84 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:85 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:86 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:87 http://deb.debian.org/debian sid/main amd64 r-cran-clipr all 0.8.0-1 [53.0 kB] Get:88 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:89 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:90 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:91 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:92 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:93 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:94 http://deb.debian.org/debian sid/main amd64 r-cran-hms all 1.1.3-1 [104 kB] Get:95 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:96 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.5-1 [621 kB] Get:97 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:98 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:99 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.9.0+dfsg-1 [463 kB] Get:100 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [420 kB] Get:101 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:102 http://deb.debian.org/debian sid/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:103 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:104 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB] Get:105 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:106 http://deb.debian.org/debian sid/main amd64 r-cran-tzdb amd64 0.4.0-2 [499 kB] Get:107 http://deb.debian.org/debian sid/main amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] Get:108 http://deb.debian.org/debian sid/main amd64 r-cran-progress all 1.2.3-1 [93.0 kB] Get:109 http://deb.debian.org/debian sid/main amd64 r-cran-vroom amd64 1.6.5-1 [830 kB] Get:110 http://deb.debian.org/debian sid/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:111 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:112 http://deb.debian.org/debian sid/main amd64 r-cran-readr amd64 2.1.5-1 [759 kB] Get:113 http://deb.debian.org/debian sid/main amd64 r-cran-xml2 amd64 1.3.6-1 [320 kB] Get:114 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:115 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-2 [1542 kB] Get:116 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.16.2+dfsg-1 [1978 kB] Get:117 http://deb.debian.org/debian sid/main amd64 r-cran-purrr amd64 1.0.2-1 [507 kB] Get:118 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.4-1 [895 kB] Get:119 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:120 http://deb.debian.org/debian sid/main amd64 r-cran-tidyr amd64 1.3.1-1 [1163 kB] Get:121 http://deb.debian.org/debian sid/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:122 http://deb.debian.org/debian sid/main amd64 r-bioc-limma amd64 3.60.6+dfsg-1 [2006 kB] Get:123 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:124 http://deb.debian.org/debian sid/main amd64 r-cran-r.methodss3 all 1.8.2-1 [84.5 kB] Get:125 http://deb.debian.org/debian sid/main amd64 r-cran-r.oo all 1.26.0-1 [961 kB] Get:126 http://deb.debian.org/debian sid/main amd64 r-cran-r.utils all 2.12.3-1 [1396 kB] Get:127 http://deb.debian.org/debian sid/main amd64 r-bioc-geoquery all 2.72.0+dfsg-1 [13.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 2s (56.9 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 ... 5153 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package ucf. Preparing to unpack .../004-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 .../005-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../006-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../007-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../008-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../009-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package libatomic1:amd64. 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Selecting previously unselected package libcairo2:amd64. Preparing to unpack .../026-libcairo2_1.18.2-2_amd64.deb ... Unpacking libcairo2:amd64 (1.18.2-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../027-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../028-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../029-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../030-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../031-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../032-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../033-libsasl2-2_2.1.28+dfsg1-8_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../034-libldap-2.5-0_2.5.18+dfsg-3+b1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../035-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../036-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../037-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../038-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../039-libcurl4t64_8.11.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.11.0-1) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../040-libdatrie1_0.2.13-3+b1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-3+b1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../041-libdeflate0_1.22-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.22-1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../042-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../043-libgfortran5_14.2.0-8_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-8) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../044-libglib2.0-0t64_2.82.2-3_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-3) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../045-libgomp1_14.2.0-8_amd64.deb ... Unpacking libgomp1:amd64 (14.2.0-8) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../046-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../047-libharfbuzz0b_10.0.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../048-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../049-libice6_2%3a1.1.1-1_amd64.deb ... Unpacking libice6:amd64 (2:1.1.1-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../050-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../051-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../052-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../053-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../054-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../055-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libthai-data. Preparing to unpack .../056-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../057-libthai0_0.1.29-2+b1_amd64.deb ... Unpacking libthai0:amd64 (0.1.29-2+b1) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../058-libpango-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../059-libpangoft2-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../060-libpangocairo-1.0-0_1.54.0+ds-3_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Selecting previously unselected package libpaper1:amd64. Preparing to unpack .../061-libpaper1_1.1.29+b2_amd64.deb ... Unpacking libpaper1:amd64 (1.1.29+b2) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../062-libpaper-utils_1.1.29+b2_amd64.deb ... Unpacking libpaper-utils (1.1.29+b2) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../063-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../064-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../065-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../066-libtcl8.6_8.6.15+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.15+dfsg-2) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../067-libwebp7_1.4.0-0.1+b1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../068-libtiff6_4.5.1+git230720-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.1+git230720-5) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../069-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../070-libtirpc3t64_1.3.4+ds-1.3+b1_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+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../071-libxft2_2.3.6-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b2) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../072-libxss1_1%3a1.2.3-1+b2_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../073-libtk8.6_8.6.15-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.15-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../074-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libxt6t64:amd64. Preparing to unpack .../075-libxt6t64_1%3a1.2.1-1.2+b1_amd64.deb ... Unpacking libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Selecting previously unselected package zip. Preparing to unpack .../076-zip_3.0-14_amd64.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package unzip. Preparing to unpack .../077-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../078-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../079-r-base-core_4.4.2-1_amd64.deb ... Unpacking r-base-core (4.4.2-1) ... Selecting previously unselected package r-cran-littler. Preparing to unpack .../080-r-cran-littler_0.3.20-1_amd64.deb ... Unpacking r-cran-littler (0.3.20-1) ... Selecting previously unselected package littler. Preparing to unpack .../081-littler_0.3.20-1_all.deb ... Unpacking littler (0.3.20-1) ... Selecting previously unselected package node-html5shiv. Preparing to unpack .../082-node-html5shiv_3.7.3+dfsg-5_all.deb ... Unpacking node-html5shiv (3.7.3+dfsg-5) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../083-r-bioc-biocgenerics_0.50.0-2_all.deb ... Unpacking r-bioc-biocgenerics (0.50.0-2) ... Selecting previously unselected package r-bioc-biobase. Preparing to unpack .../084-r-bioc-biobase_2.64.0-4_amd64.deb ... Unpacking r-bioc-biobase (2.64.0-4) ... Selecting previously unselected package r-cran-cli. Preparing to unpack .../085-r-cran-cli_3.6.3-1_amd64.deb ... Unpacking r-cran-cli (3.6.3-1) ... Selecting previously unselected package r-cran-clipr. Preparing to unpack .../086-r-cran-clipr_0.8.0-1_all.deb ... Unpacking r-cran-clipr (0.8.0-1) ... Selecting previously unselected package r-cran-crayon. Preparing to unpack .../087-r-cran-crayon_1.5.2-1_all.deb ... Unpacking r-cran-crayon (1.5.2-1) ... 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Preparing to unpack .../124-r-cran-r.oo_1.26.0-1_all.deb ... Unpacking r-cran-r.oo (1.26.0-1) ... Selecting previously unselected package r-cran-r.utils. Preparing to unpack .../125-r-cran-r.utils_2.12.3-1_all.deb ... Unpacking r-cran-r.utils (2.12.3-1) ... Selecting previously unselected package r-bioc-geoquery. Preparing to unpack .../126-r-bioc-geoquery_2.72.0+dfsg-1_all.deb ... Unpacking r-bioc-geoquery (2.72.0+dfsg-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... 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 start. Setting up node-html5shiv (3.7.3+dfsg-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up zip (3.0-14) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.3.2-2) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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 libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... 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 libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.2-1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-clipr (0.8.0-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-littler (0.3.20-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up littler (0.3.20-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-generics (0.1.3-1) ... Setting up r-cran-prettyunits (1.2.0-1) ... Setting up r-cran-fansi (1.0.5-1) ... Setting up r-cran-data.table (1.16.2+dfsg-1) ... Setting up r-cran-glue (1.7.0-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-cran-r.methodss3 (1.8.2-1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-stringi (1.8.4-1) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-bioc-limma (3.60.6+dfsg-1) ... Setting up r-cran-tzdb (0.4.0-2) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-cran-xml2 (1.3.6-1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-r.oo (1.26.0-1) ... Setting up r-cran-tidyselect (1.2.1+dfsg-1) ... Setting up r-cran-hms (1.1.3-1) ... Setting up r-cran-purrr (1.0.2-1) ... Setting up r-cran-dplyr (1.1.4-2) ... Setting up r-cran-progress (1.2.3-1) ... Setting up r-cran-r.utils (2.12.3-1) ... Setting up r-cran-vroom (1.6.5-1) ... Setting up r-cran-readr (2.1.5-1) ... Setting up r-cran-tidyr (1.3.1-1) ... Setting up r-bioc-geoquery (2.72.0+dfsg-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-y', 'install', 'r-bioc-geoquery'] 0m16.1s INFO: Running scripts post_install 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_install_exceptions'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/post_install_exceptions'] 0m16.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m16.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m16.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmppp88712c to experimental 0m16.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m16.6s INFO: Running scripts pre_distupgrade 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', 'update'] 0m17.6s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [509 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [307 kB] Fetched 917 kB in 0s (2060 kB/s) Reading package lists... 0m17.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', 'update'] 0m17.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-yf', 'dist-upgrade'] 0m17.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-yf', 'dist-upgrade'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DUMP: 29b9cbbaf4b4803fe222f6490bab03fb - 0m18.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-geoquery'] 0m18.2s DUMP: Package: r-bioc-geoquery Version: 2.72.0+dfsg-1 Installed-Size: 13435 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-bioc-biobase, r-cran-readr (>= 1.3.1), r-cran-xml2, r-cran-dplyr, r-cran-data.table, r-cran-tidyr, r-cran-magrittr, r-bioc-limma, r-cran-curl, r-cran-r.utils Suggests: r-cran-knitr, r-cran-rmarkdown, r-bioc-biocgenerics, r-cran-testthat, r-cran-covr, r-cran-markdown Description-en: Get data from NCBI Gene Expression Omnibus (GEO) The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. Description-md5: 952355a18eb44e818e0bf24162ae78a1 Homepage: https://bioconductor.org/packages/GEOquery/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-geoquery/r-bioc-geoquery_2.72.0+dfsg-1_all.deb Size: 13670876 MD5sum: a870a3f4d7efc4c51b9f632b8afeadc9 SHA256: 16b6a6f3ccfb7a55dda41fccbef0b5bde18c532c0a5cd8762a368d6d3b6a0ba2 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-geoquery'] 0m18.2s INFO: apt-cache knows about the following packages: r-bioc-geoquery 0m18.2s INFO: Running scripts pre_install 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_database-server'] 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_database-server'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_exceptions'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_exceptions'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_extras'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_extras'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy'] 0m18.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy', 'r-bioc-geoquery'] 0m18.3s DUMP: r-bioc-geoquery: Installed: 2.72.0+dfsg-1 Candidate: 2.72.0+dfsg-1 Version table: 2.74.0+dfsg-1 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 2.72.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-cache', 'policy', 'r-bioc-geoquery'] 0m18.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-y', '-t', 'experimental', 'install', 'r-bioc-geoquery'] 0m18.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-summarizedexperiment : Depends: r-api-bioc-3.19 Depends: r-bioc-genomicranges (>= 1.56.1) but it is not going to be installed Depends: r-bioc-delayedarray (>= 0.30.1) but it is not going to be installed E: Unable to correct problems, you have held broken packages. 0m18.6s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmppp88712c', 'apt-get', '-y', '-t', 'experimental', 'install', 'r-bioc-geoquery'] Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-summarizedexperiment : Depends: r-api-bioc-3.19 Depends: r-bioc-genomicranges (>= 1.56.1) but it is not going to be installed Depends: r-bioc-delayedarray (>= 0.30.1) but it is not going to be installed E: Unable to correct problems, you have held broken packages. 0m19.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/shm'] 0m19.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/shm'] 0m19.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/console'] 0m19.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/console'] 0m19.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/ptmx'] 0m19.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/ptmx'] 0m19.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/pts'] 0m19.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/dev/pts'] 0m19.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/proc'] 0m19.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppp88712c/proc'] 0m19.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m19.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppp88712c'] 0m19.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppp88712c 0m19.3s ERROR: piuparts run ends. ret=1 End: 2024-11-26 21:24:32 GMT