Start: 2025-01-14 03:41:35 GMT [testing] Package: r-bioc-sva Version: 3.52.0-1 Installed-Size: 969 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-cran-mgcv, r-bioc-genefilter (>= 1.86.0), r-bioc-biocparallel (>= 1.38.0), r-cran-matrixstats, r-bioc-limma (>= 3.60.3), r-bioc-edger (>= 4.2.0) Suggests: r-bioc-bladderbatch, r-bioc-biocstyle, r-cran-testthat Description: GNU R Surrogate Variable Analysis Homepage: https://bioconductor.org/packages/sva/ Description-md5: c05f11b1bfa8dfefd1edeafaec2b11d0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-sva/r-bioc-sva_3.52.0-1_amd64.deb Size: 455164 MD5sum: 7a4e86f23fb431096781a19c5ec7b0f9 SHA256: 8f2cc5595ac90c942fcd6a358421af2096b4d352037b5a32357b52f28ed0e0ff [sid] Package: r-bioc-sva Version: 3.54.0-2 Installed-Size: 969 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.20, r-cran-mgcv, r-bioc-genefilter, r-bioc-biocparallel, r-cran-matrixstats, r-bioc-limma, r-bioc-edger Suggests: r-bioc-bladderbatch, r-bioc-biocstyle, r-cran-testthat Description: GNU R Surrogate Variable Analysis Homepage: https://bioconductor.org/packages/sva/ Description-md5: c05f11b1bfa8dfefd1edeafaec2b11d0 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-sva/r-bioc-sva_3.54.0-2_amd64.deb Size: 454764 MD5sum: 8fca3f88c912144bcf26a150ba4175bf SHA256: 25cf898d962422f2839b1528416b6c15d5d8db4f6ce1692707e546d08c626746 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-sva=3.54.0-2 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-sva=3.54.0-2 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmp7z85s_5j 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp7z85s_5j 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/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/tmp7z85s_5j/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/tmp7z85s_5j/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie 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/tmp7z85s_5j/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'update'] 0m2.1s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [175 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9378 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6295 kB] Fetched 15.8 MB in 1s (15.4 MB/s) Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: dash libc-bin libc6 sysvinit-utils 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3566 kB of archives. After this operation, 19.5 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-11 [95.5 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.40-5 [2810 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.40-5 [627 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 sysvinit-utils amd64 3.13-1 [33.2 kB] Preconfiguring packages ... Fetched 3566 kB in 0s (36.7 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 ... 5023 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-11_amd64.deb ... Unpacking dash (0.5.12-11) over (0.5.12-9) ... Setting up dash (0.5.12-11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5023 files and directories currently installed.) Preparing to unpack .../libc6_2.40-5_amd64.deb ... Unpacking libc6:amd64 (2.40-5) over (2.40-4) ... Setting up libc6:amd64 (2.40-5) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-5_amd64.deb ... Unpacking libc-bin (2.40-5) over (2.40-4) ... Setting up libc-bin (2.40-5) ... (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 ... 5023 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.13-1_amd64.deb ... Unpacking sysvinit-utils (3.13-1) over (3.11-1) ... Setting up sysvinit-utils (3.13-1) ... Processing triggers for debianutils (5.21) ... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s DUMP: cbd74954f44e6cc367af2ae90a835577 - 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s INFO: Running scripts post_setup 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s 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 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_dummy_users'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_forbid_home'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s 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' 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_minimize'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_setup_zz_backports'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s DUMP: install ok installed apt apt 2.9.21 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.2-13 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-11 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-12 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.21 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 2.40.2-13 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 2.40-5 install ok installed libc6:amd64 libc6 2.40-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 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 0.277 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-12 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-4 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 2.40.2-13 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-13 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-12 install ok installed libsystemd0:amd64 libsystemd0 257.1-7 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257.1-7 install ok installed libuuid1:amd64 libuuid1 2.40.2-13 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.2-13 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-13 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl-base perl-base 5.40.0-8 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2024b-4 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.2-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m5.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m5.8s INFO: Running scripts is_testable 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s INFO: Running scripts pre_test 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_test_root_password'] 0m5.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_test_root_password'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-sva'] 0m6.1s DUMP: Package: r-bioc-sva Version: 3.52.0-1 Installed-Size: 969 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.19, r-cran-mgcv, r-bioc-genefilter (>= 1.86.0), r-bioc-biocparallel (>= 1.38.0), r-cran-matrixstats, r-bioc-limma (>= 3.60.3), r-bioc-edger (>= 4.2.0) Suggests: r-bioc-bladderbatch, r-bioc-biocstyle, r-cran-testthat Description-en: GNU R Surrogate Variable Analysis The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics). Description-md5: c05f11b1bfa8dfefd1edeafaec2b11d0 Homepage: https://bioconductor.org/packages/sva/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-sva/r-bioc-sva_3.52.0-1_amd64.deb Size: 455164 MD5sum: 7a4e86f23fb431096781a19c5ec7b0f9 SHA256: 8f2cc5595ac90c942fcd6a358421af2096b4d352037b5a32357b52f28ed0e0ff 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-sva'] 0m6.1s INFO: apt-cache knows about the following packages: r-bioc-sva 0m6.1s INFO: Running scripts pre_install 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m6.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m6.2s DUMP: r-bioc-sva: Installed: (none) Candidate: 3.52.0-1 Version table: 3.52.0-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva'] 0m29.3s 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 libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler openssl perl perl-modules-5.40 procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-s4vectors r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-r6 r-cran-rcpp r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libc-devtools glibc-doc manpages-dev gdbm-l10n low-memory-monitor gnutls-bin krb5-doc krb5-user libstdc++-14-doc tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-go.db r-bioc-org.hs.eg.db r-cran-runit r-bioc-biocstyle r-cran-knitr r-bioc-graph r-bioc-all r-bioc-golubesets r-bioc-genomicranges r-bioc-delayedarray r-bioc-rsamtools r-bioc-affy r-bioc-deseq2 r-cran-foreach r-cran-bbmisc r-cran-doparallel r-bioc-variantannotation r-bioc-genomicalignments r-bioc-shortread r-cran-batchtools r-cran-data.table r-bioc-pwalign r-bioc-bsgenome r-bioc-genomicfeatures r-cran-readr r-bioc-rhdf5 r-bioc-summarizedexperiment r-cran-seuratobject r-cran-class r-cran-rcolorbrewer r-cran-r.utils r-cran-markdown r-cran-biasedurn r-cran-ellipse r-cran-gplots r-cran-mass r-bioc-sparsematrixstats r-bioc-sparsearray r-bioc-delayedmatrixstats r-cran-testthat r-bioc-bladderbatch r-cran-rmariadb r-cran-rmarkdown r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-pillar r-cran-rstudioapi r-cran-rmysql r-cran-getopt r-cran-interp r-cran-gam r-cran-digest r-cran-inline r-cran-rmpi r-cran-rlecuyer r-cran-plm r-cran-zoo readline-doc Recommended packages: manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules netbase psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-callr r-cran-covr r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-tibble r-cran-whoami r-cran-withr r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-ggplot2 r-cran-lobstr r-cran-progress r-cran-scales r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-shiny r-cran-testit r-cran-dplyr r-cran-magrittr r-cran-waldo r-cran-jpeg r-cran-readr r-cran-xml2 r-cran-r.rsp r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-markdown r-cran-microbenchmark r-cran-r.devices r-cran-sodium r-cran-fs r-cran-pillar r-cran-usethis r-cran-dbitest r-cran-gert r-cran-gh r-cran-hms r-cran-rvest r-cran-generics 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 libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler openssl perl perl-modules-5.40 procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-s4vectors r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-r6 r-cran-rcpp r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 176 newly installed, 0 to remove and 0 not upgraded. Need to get 188 MB of archives. After this operation, 595 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-8 [267 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0046 [41.1 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-12 [2727 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-12 [9300 B] Get:25 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-12 [137 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-12 [25.9 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-12 [1205 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-12 [2460 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-12 [1075 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-12 [1489 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-12 [145 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-12 [2673 kB] Get:34 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kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 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libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.1.0-2 [478 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:110 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-2 [103 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-2 [16.0 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.64.0-4 [2132 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1894 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.38.1-1 [2305 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 r-cran-dbi all 1.2.3-1 [852 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.0-1 [213 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 r-cran-rsqlite amd64 2.3.7-2 [1187 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 5.2.3+dfsg-1 [178 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.2.0+dfsg-1 [401 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.50.0+dfsg-2 [9876 B] Get:143 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.44.0-1 [622 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.0.0+ds-2 [77.0 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] Get:146 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.40.1+dfsg-1 [3843 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.72.1+dfsg-1 [13.3 MB] Get:149 http://deb.debian.org/debian trixie/main amd64 r-bioc-keggrest all 1.44.1+dfsg-1 [183 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotationdbi all 1.66.0-1 [4682 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-cran-xml amd64 3.99-0.18-1 [1762 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-bioc-annotate all 1.82.0+dfsg-1 [1763 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-cran-formatr all 1.14-2 [152 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-cran-bh all 1.84.0-1 [5912 B] Get:161 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocparallel amd64 1.38.0-2 [1325 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-cran-statmod amd64 1.5.0-1 [295 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-bioc-limma amd64 3.60.6+dfsg-1 [2006 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-6-1 [1392 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-cran-locfit amd64 1.5-9.10-1 [515 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 r-bioc-edger amd64 4.2.2+dfsg-1 [1182 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-matrixstats amd64 1.4.1-1 [510 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-bioc-matrixgenerics all 1.16.0-2 [423 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-1-1 [4138 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.8-3-1 [8265 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-bioc-genefilter amd64 1.86.0-1 [1109 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.166-1 [2330 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-1-1 [3233 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 r-bioc-sva amd64 3.52.0-1 [455 kB] Preconfiguring packages ... Fetched 188 MB in 1s (233 MB/s) Selecting previously unselected package libncursesw6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5027 files and directories currently installed.) Preparing to unpack .../000-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... 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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 (8.2-6) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../093-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 .../094-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... Selecting previously unselected package libtcl8.6:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../100-libxft2_2.3.6-1+b3_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b3) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../101-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../102-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../103-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblsan0:amd64 (14.2.0-12) ... Setting up libitm1:amd64 (14.2.0-12) ... 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+b3) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up perl (5.40.0-8) ... Setting up libglib2.0-0t64:amd64 (2.82.4-1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0046) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libc6-dev:amd64 (2.40-5) ... Setting up libharfbuzz0b:amd64 (10.1.0-2) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libgcc-14-dev:amd64 (14.2.0-12) ... Setting up libstdc++-14-dev:amd64 (14.2.0-12) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up libboost1.83-dev:amd64 (1.83.0-4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libldap-2.5-0:amd64 (2.5.19+dfsg-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... 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-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.22-6-1) ... Setting up r-cran-nlme (3.1.166-1) ... Setting up r-cran-formatr (1.14-2) ... Setting up r-cran-xml (3.99-0.18-1) ... Setting up r-cran-locfit (1.5-9.10-1) ... Setting up r-cran-statmod (1.5.0-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-bioc-genomeinfodbdata (1.2.13-2) ... Setting up r-cran-littler (0.3.20-2) ... Setting up r-cran-bh (1.84.0-1) ... Setting up r-cran-rcpp (1.0.13-1-1) ... Setting up r-cran-curl (5.2.3+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up r-cran-rlang (1.1.4-1) ... Setting up r-cran-matrixstats (1.4.1-1) ... Setting up littler (0.3.20-2) ... Setting up r-bioc-matrixgenerics (1.16.0-2) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-plogr (0.2.0-3) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-dbi (1.2.3-1) ... Setting up r-cran-snow (1:0.4.4-2) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-bit (4.0.5-1) ... Setting up r-cran-xtable (1:1.8-4-2) ... Setting up r-cran-cli (3.6.3-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-cran-bit64 (4.0.5-1) ... Setting up r-bioc-zlibbioc (1.50.0+dfsg-2) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-cran-fastmap (1.2.0-1) ... Setting up r-cran-png (0.1-8-1+b1) ... Setting up r-bioc-biobase (2.64.0-4) ... Setting up r-cran-jsonlite (1.8.9+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-cpp11 (0.5.0-1) ... Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-bioc-limma (3.60.6+dfsg-1) ... Setting up r-cran-matrix (1.7-1-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-bioc-iranges (2.38.1-1) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-openssl (2.2.0+dfsg-1) ... Setting up r-bioc-biocparallel (1.38.0-2) ... Setting up r-bioc-edger (4.2.2+dfsg-1) ... Setting up r-cran-survival (3.8-3-1) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-blob (1.2.4-1) ... Setting up r-bioc-xvector (0.44.0-1) ... Setting up r-cran-rsqlite (2.3.7-2) ... Setting up r-bioc-ucsc.utils (1.0.0+ds-2) ... Setting up r-bioc-genomeinfodb (1.40.1+dfsg-1) ... Setting up r-bioc-biostrings (2.72.1+dfsg-1) ... Setting up r-bioc-keggrest (1.44.1+dfsg-1) ... Setting up r-bioc-annotationdbi (1.66.0-1) ... Setting up r-bioc-annotate (1.82.0+dfsg-1) ... Setting up r-bioc-genefilter (1.86.0-1) ... Setting up r-bioc-sva (3.52.0-1) ... Processing triggers for libc-bin (2.40-5) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva'] 0m29.3s INFO: Running scripts post_install 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m29.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m30.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m30.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp7z85s_5j to sid 0m30.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m30.7s INFO: Running scripts pre_distupgrade 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'update'] 0m33.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 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 [7322 kB] Fetched 17.5 MB in 2s (9184 kB/s) Reading package lists... 0m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'update'] 0m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-yf', 'dist-upgrade'] 0m41.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils dpkg gcc-14-base libasan8 libatomic1 libblkid1 libgcc-14-dev libgcc-s1 libgfortran5 libgomp1 libhwasan0 libitm1 liblsan0 libmount1 libpng16-16t64 libquadmath0 libsharpyuv0 libsmartcols1 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtsan2 libubsan1 libudev1 libuuid1 libwebp7 libxxhash0 linux-libc-dev login mount openssl openssl-provider-legacy r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-s4vectors r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-rcpp tzdata util-linux x11-common 55 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 68.6 MB of archives. After this operation, 814 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.3-1 [106 kB] Get:2 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.13 [1534 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.3-1 [36.2 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.3-1 [169 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.3-1 [200 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.3-1 [140 kB] Get:7 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.3-1 [1212 kB] Get:8 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.3-1 [155 kB] Get:9 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.3-1 [88.4 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-13 [2728 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-13 [1075 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-13 [137 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-13 [25.9 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-13 [9280 B] Get:15 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-13 [1205 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-13 [1489 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-13 [145 kB] Get:18 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-13 [48.6 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-13 [713 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-13 [2374 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-13 [2675 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-13 [2461 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-13 [837 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-13 [72.7 kB] Get:25 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.4.0-2 [301 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.4.0-2 [2302 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257.2-1 [449 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257.2-1 [148 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB] Get:30 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-6 [257 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.45-1 [281 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:34 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.9-1 [2488 kB] Get:35 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.4.0-2 [1422 kB] Get:36 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B] Get:37 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB] Get:38 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.40.1-2 [2309 kB] Get:39 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB] Get:40 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB] Get:41 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.18.0-2 [446 kB] Get:42 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB] Get:43 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.42.1+dfsg-2 [3844 kB] Get:44 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.4 MB] Get:45 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.46.0+dfsg-2 [184 kB] Get:46 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.68.0-2 [4703 kB] Get:47 http://deb.debian.org/debian sid/main amd64 r-bioc-genefilter amd64 1.88.0-2 [1233 kB] Get:48 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.40.0-2 [1326 kB] Get:49 http://deb.debian.org/debian sid/main amd64 r-bioc-limma amd64 3.62.1+dfsg-2 [2022 kB] Get:50 http://deb.debian.org/debian sid/main amd64 r-bioc-edger amd64 4.4.1+dfsg-2 [1116 kB] Get:51 http://deb.debian.org/debian sid/main amd64 r-bioc-sva amd64 3.54.0-2 [455 kB] Get:52 http://deb.debian.org/debian sid/main amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1865 kB] Get:53 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB] Get:54 http://deb.debian.org/debian sid/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get:55 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.2 [216 kB] Preconfiguring packages ... Fetched 68.6 MB in 0s (172 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 ... 37747 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.3-1_amd64.deb ... Unpacking bsdutils (1:2.40.3-1) over (1:2.40.2-13) ... Setting up bsdutils (1:2.40.3-1) ... (Reading database ... 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Setting up gcc-14-base:amd64 (14.2.0-13) ... (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 ... 37749 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.2.0-13_amd64.deb ... Unpacking libstdc++6:amd64 (14.2.0-13) over (14.2.0-12) ... Setting up libstdc++6:amd64 (14.2.0-13) ... (Reading database ... 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Unpacking openssl-provider-legacy (3.4.0-2) over (3.3.2-2) ... Setting up openssl-provider-legacy (3.4.0-2) ... (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 ... 37749 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.4.0-2_amd64.deb ... Unpacking libssl3t64:amd64 (3.4.0-2) over (3.3.2-2) ... Setting up libssl3t64:amd64 (3.4.0-2) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37748 files and directories currently installed.) Preparing to unpack .../00-tzdata_2024b-6_all.deb ... Unpacking tzdata (2024b-6) over (2024b-4) ... Preparing to unpack .../01-libpng16-16t64_1.6.45-1_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.45-1) over (1.6.44-3) ... Preparing to unpack .../02-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) over (1.4.0-0.1+b1) ... Preparing to unpack .../03-libwebp7_1.5.0-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.5.0-0.1) over (1.4.0-0.1+b1) ... Preparing to unpack .../04-linux-libc-dev_6.12.9-1_all.deb ... Unpacking linux-libc-dev (6.12.9-1) over (6.12.6-1) ... Preparing to unpack .../05-openssl_3.4.0-2_amd64.deb ... Unpacking openssl (3.4.0-2) over (3.3.2-2) ... Preparing to unpack .../06-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ... Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) over (1.50.0+dfsg-2) ... Preparing to unpack .../07-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ... Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) over (0.42.1+dfsg-2) ... Preparing to unpack .../08-r-bioc-iranges_2.40.1-2_amd64.deb ... Unpacking r-bioc-iranges (2.40.1-2) over (2.38.1-1) ... Preparing to unpack .../09-r-bioc-xvector_0.46.0-2_amd64.deb ... Unpacking r-bioc-xvector (0.46.0-2) over (0.44.0-1) ... Preparing to unpack .../10-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ... Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) over (1.0.0+ds-2) ... 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Preparing to unpack .../18-r-bioc-biocparallel_1.40.0-2_amd64.deb ... Unpacking r-bioc-biocparallel (1.40.0-2) over (1.38.0-2) ... Preparing to unpack .../19-r-bioc-limma_3.62.1+dfsg-2_amd64.deb ... Unpacking r-bioc-limma (3.62.1+dfsg-2) over (3.60.6+dfsg-1) ... Preparing to unpack .../20-r-bioc-edger_4.4.1+dfsg-2_amd64.deb ... Unpacking r-bioc-edger (4.4.1+dfsg-2) over (4.2.2+dfsg-1) ... Preparing to unpack .../21-r-bioc-sva_3.54.0-2_amd64.deb ... Unpacking r-bioc-sva (3.54.0-2) over (3.52.0-1) ... Preparing to unpack .../22-r-bioc-annotate_1.84.0+dfsg-2_all.deb ... Unpacking r-bioc-annotate (1.84.0+dfsg-2) over (1.82.0+dfsg-1) ... Preparing to unpack .../23-r-bioc-biocgenerics_0.52.0-2_all.deb ... Unpacking r-bioc-biocgenerics (0.52.0-2) over (0.50.0-2) ... Preparing to unpack .../24-r-cran-rcpp_1.0.14-1_amd64.deb ... Unpacking r-cran-rcpp (1.0.14-1) over (1.0.13-1-1) ... Preparing to unpack .../25-x11-common_1%3a7.7+23.2_all.deb ... Unpacking x11-common (1:7.7+23.2) over (1:7.7+23.1) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up r-bioc-biocgenerics (0.52.0-2) ... Setting up r-bioc-biocparallel (1.40.0-2) ... Setting up r-bioc-matrixgenerics (1.18.0-2) ... Setting up x11-common (1:7.7+23.2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up linux-libc-dev (6.12.9-1) ... Setting up libgomp1:amd64 (14.2.0-13) ... Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 14 03:42:17 UTC 2025. Universal Time is now: Tue Jan 14 03:42:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up r-bioc-biobase (2.66.0-2) ... Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... Setting up libquadmath0:amd64 (14.2.0-13) ... Setting up r-bioc-limma (3.62.1+dfsg-2) ... Setting up libpng16-16t64:amd64 (1.6.45-1) ... Setting up libatomic1:amd64 (14.2.0-13) ... Setting up libgfortran5:amd64 (14.2.0-13) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libubsan1:amd64 (14.2.0-13) ... Setting up mount (2.40.3-1) ... Setting up libhwasan0:amd64 (14.2.0-13) ... Setting up libasan8:amd64 (14.2.0-13) ... Setting up r-bioc-iranges (2.40.1-2) ... Setting up libtsan2:amd64 (14.2.0-13) ... Setting up openssl (3.4.0-2) ... Setting up liblsan0:amd64 (14.2.0-13) ... Setting up libitm1:amd64 (14.2.0-13) ... Setting up login (1:4.16.0-2+really2.40.3-1) ... Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... Setting up r-bioc-edger (4.4.1+dfsg-2) ... Setting up r-bioc-genomeinfodb (1.42.1+dfsg-2) ... Setting up r-bioc-xvector (0.46.0-2) ... Setting up libgcc-14-dev:amd64 (14.2.0-13) ... Setting up libstdc++-14-dev:amd64 (14.2.0-13) ... Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... Setting up r-bioc-keggrest (1.46.0+dfsg-2) ... Setting up r-bioc-annotationdbi (1.68.0-2) ... Setting up r-bioc-annotate (1.84.0+dfsg-2) ... Setting up r-bioc-genefilter (1.88.0-2) ... Setting up r-bioc-sva (3.54.0-2) ... Processing triggers for libc-bin (2.40-5) ... 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-yf', 'dist-upgrade'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m42.1s DUMP: 5eb98ccbc27fdf77a68f6f40e15c3a09 - 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-sva'] 0m42.3s DUMP: Package: r-bioc-sva Version: 3.54.0-2 Installed-Size: 969 Maintainer: Debian R Packages Maintainers Architecture: amd64 Depends: r-api-4.0, r-api-bioc-3.20, r-cran-mgcv, r-bioc-genefilter, r-bioc-biocparallel, r-cran-matrixstats, r-bioc-limma, r-bioc-edger Suggests: r-bioc-bladderbatch, r-bioc-biocstyle, r-cran-testthat Description-en: GNU R Surrogate Variable Analysis The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics). Description-md5: c05f11b1bfa8dfefd1edeafaec2b11d0 Homepage: https://bioconductor.org/packages/sva/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-sva/r-bioc-sva_3.54.0-2_amd64.deb Size: 454764 MD5sum: 8fca3f88c912144bcf26a150ba4175bf SHA256: 25cf898d962422f2839b1528416b6c15d5d8db4f6ce1692707e546d08c626746 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-sva'] 0m42.3s INFO: apt-cache knows about the following packages: r-bioc-sva 0m42.3s INFO: Running scripts pre_install 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m42.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m42.4s 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: 0m42.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m42.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m42.5s DUMP: r-bioc-sva: Installed: 3.54.0-2 Candidate: 3.54.0-2 Version table: *** 3.54.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m42.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m42.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva'] 0m42.9s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-sva is already the newest version (3.54.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva'] 0m42.9s INFO: Running scripts post_install 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m42.9s INFO: Running scripts post_distupgrade 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_exceptions'] 0m42.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_distupgrade_zz_backports'] 0m43.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m44.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m44.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m46.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m46.0s INFO: Running scripts pre_install 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_database-server'] 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_exceptions'] 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_extras'] 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture'] 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m46.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m46.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m46.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy'] 0m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m46.1s DUMP: r-bioc-sva: Installed: 3.54.0-2 Candidate: 3.54.0-2 Version table: *** 3.54.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m46.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-cache', 'policy', 'r-bioc-sva'] 0m46.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva=3.54.0-2'] 0m46.6s DUMP: Reading package lists... Building dependency tree... Reading state information... r-bioc-sva is already the newest version (3.54.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', '-y', 'install', 'r-bioc-sva=3.54.0-2'] 0m46.6s INFO: Running scripts post_install 0m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_install_exceptions'] 0m46.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m48.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 0m50.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', '-ac', '--ignore-obsolete'] 0m53.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', '-ac', '--ignore-obsolete'] 0m53.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.1s DUMP: 0.15.6 0m53.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.1s INFO: Running adequate version 0.15.6 now. 0m53.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'r-bioc-sva'] 0m53.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'r-bioc-sva'] 0m53.2s INFO: Running scripts pre_remove 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m57.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m57.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m57.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m57.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_exceptions'] 0m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/pre_remove_exceptions'] 0m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.5s DUMP: install ok installed apt apt 2.9.21 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1 install ok installed bsdutils bsdutils 1:2.40.3-1 install ok installed ca-certificates ca-certificates 20241223 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-11 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.13 install ok installed e2fsprogs e2fsprogs 1.47.2-1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-2 install ok installed fontconfig-config fontconfig-config 2.15.0-2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-13 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.2 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.21 install ok installed libasan8:amd64 libasan8 14.2.0-13 install ok installed libatomic1:amd64 libatomic1 14.2.0-13 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 libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.3-1 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-4 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 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 2.40-5 install ok installed libc-dev-bin libc-dev-bin 2.40-5 install ok installed libc6:amd64 libc6 2.40-5 install ok installed libc6-dev:amd64 libc6-dev 2.40-5 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1 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 8.11.1-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-13 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-13 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 14.2.0-13 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.4-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-13 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.1.0-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-13 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-6 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libitm1:amd64 libitm1 14.2.0-13 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 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 3.12.0-4 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.19+dfsg-1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed liblsan0:amd64 liblsan0 14.2.0-13 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-4 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 2.40.3-1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3 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 libpango-1.0-0:amd64 libpango-1.0-0 1.55.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.55.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.55.0+ds-3 install ok installed libpaper-utils libpaper-utils 2.2.5-0.3 install ok installed libpaper2:amd64 libpaper2 2.2.5-0.3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-5 install ok installed libperl5.40:amd64 libperl5.40 5.40.0-8 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.45-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-13 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 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 libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.3-1 install ok installed libss2:amd64 libss2 1.47.2-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.4.0-2 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-13 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-13 install ok installed libsystemd0:amd64 libsystemd0 257.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-13 install ok installed libubsan1:amd64 libubsan1 14.2.0-13 install ok installed libudev1:amd64 libudev1 257.2-1 install ok installed libunistring5:amd64 libunistring5 1.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.3-1 install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxft2:amd64 libxft2 2.3.6-1+b3 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b3 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3 install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed linux-libc-dev linux-libc-dev 6.12.9-1 install ok installed littler littler 0.3.20-2 install ok installed login login 1:4.16.0-2+really2.40.3-1 install ok installed login.defs login.defs 1:4.16.0-7 install ok installed logsave logsave 1.47.2-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.3-1 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 openssl 3.4.0-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.0-2 install ok installed passwd passwd 1:4.16.0-7 install ok installed perl perl 5.40.0-8 install ok installed perl-base perl-base 5.40.0-8 install ok installed perl-modules-5.40 perl-modules-5.40 5.40.0-8 install ok installed procps procps 2:4.0.4-6 install ok installed r-base-core r-base-core 4.4.2-1 install ok installed r-bioc-annotate r-bioc-annotate 1.84.0+dfsg-2 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.68.0-2 install ok installed r-bioc-biobase r-bioc-biobase 2.66.0-2 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.52.0-2 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.40.0-2 install ok installed r-bioc-biostrings r-bioc-biostrings 2.74.1+dfsg-2 install ok installed r-bioc-edger r-bioc-edger 4.4.1+dfsg-2 install ok installed r-bioc-genefilter r-bioc-genefilter 1.88.0-2 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.42.1+dfsg-2 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.13-2 install ok installed r-bioc-iranges r-bioc-iranges 2.40.1-2 install ok installed r-bioc-keggrest r-bioc-keggrest 1.46.0+dfsg-2 install ok installed r-bioc-limma r-bioc-limma 3.62.1+dfsg-2 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.18.0-2 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.44.0+dfsg-2 install ok installed r-bioc-sva r-bioc-sva 3.54.0-2 install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.2.0+ds-2 install ok installed r-bioc-xvector r-bioc-xvector 0.46.0-2 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.52.0+dfsg-2 install ok installed r-cran-askpass r-cran-askpass 1.2.1-1 install ok installed r-cran-bh r-cran-bh 1.84.0-1 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-blob r-cran-blob 1.2.4-1 install ok installed r-cran-cachem r-cran-cachem 1.1.0-1 install ok installed r-cran-cli r-cran-cli 3.6.3-1 install ok installed r-cran-codetools r-cran-codetools 0.2-20-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.5.0-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.2.3+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.2.3-1 install ok installed r-cran-fastmap r-cran-fastmap 1.2.0-1 install ok installed r-cran-formatr r-cran-formatr 1.14-2 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-glue r-cran-glue 1.8.0-1 install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.9+dfsg-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.22-6-1 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.20-2 install ok installed r-cran-locfit r-cran-locfit 1.5-9.10-1 install ok installed r-cran-matrix r-cran-matrix 1.7-1-1 install ok installed r-cran-matrixstats r-cran-matrixstats 1.4.1-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.9-1-1 install ok installed r-cran-mime r-cran-mime 0.12-2 install ok installed r-cran-nlme r-cran-nlme 3.1.166-1 install ok installed r-cran-openssl r-cran-openssl 2.2.0+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.4-1 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-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.14-1 install ok installed r-cran-rlang r-cran-rlang 1.1.4-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.7-2 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-statmod r-cran-statmod 1.5.0-1 install ok installed r-cran-survival r-cran-survival 3.8-3-1 install ok installed r-cran-sys r-cran-sys 3.4.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1 install ok installed r-cran-xml r-cran-xml 3.99-0.18-1 install ok installed r-cran-xtable r-cran-xtable 1:1.8-4-2 install ok installed readline-common readline-common 8.2-6 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 sqv sqv 1.2.1-5 install ok installed sysvinit-utils sysvinit-utils 3.13-1 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2024b-6 install ok installed ucf ucf 3.0046 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.3-1 install ok installed x11-common x11-common 1:7.7+23.2 install ok installed xdg-utils xdg-utils 1.2.1-2 install ok installed zip zip 3.0-14 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1 0m57.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', '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', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'openssl', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-s4vectors', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-r6', 'r-cran-rcpp', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-statmod', 'r-cran-survival', 'r-cran-sys', 'r-cran-vctrs', 'r-cran-xml', 'r-cran-xtable', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-sva'] 0m60.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-14-dev libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu72 libidn2-0 libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libncursesw6 libnghttp2-14 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libperl5.40 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler openssl perl perl-modules-5.40 procps r-base-core r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-edger r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics r-bioc-s4vectors r-bioc-sva r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv r-cran-mime r-cran-nlme r-cran-openssl r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-r6 r-cran-rcpp r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-statmod r-cran-survival r-cran-sys r-cran-vctrs r-cran-xml r-cran-xtable readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 176 to remove and 0 not upgraded. After this operation, 596 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 ... 37757 files and directories currently installed.) Removing r-bioc-sva (3.54.0-2) ... Removing r-bioc-genefilter (1.88.0-2) ... Removing r-cran-survival (3.8-3-1) ... Removing r-cran-mgcv (1.9-1-1) ... Removing r-cran-matrix (1.7-1-1) ... Removing r-bioc-biocparallel (1.40.0-2) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-bioc-annotate (1.84.0+dfsg-2) ... Removing r-cran-xtable (1:1.8-4-2) ... Removing r-cran-rcpp (1.0.14-1) ... Removing r-cran-bh (1.84.0-1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-4) ... Removing libstdc++-14-dev:amd64 (14.2.0-13) ... Removing libgcc-14-dev:amd64 (14.2.0-13) ... Removing libasan8:amd64 (14.2.0-13) ... Removing r-bioc-edger (4.4.1+dfsg-2) ... Removing r-bioc-annotationdbi (1.68.0-2) ... Removing r-bioc-keggrest (1.46.0+dfsg-2) ... Removing r-bioc-biostrings (2.74.1+dfsg-2) ... Removing r-bioc-genomeinfodb (1.42.1+dfsg-2) ... Removing r-bioc-ucsc.utils (1.2.0+ds-2) ... Removing r-cran-httr (1.4.7+dfsg-1) ... Removing r-cran-curl (5.2.3+dfsg-1) ... Removing r-bioc-xvector (0.46.0-2) ... Removing r-bioc-zlibbioc (1.52.0+dfsg-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libc6-dev:amd64 (2.40-5) ... Removing libc-dev-bin (2.40-5) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libhwasan0:amd64 (14.2.0-13) ... Removing r-cran-xml (3.99-0.18-1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libitm1:amd64 (14.2.0-13) ... Removing liblsan0:amd64 (14.2.0-13) ... Removing r-cran-png (0.1-8-1+b1) ... Removing libquadmath0:amd64 (14.2.0-13) ... Removing libtsan2:amd64 (14.2.0-13) ... Removing libubsan1:amd64 (14.2.0-13) ... Removing linux-libc-dev (6.12.9-1) ... Removing littler (0.3.20-2) ... Removing r-bioc-biobase (2.66.0-2) ... Removing r-bioc-iranges (2.40.1-2) ... Removing r-bioc-s4vectors (0.44.0+dfsg-2) ... Removing r-bioc-matrixgenerics (1.18.0-2) ... Removing r-bioc-limma (3.62.1+dfsg-2) ... Removing r-bioc-biocgenerics (0.52.0-2) ... Removing r-bioc-genomeinfodbdata (1.2.13-2) ... Removing r-cran-openssl (2.2.0+dfsg-1) ... Removing r-cran-askpass (1.2.1-1) ... 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-memoise (2.0.1-1) ... Removing r-cran-cachem (1.1.0-1) ... Removing r-cran-vctrs (0.6.5-1) ... Removing r-cran-lifecycle (1.0.4+dfsg-1) ... Removing r-cran-cli (3.6.3-1) ... Removing r-cran-codetools (0.2-20-1) ... Removing r-cran-cpp11 (0.5.0-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-dbi (1.2.3-1) ... Removing r-cran-fastmap (1.2.0-1) ... 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-glue (1.8.0-1) ... Removing r-cran-jsonlite (1.8.9+dfsg-1) ... Removing r-cran-locfit (1.5-9.10-1) ... Removing r-cran-nlme (3.1.166-1) ... Removing r-cran-lattice (0.22-6-1) ... Removing r-cran-littler (0.3.20-2) ... Removing r-cran-matrixstats (1.4.1-1) ... Removing r-cran-mime (0.12-2) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.4-1) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rlang (1.1.4-1) ... Removing r-cran-statmod (1.5.0-1) ... Removing r-cran-sys (3.4.3-1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-base-core (4.4.2-1) ... Removing ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.55.0+ds-3) ... Removing fontconfig (2.15.0-2) ... Removing libtk8.6:amd64 (8.6.16-1) ... Removing libxft2:amd64 (2.3.6-1+b3) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing libfontconfig1:amd64 (2.15.0-2) ... Removing fontconfig-config (2.15.0-2) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libharfbuzz0b:amd64 (10.1.0-2) ... Removing libglib2.0-0t64:amd64 (2.82.4-1) ... Removing libatomic1:amd64 (14.2.0-13) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libcurl4t64:amd64 (8.11.1-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libldap-2.5-0:amd64 (2.5.19+dfsg-1) ... Removing libgnutls30t64:amd64 (3.8.8-2) ... Removing libp11-kit0:amd64 (0.25.5-3) ... Removing libffi8:amd64 (3.4.6-1) ... Removing libfribidi0:amd64 (1.0.16-1) ... Removing ucf (3.0046) ... Removing perl (5.40.0-8) ... Removing libperl5.40:amd64 (5.40.0-8) ... Removing libgdbm-compat4t64:amd64 (1.24-2) ... Removing libgdbm6t64:amd64 (1.24-2) ... Removing libgfortran5:amd64 (14.2.0-13) ... Removing libgomp1:amd64 (14.2.0-13) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... 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+b2) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libicu72:amd64 (72.1-6) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libidn2-0:amd64 (2.3.7-2+b1) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing procps (2:4.0.4-6) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpaper-utils (2.2.5-0.3) ... Removing libpaper2:amd64 (2.2.5-0.3) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libpng16-16t64:amd64 (1.6.45-1) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... Removing libreadline8t64:amd64 (8.2-6) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libwebp7:amd64 (1.5.0-0.1) ... Removing libsharpyuv0:amd64 (1.5.0-0.1) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtasn1-6:amd64 (4.19.0-3+b3) ... Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing libunistring5:amd64 (1.3-1) ... Removing libxss1:amd64 (1:1.2.3-1+b3) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b3) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing openssl (3.4.0-2) ... Removing perl-modules-5.40 (5.40.0-8) ... Removing readline-common (8.2-6) ... Removing sensible-utils (0.0.24) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23.2) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.2.1-2) ... Removing zip (3.0-14) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Processing triggers for libc-bin (2.40-5) ... 0m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', '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', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'openssl', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-s4vectors', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-r6', 'r-cran-rcpp', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-statmod', 'r-cran-survival', 'r-cran-sys', 'r-cran-vctrs', 'r-cran-xml', 'r-cran-xtable', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-sva'] 0m60.0s INFO: Running scripts post_remove 0m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_remove_exceptions'] 0m60.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_remove_exceptions'] 0m60.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', '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', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'openssl', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-s4vectors', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-r6', 'r-cran-rcpp', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-statmod', 'r-cran-survival', 'r-cran-sys', 'r-cran-vctrs', 'r-cran-xml', 'r-cran-xtable', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m0.4s DUMP: (Reading database ... 5084 files and directories currently installed.) Purging configuration files for ca-certificates (20241223) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.15.0-2) ... Purging configuration files for fontconfig-config (2.15.0-2) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove 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 libffi8 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-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 (2.82.4-1) ... dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed 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 libidn2-0 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 libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 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 libpaper2:amd64 (2.2.5-0.3) ... dpkg: warning: ignoring request to remove libperl5.40 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 libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-6) ... 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++-14-dev which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... 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 libunistring5 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6t64 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed Purging configuration files for openssl (3.4.0-2) ... Purging configuration files for perl (5.40.0-8) ... dpkg: warning: ignoring request to remove perl-modules-5.40 which isn't installed Purging configuration files for procps (2:4.0.4-6) ... Purging configuration files for r-base-core (4.4.2-1) ... dpkg: warning: ignoring request to remove r-bioc-annotate which isn't installed dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics 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-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-edger which isn't installed dpkg: warning: ignoring request to remove r-bioc-genefilter 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-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-limma 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-s4vectors 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-askpass which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-locfit 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-mgcv 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-nlme 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-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-r6 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-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-statmod which isn't installed dpkg: warning: ignoring request to remove r-cran-survival 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-vctrs 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-xtable which isn't installed Purging configuration files for readline-common (8.2-6) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for ucf (3.0046) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23.2) ... 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 1m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', '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', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libperl5.40:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'littler', 'openssl', 'perl', 'perl-modules-5.40', 'procps', 'r-base-core', 'r-bioc-annotate', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-edger', 'r-bioc-genefilter', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-limma', 'r-bioc-matrixgenerics', 'r-bioc-s4vectors', 'r-bioc-ucsc.utils', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-locfit', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mgcv', 'r-cran-mime', 'r-cran-nlme', 'r-cran-openssl', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-r6', 'r-cran-rcpp', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-statmod', 'r-cran-survival', 'r-cran-sys', 'r-cran-vctrs', 'r-cran-xml', 'r-cran-xtable', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', 'r-bioc-sva'] 1m0.4s DUMP: dpkg: warning: ignoring request to remove r-bioc-sva which isn't installed 1m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', 'r-bioc-sva'] 1m0.4s INFO: Running scripts post_purge 1m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_purge_exceptions'] 1m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_purge_exceptions'] 1m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', '--pending'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--purge', '--pending'] 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--remove', '--pending'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg', '--remove', '--pending'] 1m0.5s INFO: Running scripts post_test 1m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_test_exceptions'] 1m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'tmp/scripts/post_test_exceptions'] 1m0.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 1m0.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-divert', '--list'] 1m0.8s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /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 /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'dpkg-divert', '--list'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'clean'] 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j', 'apt-get', 'clean'] 1m0.9s DEBUG: Recording chroot state 1m1.4s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 1m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/shm'] 1m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/shm'] 1m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/console'] 1m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/console'] 1m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/ptmx'] 1m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/ptmx'] 1m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/pts'] 1m1.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/dev/pts'] 1m1.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/proc'] 1m1.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j/proc'] 1m1.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 1m1.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp7z85s_5j'] 1m1.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp7z85s_5j 1m1.9s INFO: PASS: Upgrading between Debian distributions. 1m1.9s INFO: PASS: All tests. 1m1.9s INFO: piuparts run ends. ret=0 End: 2025-01-14 03:42:38 GMT