Start: 2024-01-08 08:44:22 GMT Package: r-bioc-structuralvariantannotation Version: 1.13.0+ds-1 Installed-Size: 1298 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.2.2.20221110-1), r-api-4.0, r-bioc-genomicranges, r-bioc-rtracklayer, r-bioc-variantannotation, r-bioc-biocgenerics, r-cran-assertthat, r-bioc-biostrings, r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures, r-bioc-iranges, r-bioc-s4vectors, r-bioc-summarizedexperiment, r-bioc-genomeinfodb Suggests: r-cran-ggplot2, r-cran-devtools, r-cran-testthat (>= 2.1.0), r-cran-roxygen2, r-cran-rmarkdown, r-cran-tidyverse, r-cran-knitr, r-bioc-ggbio, r-bioc-biovizbase Description: Variant annotations for structural variants Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/ Description-md5: da0d30e1c2fddfc05ec9f7a5a97d4001 Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-structuralvariantannotation/r-bioc-structuralvariantannotation_1.13.0+ds-1_all.deb Size: 401832 MD5sum: 9d89c695d419b070c16f0e7900808c34 SHA256: afeba703d50595004f566791223017de6ece871f38a02adc3d11f6e0f128c907 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.13.0+ds-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.13.0+ds-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpl9d3m2yz 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl9d3m2yz 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpl9d3m2yz/tmp/scripts/ 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpl9d3m2yz/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'update'] 0m3.1s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'update'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', '-yf', 'dist-upgrade'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s INFO: Running scripts post_setup 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_dummy_users'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_forbid_home'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'clean'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'clean'] 0m4.9s DEBUG: Recording chroot state 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.19-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-divert', '--list'] 0m5.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-divert', '--list'] 0m5.6s INFO: Running scripts is_testable 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s INFO: apt-cache does not know about any of the requested packages 0m5.6s INFO: Running scripts pre_test 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_test_root_password'] 0m5.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_test_root_password'] 0m5.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m6.8s DEBUG: No broken symlinks as far as we can find. 0m6.8s INFO: Running scripts pre_install 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_database-server'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_database-server'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_exceptions'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_exceptions'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_extras'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_extras'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_log_alternatives'] 0m6.9s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_install_log_alternatives'] 0m6.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m7.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m8.2s DEBUG: No broken symlinks as far as we can find. 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-cache', 'policy'] 0m9.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.4,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-cache', 'policy'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation'] 0m9.1s DUMP: r-bioc-structuralvariantannotation: Installed: (none) Candidate: 1.13.0+ds-1 Version table: 1.13.0+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.13.0+ds-1'] 0m41.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan8 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc manpages-dev low-memory-monitor krb5-doc krb5-user libstdc++-12-doc tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-go.db r-cran-runit r-bioc-org.hs.eg.db r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-testthat r-cran-rmarkdown r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi r-bioc-shortread r-cran-batchtools r-cran-data.table r-cran-mockery r-cran-webmockr r-cran-biocmanager r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr r-bioc-delayedmatrixstats r-bioc-edger r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-limma r-cran-ggplot2 r-cran-devtools r-cran-roxygen2 r-cran-tidyverse r-bioc-ggbio r-bioc-biovizbase r-bioc-rhdf5 r-bioc-snpstats r-cran-covr r-cran-ff r-cran-callr r-cran-htmltools r-cran-htmlwidgets r-cran-processx r-cran-ps r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-bench r-cran-desc r-cran-scales r-cran-spelling r-cran-rmysql r-cran-unitizer r-cran-shiny r-cran-forcats r-cran-r.utils r-cran-waldo r-cran-lubridate r-cran-httpuv r-cran-jpeg r-cran-readr r-cran-r.rsp r-cran-sf r-cran-lintr r-cran-getopt r-cran-base64enc r-cran-r.devices r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-survival r-cran-units r-cran-vdiffr r-cran-inline r-cran-fs r-cran-usethis r-cran-gert r-cran-gh r-cran-rvest r-cran-rlecuyer r-cran-brio r-cran-evaluate r-cran-pkgbuild r-cran-pkgload r-cran-tidyr r-cran-pkgdown r-cran-zeallot readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-bioc-biovizbase r-cran-testthat r-cran-mockery r-cran-decor r-cran-knitr r-cran-brio r-cran-httpuv r-cran-webutils r-cran-rmysql r-cran-rpostgresql r-cran-tidyr r-cran-bench r-cran-broom r-cran-callr r-cran-covr r-cran-ggplot2 r-cran-lobstr r-cran-rmarkdown r-cran-testit r-cran-survival r-cran-pkgload r-cran-sp r-cran-runit r-cran-sodium r-cran-lubridate r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-mockr r-cran-formattable r-cran-waldo libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan8 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-structuralvariantannotation r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 194 newly installed, 0 to remove and 0 not upgraded. Need to get 189 MB of archives. After this operation, 534 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:17 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u3 [45.2 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.66-1 [1905 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:31 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u3 [1898 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:43 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:85 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:100 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocgenerics all 0.44.0-2 [600 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biobase amd64 2.58.0-2 [2112 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 r-bioc-s4vectors amd64 0.36.1-1 [2026 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 r-bioc-iranges amd64 2.32.0-1 [2222 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbi all 1.1.3-1 [687 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit amd64 4.0.5-1 [1070 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 r-cran-bit64 amd64 4.0.5-1 [463 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 r-cran-blob all 1.2.3-1 [49.5 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 r-cran-fastmap amd64 1.1.1-1 [68.9 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 r-cran-cachem amd64 1.0.7-1 [71.6 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 r-cran-rsqlite amd64 2.2.20-1 [1123 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 r-cran-curl amd64 5.0.0+dfsg-1 [172 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 r-cran-jsonlite amd64 1.8.4+dfsg-1 [442 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 r-cran-mime amd64 0.12-1+b1 [36.0 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 r-cran-sys amd64 3.4.1-1 [42.7 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 r-cran-askpass amd64 1.1-2 [22.2 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 r-cran-openssl amd64 2.0.5+dfsg-1 [391 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 r-cran-httr all 1.4.5+dfsg-1 [465 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 r-cran-png amd64 0.1-8-1 [41.1 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 r-bioc-zlibbioc all 1.44.0+dfsg-1 [9200 B] Get:133 http://deb.debian.org/debian bookworm/main amd64 r-bioc-xvector amd64 0.38.0-1 [618 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 r-cran-bitops amd64 1.0-7-1 [30.2 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcurl amd64 1.98-1.10+dfsg-1 [783 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodbdata all 1.2.9-1 [11.7 MB] Get:137 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomeinfodb all 1.34.9-1 [3938 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biostrings amd64 2.66.0-1 [13.8 MB] Get:140 http://deb.debian.org/debian bookworm/main amd64 r-bioc-keggrest all 1.38.0+dfsg-1 [179 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 r-bioc-annotationdbi all 1.60.0-1 [4696 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [219 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 r-cran-dplyr amd64 1.0.10-1 [1227 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 r-cran-dbplyr all 2.3.0+dfsg-1 [1055 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 r-cran-filelock amd64 1.0.2-2 [24.6 kB] Get:156 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocfilecache all 2.6.1+dfsg-1 [296 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocio all 1.8.0+dfsg-1 [201 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 r-cran-formatr all 1.14-1 [152 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 r-cran-codetools all 0.2-19-1 [90.9 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 r-cran-bh all 1.74.0-2 [5524 B] Get:165 http://deb.debian.org/debian bookworm/main amd64 r-cran-cpp11 all 0.4.3-1 [223 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biocparallel amd64 1.32.5-1 [1337 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml amd64 3.99-0.13-1 [1717 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 r-cran-ellipsis amd64 0.3.2-2 [35.1 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 r-cran-hms all 1.1.2-1 [104 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:171 http://deb.debian.org/debian bookworm/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringi amd64 1.7.12-1 [858 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 r-cran-stringr all 1.5.0-1 [295 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 r-cran-digest amd64 0.6.31-1 [184 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 r-cran-xml2 amd64 1.3.3-1+b1 [280 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 r-bioc-biomart all 2.54.0+dfsg-1 [442 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicranges amd64 1.50.2+dfsg-1 [1796 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rhtslib amd64 2.0.0+dfsg-1 [1287 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rsamtools amd64 2.14.0-1 [3755 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrixstats amd64 0.63.0-1 [470 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 r-bioc-matrixgenerics all 1.10.0-1 [302 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 r-bioc-delayedarray amd64 0.24.0+dfsg-1 [1937 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 r-bioc-summarizedexperiment all 1.28.0+dfsg-1 [2018 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicalignments amd64 1.34.0-1 [2112 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjson amd64 0.2.21-1 [139 kB] Get:188 http://deb.debian.org/debian bookworm/main amd64 r-cran-yaml amd64 2.3.7-1 [104 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 r-bioc-rtracklayer amd64 1.58.0-1 [5104 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 r-bioc-bsgenome all 1.66.3-1 [6997 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 r-bioc-genomicfeatures all 1.50.4+dfsg-1 [1676 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 r-bioc-variantannotation amd64 1.44.1-1 [3642 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 r-bioc-structuralvariantannotation all 1.13.0+ds-1 [402 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 189 MB in 1s (152 MB/s) Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6101 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../002-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.11-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../006-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../007-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../008-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../009-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../010-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../011-fontconfig-config_2.14.1-4_amd64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../012-libfontconfig1_2.14.1-4_amd64.deb ... Unpacking libfontconfig1:amd64 (2.14.1-4) ... Selecting previously unselected package fontconfig. Preparing to unpack .../013-fontconfig_2.14.1-4_amd64.deb ... Unpacking fontconfig (2.14.1-4) ... Selecting previously unselected package libasan8:amd64. Preparing to unpack .../014-libasan8_12.2.0-14_amd64.deb ... Unpacking libasan8:amd64 (12.2.0-14) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../015-libatomic1_12.2.0-14_amd64.deb ... Unpacking libatomic1:amd64 (12.2.0-14) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../016-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../017-libgomp1_12.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (12.2.0-14) ... Selecting previously unselected package libitm1:amd64. Preparing to unpack .../018-libitm1_12.2.0-14_amd64.deb ... Unpacking libitm1:amd64 (12.2.0-14) ... Selecting previously unselected package liblsan0:amd64. Preparing to unpack .../019-liblsan0_12.2.0-14_amd64.deb ... Unpacking liblsan0:amd64 (12.2.0-14) ... Selecting previously unselected package libtsan2:amd64. Preparing to unpack .../020-libtsan2_12.2.0-14_amd64.deb ... Unpacking libtsan2:amd64 (12.2.0-14) ... Selecting previously unselected package libubsan1:amd64. Preparing to unpack .../021-libubsan1_12.2.0-14_amd64.deb ... Unpacking libubsan1:amd64 (12.2.0-14) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../022-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgcc-12-dev:amd64. Preparing to unpack .../023-libgcc-12-dev_12.2.0-14_amd64.deb ... Unpacking libgcc-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package libc-dev-bin. Preparing to unpack .../024-libc-dev-bin_2.36-9+deb12u3_amd64.deb ... Unpacking libc-dev-bin (2.36-9+deb12u3) ... Selecting previously unselected package linux-libc-dev:amd64. Preparing to unpack .../025-linux-libc-dev_6.1.66-1_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.1.66-1) ... Selecting previously unselected package libcrypt-dev:amd64. Preparing to unpack .../026-libcrypt-dev_1%3a4.4.33-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.33-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../027-libkrb5support0_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../028-libk5crypto3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../029-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../030-libkrb5-3_1.20.1-2+deb12u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../031-libgssapi-krb5-2_1.20.1-2+deb12u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../032-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3:amd64. Preparing to unpack .../033-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../034-libnsl2_1.3.0-2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:amd64. Preparing to unpack .../035-libtirpc-dev_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:amd64. Preparing to unpack .../036-libnsl-dev_1.3.0-2_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-2) ... Selecting previously unselected package rpcsvc-proto. 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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 (0.20-45-3) ... Setting up r-cran-formatr (1.14-1) ... Setting up r-cran-xml (3.99-0.13-1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u3) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.2-2) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-rappdirs (0.3.3-1) ... Setting up r-cran-filelock (1.0.2-2) ... Setting up r-bioc-genomeinfodbdata (1.2.9-1) ... Setting up r-cran-littler (0.3.17-1) ... Setting up r-cran-rcpp (1.0.10-1) ... Setting up r-cran-curl (5.0.0+dfsg-1) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-bioc-biocgenerics (0.44.0-2) ... Setting up r-cran-rlang (1.0.6-1) ... Setting up r-cran-matrixstats (0.63.0-1) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up r-bioc-matrixgenerics (1.10.0-1) ... 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Setting up r-cran-tidyselect (1.2.0+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.34.9-1) ... Setting up r-cran-httr (1.4.5+dfsg-1) ... Setting up r-cran-hms (1.1.2-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-purrr (1.0.1-1) ... Setting up r-cran-blob (1.2.3-1) ... Setting up r-bioc-xvector (0.38.0-1) ... Setting up r-cran-dplyr (1.0.10-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up r-cran-dbplyr (2.3.0+dfsg-1) ... Setting up r-cran-rsqlite (2.2.20-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-cran-bh (1.74.0-2) ... Setting up r-bioc-biocparallel (1.32.5-1) ... Setting up r-bioc-biocfilecache (2.6.1+dfsg-1) ... Setting up r-bioc-genomicranges (1.50.2+dfsg-1) ... Setting up r-bioc-rhtslib (2.0.0+dfsg-1) ... Setting up r-bioc-biostrings (2.66.0-1) ... Setting up r-bioc-rsamtools (2.14.0-1) ... Setting up r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Setting up r-bioc-keggrest (1.38.0+dfsg-1) ... Setting up r-bioc-annotationdbi (1.60.0-1) ... Setting up r-bioc-biomart (2.54.0+dfsg-1) ... Setting up r-bioc-genomicalignments (1.34.0-1) ... Setting up r-bioc-rtracklayer (1.58.0-1) ... Setting up r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Setting up r-bioc-bsgenome (1.66.3-1) ... Setting up r-bioc-variantannotation (1.44.1-1) ... Setting up r-bioc-structuralvariantannotation (1.13.0+ds-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m41.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.13.0+ds-1'] 0m41.5s INFO: Running scripts post_install 0m41.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_install_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_install_exceptions'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_install_log_alternatives'] 0m41.6s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=libblas3: piuparts=r-bioc-structuralvariantannotation=1.13.0+ds-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=xdg-utils: piuparts=r-bioc-structuralvariantannotation=1.13.0+ds-1: /usr/bin/update-alternatives --install /usr/bin/open open /usr/bin/xdg-open 50 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/xdg-open.1.gz LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=r-bioc-structuralvariantannotation=1.13.0+ds-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_install_log_alternatives'] 0m41.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m43.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 0m47.0s DEBUG: No broken symlinks as far as we can find. 0m47.0s INFO: /bin converted to /usr/bin by /usr merge 0m47.0s INFO: /lib converted to /usr/lib by /usr merge 0m47.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m47.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m47.0s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m47.0s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m47.0s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m47.0s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m47.0s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m47.0s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m47.0s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m47.0s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m47.0s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m47.0s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m47.0s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m47.0s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m47.0s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m47.0s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m47.0s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m47.0s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m47.0s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m47.0s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m47.0s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m47.0s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m47.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m47.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m47.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m47.1s INFO: /sbin converted to /usr/sbin by /usr merge 0m48.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', '-ac', '--ignore-obsolete'] 0m52.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', '-ac', '--ignore-obsolete'] 0m52.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.0s DUMP: 0.15.6 0m53.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.0s INFO: Running adequate version 0.15.6 now. 0m53.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'r-bioc-structuralvariantannotation'] 0m53.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'r-bioc-structuralvariantannotation'] 0m53.1s INFO: Running scripts pre_remove 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m53.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m58.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m58.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_exceptions'] 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/pre_remove_exceptions'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m58.9s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed ca-certificates ca-certificates 20230311 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed fontconfig fontconfig 2.14.1-4 install ok installed fontconfig-config fontconfig-config 2.14.1-4 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-6 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libasan8:amd64 libasan8 12.2.0-14 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0+ds1-21 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u3 install ok installed libc-dev-bin libc-dev-bin 2.36-9+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 install ok installed libc6-dev:amd64 libc6-dev 2.36-9+deb12u3 install ok installed libcairo2:amd64 libcairo2 1.16.0-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.33-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u4 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-2+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.1-4 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.2.0-14 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.74.6-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u1 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libitm1:amd64 libitm1 12.2.0-14 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u1 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblsan0:amd64 liblsan0 12.2.0-14 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.50.12+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.50.12+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.50.12+ds-1 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.11-1~deb12u2 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.2.0-14 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.19-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-1 install ok installed libthai0:amd64 libthai0 0.1.29-1 install ok installed libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtsan2:amd64 libtsan2 12.2.0-14 install ok installed libubsan1:amd64 libubsan1 12.2.0-14 install ok installed libudev1:amd64 libudev1 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libx11-6:amd64 libx11-6 2:1.8.4-2+deb12u2 install ok installed libx11-data libx11-data 2:1.8.4-2+deb12u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3~deb12u1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed linux-libc-dev:amd64 linux-libc-dev 6.1.66-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed node-html5shiv node-html5shiv 3.7.3+dfsg-5 install ok installed openssl openssl 3.0.11-1~deb12u2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed r-base-core r-base-core 4.2.2.20221110-2 install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.60.0-1 install ok installed r-bioc-biobase r-bioc-biobase 2.58.0-2 install ok installed r-bioc-biocfilecache r-bioc-biocfilecache 2.6.1+dfsg-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.44.0-2 install ok installed r-bioc-biocio r-bioc-biocio 1.8.0+dfsg-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.32.5-1 install ok installed r-bioc-biomart r-bioc-biomart 2.54.0+dfsg-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.66.0-1 install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.66.3-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.24.0+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.34.9-1 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.9-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.34.0-1 install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.50.4+dfsg-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.50.2+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.32.0-1 install ok installed r-bioc-keggrest r-bioc-keggrest 1.38.0+dfsg-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.10.0-1 install ok installed r-bioc-rhtslib r-bioc-rhtslib 2.0.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.14.0-1 install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.58.0-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.36.1-1 install ok installed r-bioc-structuralvariantannotation r-bioc-structuralvariantannotation 1.13.0+ds-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.28.0+dfsg-1 install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.44.1-1 install ok installed r-bioc-xvector r-bioc-xvector 0.38.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.44.0+dfsg-1 install ok installed r-cran-askpass r-cran-askpass 1.1-2 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.74.0-2 install ok installed r-cran-bit r-cran-bit 4.0.5-1 install ok installed r-cran-bit64 r-cran-bit64 4.0.5-1 install ok installed r-cran-bitops r-cran-bitops 1.0-7-1 install ok installed r-cran-blob r-cran-blob 1.2.3-1 install ok installed r-cran-cachem r-cran-cachem 1.0.7-1 install ok installed r-cran-cli r-cran-cli 3.6.0-1 install ok installed r-cran-codetools r-cran-codetools 0.2-19-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.4.3-1 install ok installed r-cran-crayon r-cran-crayon 1.5.2-1 install ok installed r-cran-curl r-cran-curl 5.0.0+dfsg-1 install ok installed r-cran-dbi r-cran-dbi 1.1.3-1 install ok installed r-cran-dbplyr r-cran-dbplyr 2.3.0+dfsg-1 install ok installed r-cran-digest r-cran-digest 0.6.31-1 install ok installed r-cran-dplyr r-cran-dplyr 1.0.10-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.2-2 install ok installed r-cran-fansi r-cran-fansi 1.0.4-1 install ok installed r-cran-fastmap r-cran-fastmap 1.1.1-1 install ok installed r-cran-filelock r-cran-filelock 1.0.2-2 install ok installed r-cran-formatr r-cran-formatr 1.14-1 install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4 install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3 install ok installed r-cran-generics r-cran-generics 0.1.3-1 install ok installed r-cran-glue r-cran-glue 1.6.2-1 install ok installed r-cran-hms r-cran-hms 1.1.2-1 install ok installed r-cran-httr r-cran-httr 1.4.5+dfsg-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.8.4+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 0.20-45-3 install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.3+dfsg-1 install ok installed r-cran-littler r-cran-littler 0.3.17-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1 install ok installed r-cran-matrix r-cran-matrix 1.5-3-1 install ok installed r-cran-matrixstats r-cran-matrixstats 0.63.0-1 install ok installed r-cran-memoise r-cran-memoise 2.0.1-1 install ok installed r-cran-mime r-cran-mime 0.12-1+b1 install ok installed r-cran-openssl r-cran-openssl 2.0.5+dfsg-1 install ok installed r-cran-pillar r-cran-pillar 1.8.1+dfsg-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.2-2 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 install ok installed r-cran-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-progress r-cran-progress 1.2.2-2 install ok installed r-cran-purrr r-cran-purrr 1.0.1-1 install ok installed r-cran-r6 r-cran-r6 2.5.1-1 install ok installed r-cran-rappdirs r-cran-rappdirs 0.3.3-1 install ok installed r-cran-rcpp r-cran-rcpp 1.0.10-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.10+dfsg-1 install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1 install ok installed r-cran-rjson r-cran-rjson 0.2.21-1 install ok installed r-cran-rlang r-cran-rlang 1.0.6-1 install ok installed r-cran-rsqlite r-cran-rsqlite 2.2.20-1 install ok installed r-cran-snow r-cran-snow 1:0.4.4-2 install ok installed r-cran-stringi r-cran-stringi 1.7.12-1 install ok installed r-cran-stringr r-cran-stringr 1.5.0-1 install ok installed r-cran-sys r-cran-sys 3.4.1-1 install ok installed r-cran-tibble r-cran-tibble 3.1.8+dfsg-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.0+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.2.3-1 install ok installed r-cran-vctrs r-cran-vctrs 0.5.2-1 install ok installed r-cran-withr r-cran-withr 2.5.0-1 install ok installed r-cran-xml r-cran-xml 3.99-0.13-1 install ok installed r-cran-xml2 r-cran-xml2 1.3.3-1+b1 install ok installed r-cran-yaml r-cran-yaml 2.3.7-1 install ok installed readline-common readline-common 8.2-1.3 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-1 install ok installed sensible-utils sensible-utils 0.0.17+nmu1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.13.dfsg-1 0m58.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m58.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-structuralvariantannotation'] 1m2.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan8 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-12-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 liblsan0 libnghttp2-14 libnsl-dev libnsl2 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl3 libstdc++-12-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev node-html5shiv openssl r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4vectors r-bioc-structuralvariantannotation r-bioc-summarizedexperiment r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-assertthat r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-ellipsis r-cran-fansi r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr r-cran-xml r-cran-xml2 r-cran-yaml readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 194 to remove and 0 not upgraded. After this operation, 534 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 ... 35746 files and directories currently installed.) Removing r-bioc-structuralvariantannotation (1.13.0+ds-1) ... Removing r-bioc-variantannotation (1.44.1-1) ... Removing r-bioc-genomicfeatures (1.50.4+dfsg-1) ... Removing r-bioc-biomart (2.54.0+dfsg-1) ... Removing r-bioc-biocfilecache (2.6.1+dfsg-1) ... Removing r-bioc-annotationdbi (1.60.0-1) ... Removing r-bioc-keggrest (1.38.0+dfsg-1) ... Removing r-cran-httr (1.4.5+dfsg-1) ... Removing r-cran-curl (5.0.0+dfsg-1) ... Removing r-bioc-bsgenome (1.66.3-1) ... Removing r-cran-stringr (1.5.0-1) ... Removing r-cran-stringi (1.7.12-1) ... Removing r-cran-xml2 (1.3.3-1+b1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing r-cran-png (0.1-8-1) ... Removing r-cran-openssl (2.0.5+dfsg-1) ... Removing node-html5shiv (3.7.3+dfsg-5) ... Removing r-cran-askpass (1.1-2) ... Removing r-cran-dbplyr (2.3.0+dfsg-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-progress (1.2.2-2) ... Removing r-cran-hms (1.1.2-1) ... Removing r-cran-dplyr (1.0.10-1) ... Removing r-cran-tidyselect (1.2.0+dfsg-1) ... Removing r-cran-purrr (1.0.1-1) ... Removing r-cran-digest (0.6.31-1) ... Removing r-cran-ellipsis (0.3.2-2) ... Removing r-cran-tibble (3.1.8+dfsg-1) ... Removing r-cran-pillar (1.8.1+dfsg-1) ... Removing r-cran-fansi (1.0.4-1) ... Removing r-cran-filelock (1.0.2-2) ... Removing r-cran-generics (0.1.3-1) ... Removing r-cran-jsonlite (1.8.4+dfsg-1) ... Removing r-cran-magrittr (2.0.3-1) ... Removing r-cran-mime (0.12-1+b1) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-r6 (2.5.1-1) ... Removing r-cran-rappdirs (0.3.3-1) ... Removing r-cran-sys (3.4.1-1) ... Removing r-cran-utf8 (1.2.3-1) ... Removing r-cran-withr (2.5.0-1) ... Removing r-bioc-rtracklayer (1.58.0-1) ... Removing r-bioc-genomicalignments (1.34.0-1) ... Removing r-bioc-summarizedexperiment (1.28.0+dfsg-1) ... Removing r-bioc-delayedarray (0.24.0+dfsg-1) ... Removing r-cran-matrix (1.5-3-1) ... Removing r-cran-rsqlite (2.2.20-1) ... Removing r-cran-rcpp (1.0.10-1) ... Removing r-cran-restfulr (0.0.15-1) ... Removing r-cran-yaml (2.3.7-1) ... Removing r-cran-xml (3.99-0.13-1) ... Removing r-bioc-biobase (2.58.0-2) ... Removing r-bioc-biocio (1.8.0+dfsg-1) ... Removing r-bioc-matrixgenerics (1.10.0-1) ... Removing r-cran-bit64 (4.0.5-1) ... Removing r-cran-bit (4.0.5-1) ... Removing r-cran-blob (1.2.3-1) ... Removing r-cran-memoise (2.0.1-1) ... Removing r-cran-cachem (1.0.7-1) ... Removing r-cran-vctrs (0.5.2-1) ... Removing r-cran-dbi (1.1.3-1) ... Removing r-cran-fastmap (1.1.1-1) ... Removing r-cran-lifecycle (1.0.3+dfsg-1) ... Removing r-cran-glue (1.6.2-1) ... Removing r-cran-lattice (0.20-45-3) ... Removing r-cran-rjson (0.2.21-1) ... Removing r-cran-littler (0.3.17-1) ... Removing r-cran-matrixstats (0.63.0-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-pkgkitten (0.2.2-2) ... Removing r-cran-plogr (0.2.0-3) ... Removing r-cran-rlang (1.0.6-1) ... Removing r-bioc-rsamtools (2.14.0-1) ... Removing r-bioc-biocparallel (1.32.5-1) ... Removing r-cran-snow (1:0.4.4-2) ... Removing r-cran-bh (1.74.0-2) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Removing libstdc++-12-dev:amd64 (12.2.0-14) ... Removing libgcc-12-dev:amd64 (12.2.0-14) ... Removing libasan8:amd64 (12.2.0-14) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing r-bioc-genomicranges (1.50.2+dfsg-1) ... Removing r-bioc-rhtslib (2.0.0+dfsg-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Removing libitm1:amd64 (12.2.0-14) ... Removing liblsan0:amd64 (12.2.0-14) ... Removing libtsan2:amd64 (12.2.0-14) ... Removing libubsan1:amd64 (12.2.0-14) ... Removing r-bioc-biostrings (2.66.0-1) ... Removing r-bioc-genomeinfodb (1.34.9-1) ... Removing r-bioc-genomeinfodbdata (1.2.9-1) ... Removing r-cran-rcurl (1.98-1.10+dfsg-1) ... Removing r-cran-bitops (1.0-7-1) ... Removing r-cran-cli (3.6.0-1) ... Removing r-cran-codetools (0.2-19-1) ... Removing r-cran-cpp11 (0.4.3-1) ... Removing r-cran-crayon (1.5.2-1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.14-1) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-bioc-xvector (0.38.0-1) ... Removing r-bioc-zlibbioc (1.44.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Removing libc6-dev:amd64 (2.36-9+deb12u3) ... Removing libc-dev-bin (2.36-9+deb12u3) ... Removing libcrypt-dev:amd64 (1:4.4.33-2) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.3+ds-1) ... Removing libnsl2:amd64 (1.3.0-2) ... Removing linux-libc-dev:amd64 (6.1.66-1) ... Removing r-bioc-iranges (2.32.0-1) ... Removing r-bioc-s4vectors (0.36.1-1) ... Removing r-bioc-biocgenerics (0.44.0-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing r-base-core (4.2.2.20221110-2) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Removing libpango-1.0-0:amd64 (1.50.12+ds-1) ... Removing fontconfig (2.14.1-4) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.16.0-7) ... Removing libfontconfig1:amd64 (2.14.1-4) ... Removing fontconfig-config (2.14.1-4) ... Removing fonts-dejavu-core (2.37-6) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libfreetype6:amd64 (2.12.1+dfsg-5) ... Removing libcurl4:amd64 (7.88.1-10+deb12u4) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.29-1) ... Removing libdatrie1:amd64 (0.2.13-2+b1) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libglib2.0-0:amd64 (2.74.6-2) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Removing libicu72:amd64 (72.1-3) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpng16-16:amd64 (1.6.39-2) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing openssl (3.0.11-1~deb12u2) ... Removing libssl3:amd64 (3.0.11-1~deb12u2) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libthai-data (0.1.29-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing readline-common (8.2-1.3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.17+nmu1) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libx11-data (2:1.8.4-2+deb12u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... 1m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-structuralvariantannotation'] 1m2.0s INFO: Running scripts post_remove 1m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_remove_exceptions'] 1m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_remove_exceptions'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m2.9s DUMP: (Reading database ... 6147 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.14.1-4) ... Purging configuration files for fontconfig-config (2.14.1-4) ... Purging configuration files for fonts-dejavu-core (2.37-6) ... 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 libboost1.74-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.33-2) ... dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-12-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.74.6-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... dpkg: warning: ignoring request to remove libharfbuzz0b 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 libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove 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 libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libstdc++-12-dev which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtirpc3 which isn't installed 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 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 libxt6 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove node-html5shiv which isn't installed Purging configuration files for openssl (3.0.11-1~deb12u2) ... Purging configuration files for r-base-core (4.2.2.20221110-2) ... dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocfilecache which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocio which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biomart which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-bsgenome which isn't installed dpkg: warning: ignoring request to remove r-bioc-delayedarray which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodb which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomeinfodbdata which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicalignments which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicfeatures which isn't installed dpkg: warning: ignoring request to remove r-bioc-genomicranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-iranges which isn't installed dpkg: warning: ignoring request to remove r-bioc-keggrest which isn't installed dpkg: warning: ignoring request to remove r-bioc-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-variantannotation 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-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-bh which isn't installed dpkg: warning: ignoring request to remove r-cran-bit which isn't installed dpkg: warning: ignoring request to remove r-cran-bit64 which isn't installed dpkg: warning: ignoring request to remove r-cran-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-blob which isn't installed dpkg: warning: ignoring request to remove r-cran-cachem which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-codetools which isn't installed dpkg: warning: ignoring request to remove r-cran-cpp11 which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-curl which isn't installed dpkg: warning: ignoring request to remove r-cran-dbi which isn't installed dpkg: warning: ignoring request to remove r-cran-dbplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-fastmap which isn't installed dpkg: warning: ignoring request to remove r-cran-filelock which isn't installed dpkg: warning: ignoring request to remove r-cran-formatr which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.logger which isn't installed dpkg: warning: ignoring request to remove r-cran-futile.options which isn't installed dpkg: warning: ignoring request to remove r-cran-generics which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-httr which isn't installed dpkg: warning: ignoring request to remove r-cran-jsonlite which isn't installed dpkg: warning: ignoring request to remove r-cran-lambda.r which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-matrixstats which isn't installed dpkg: warning: ignoring request to remove r-cran-memoise which isn't installed dpkg: warning: ignoring request to remove r-cran-mime which isn't installed dpkg: warning: ignoring request to remove r-cran-openssl which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plogr which isn't installed dpkg: warning: ignoring request to remove r-cran-png which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rappdirs which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-rcurl which isn't installed dpkg: warning: ignoring request to remove r-cran-restfulr which isn't installed dpkg: warning: ignoring request to remove r-cran-rjson which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-rsqlite which isn't installed dpkg: warning: ignoring request to remove r-cran-snow which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-sys which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-tidyselect which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-vctrs which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed dpkg: warning: ignoring request to remove r-cran-xml which isn't installed dpkg: warning: ignoring request to remove r-cran-xml2 which isn't installed dpkg: warning: ignoring request to remove r-cran-yaml which isn't installed Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: 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 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-12-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu72:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libstdc++-12-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1: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', 'libxt6:amd64', 'linux-libc-dev:amd64', 'node-html5shiv', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocfilecache', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', 'r-bioc-biomart', 'r-bioc-biostrings', 'r-bioc-bsgenome', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicfeatures', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-keggrest', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-askpass', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bit', 'r-cran-bit64', 'r-cran-bitops', 'r-cran-blob', 'r-cran-cachem', 'r-cran-cli', 'r-cran-codetools', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-curl', 'r-cran-dbi', 'r-cran-dbplyr', 'r-cran-digest', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-filelock', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-hms', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-memoise', 'r-cran-mime', 'r-cran-openssl', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plogr', 'r-cran-png', 'r-cran-prettyunits', 'r-cran-progress', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rappdirs', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-restfulr', 'r-cran-rjson', 'r-cran-rlang', 'r-cran-rsqlite', 'r-cran-snow', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-sys', 'r-cran-tibble', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-withr', 'r-cran-xml', 'r-cran-xml2', 'r-cran-yaml', 'readline-common', 'rpcsvc-proto', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation'] 1m2.9s DUMP: dpkg: warning: ignoring request to remove r-bioc-structuralvariantannotation which isn't installed 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation'] 1m2.9s INFO: Running scripts post_purge 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_purge_exceptions'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_purge_exceptions'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', '--pending'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--purge', '--pending'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--remove', '--pending'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg', '--remove', '--pending'] 1m2.9s INFO: Running scripts post_test 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_test_exceptions'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'tmp/scripts/post_test_exceptions'] 1m2.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 1m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 1m4.1s DEBUG: No broken symlinks as far as we can find. 1m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-divert', '--list'] 1m4.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'dpkg-divert', '--list'] 1m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'clean'] 1m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz', 'apt-get', 'clean'] 1m4.2s DEBUG: Recording chroot state 1m4.9s INFO: PASS: Installation and purging test. 1m5.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/shm'] 1m5.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/shm'] 1m5.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/console'] 1m5.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/console'] 1m5.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/ptmx'] 1m5.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/ptmx'] 1m5.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts'] 1m5.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/dev/pts'] 1m5.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/proc'] 1m5.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz/proc'] 1m5.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 1m5.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl9d3m2yz'] 1m5.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl9d3m2yz 1m5.6s INFO: PASS: All tests. 1m5.6s INFO: piuparts run ends. ret=0 End: 2024-01-08 08:45:28 GMT