Start: 2024-11-26 15:16:35 GMT [testing] Package: r-bioc-biocstyle Version: 2.32.1+dfsg-1 Installed-Size: 637 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-bookdown, r-cran-knitr (>= 1.30), r-cran-rmarkdown (>= 1.2), r-cran-yaml, r-cran-biocmanager, texlive-bibtex-extra, xdg-utils, r-bioc-biocversion (>= 3.19.1), r-bioc-biocgenerics (>= 0.50.0) Suggests: r-cran-runit, r-cran-htmltools Description: standard styles for vignettes and other Bioconductor documents Homepage: https://bioconductor.org/packages/BiocStyle/ Description-md5: 3039a52b9b0668021ed645f7222b1fde Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-biocstyle/r-bioc-biocstyle_2.32.1+dfsg-1_all.deb Size: 452876 MD5sum: 9935308381a88599b01ac7086cca90b2 SHA256: d41b4a02df1d6a7895f1bddbb6f293871a579409c953f3cfcaf09c8f90f02658 [sid] Package: r-bioc-biocstyle Version: 2.34.0+dfsg-1 Installed-Size: 637 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-cran-bookdown, r-cran-knitr (>= 1.30), r-cran-rmarkdown (>= 1.2), r-cran-yaml, r-cran-biocmanager, texlive-bibtex-extra, xdg-utils, r-bioc-biocversion (>= 3.19.1), r-bioc-biocgenerics (>= 0.50.0) Suggests: r-cran-runit, r-cran-htmltools Description: standard styles for vignettes and other Bioconductor documents Homepage: https://bioconductor.org/packages/BiocStyle/ Description-md5: 3039a52b9b0668021ed645f7222b1fde Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-biocstyle/r-bioc-biocstyle_2.34.0+dfsg-1_all.deb Size: 452448 MD5sum: 6f4e648de063436a28307c0dd732929c SHA256: 9e632947f96c6469bc68c08f6febd554b41fe2c4a5d0f532d5b31ab8938c657b Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-biocstyle=2.34.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt r-bioc-biocstyle=2.34.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmppfzi933f 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppfzi933f 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppfzi933f', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppfzi933f', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppfzi933f/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppfzi933f/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmppfzi933f/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9378 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6273 kB] Fetched 15.8 MB in 1s (18.0 MB/s) Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-yf', 'dist-upgrade'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s DUMP: 246f15cab0f95f517c9ee1951f6a1e38 - 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s INFO: Running scripts post_setup 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_dummy_users'] 0m2.4s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_dummy_users'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_forbid_home'] 0m2.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_forbid_home'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-7 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m2.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m2.7s INFO: Running scripts is_testable 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/is_testable_uninstallable'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/is_testable_uninstallable'] 0m2.7s INFO: Running scripts pre_test 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_test_exceptions'] 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_test_exceptions'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_test_root_password'] 0m2.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_test_root_password'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-biocstyle'] 0m2.8s DUMP: Package: r-bioc-biocstyle Version: 2.32.1+dfsg-1 Installed-Size: 637 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.19, r-cran-bookdown, r-cran-knitr (>= 1.30), r-cran-rmarkdown (>= 1.2), r-cran-yaml, r-cran-biocmanager, texlive-bibtex-extra, xdg-utils, r-bioc-biocversion (>= 3.19.1), r-bioc-biocgenerics (>= 0.50.0) Suggests: r-cran-runit, r-cran-htmltools Description-en: standard styles for vignettes and other Bioconductor documents Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality. Description-md5: 3039a52b9b0668021ed645f7222b1fde Homepage: https://bioconductor.org/packages/BiocStyle/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-biocstyle/r-bioc-biocstyle_2.32.1+dfsg-1_all.deb Size: 452876 MD5sum: 9935308381a88599b01ac7086cca90b2 SHA256: d41b4a02df1d6a7895f1bddbb6f293871a579409c953f3cfcaf09c8f90f02658 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-biocstyle'] 0m2.8s INFO: apt-cache knows about the following packages: r-bioc-biocstyle 0m2.8s INFO: Running scripts pre_install 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_database-server'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_database-server'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_exceptions'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_extras'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy'] 0m2.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy', 'r-bioc-biocstyle'] 0m2.9s DUMP: r-bioc-biocstyle: Installed: (none) Candidate: 2.32.1+dfsg-1 Version table: 2.32.1+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy', 'r-bioc-biocstyle'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-y', 'install', 'r-bioc-biocstyle'] 0m35.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libatomic1 libbibtex-parser-perl libblas3 libbrotli1 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libio-string-perl libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.40 r-base-core r-bioc-biocgenerics r-bioc-biocversion r-cran-base64enc r-cran-biocmanager r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-commonmark r-cran-crayon r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-later r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-memoise r-cran-mime r-cran-pkgkitten r-cran-promises r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rlang r-cran-rmarkdown r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-tinytex r-cran-withr r-cran-xfun r-cran-xtable r-cran-yaml readline-common sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip Suggested packages: apache2 | lighttpd | httpd gdbm-l10n low-memory-monitor krb5-doc krb5-user libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc libmpfi-doc tcl8.6 tk8.6 nodejs texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin groff ghc php python ruby libjs-katex citation-style-language-styles perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-runit r-cran-rstudioapi r-cran-testthat r-cran-getopt r-cran-covr r-cran-httr r-cran-roxygen2 r-cran-inline r-cran-plm r-cran-zoo r-cran-survival readline-doc debhelper ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview texlive-latex-base-doc wp2latex Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs node-jquery krb5-locales libldap-common publicsuffix libsasl2-modules netbase r-recommended r-base-dev r-doc-html r-cran-remotes r-cran-testthat r-cran-curl r-cran-downlit r-cran-htmlwidgets r-cran-rstudioapi r-cran-miniui r-cran-rsconnect r-cran-tibble r-cran-testit r-cran-tufte r-cran-xml2 r-cran-webshot r-cran-future r-cran-ggplot2 r-cran-thematic r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps r-cran-rprojroot r-cran-whoami r-cran-lattice r-cran-dplyr r-cran-rsvg r-cran-pillar r-cran-spelling r-cran-vctrs r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-markdown r-cran-cairo r-cran-ragg r-cran-httr r-cran-r.rsp r-cran-sf r-cran-codetools r-cran-formatr r-cran-gridsvg r-cran-jpeg r-cran-magick r-cran-png r-cran-reticulate r-cran-rgl r-cran-tikzdevice r-cran-svglite node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-purrr r-cran-usethis r-cran-dygraphs r-cran-dt r-cran-renv r-cran-runit lmodern dvisvgm libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax javascript-common libatomic1 libbibtex-parser-perl libblas3 libbrotli1 libcairo2 libcurl4t64 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4t64 libgdbm6t64 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu72 libio-string-perl libjbig0 libjpeg62-turbo libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblapack3 liblatex-tounicode-perl libldap-2.5-0 liblerc4 liblua5.4-0 libmpfi0 libmpfr6 libnghttp2-14 libnuma1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.40 libpixman-1-0 libpng16-16t64 libpotrace0 libpsl5t64 libptexenc1 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libuv1t64 libwebp7 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libyaml-0-2 libzzip-0-13t64 littler node-bootstrap-sass node-html5shiv node-normalize.css openssl pandoc pandoc-data perl perl-modules-5.40 r-base-core r-bioc-biocgenerics r-bioc-biocstyle r-bioc-biocversion r-cran-base64enc r-cran-biocmanager r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli r-cran-commonmark r-cran-crayon r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-later r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-memoise r-cran-mime r-cran-pkgkitten r-cran-promises r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rlang r-cran-rmarkdown r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-tinytex r-cran-withr r-cran-xfun r-cran-xtable r-cran-yaml readline-common sensible-utils t1utils tex-common texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base ucf unzip x11-common xdg-utils zip 0 upgraded, 182 newly installed, 0 to remove and 0 not upgraded. Need to get 248 MB of archives. After this operation, 787 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 perl-modules-5.40 all 5.40.0-7 [3017 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libgdbm6t64 amd64 1.24-2 [75.2 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libgdbm-compat4t64 amd64 1.24-2 [50.3 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libperl5.40 amd64 5.40.0-7 [4324 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 perl amd64 5.40.0-7 [267 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 javascript-common all 11+nmu1 [6260 B] Get:25 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:26 http://deb.debian.org/debian trixie/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 liblatex-tounicode-perl all 0.55-1 [28.8 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libbibtex-parser-perl all 1.05+dfsg-1 [17.4 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:44 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libjs-popper.js all 1.16.1+ds-6 [52.4 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [517 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libjs-d3 all 3.5.17-4 [132 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libjs-es5-shim all 4.6.7-2 [47.4 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [397 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [144 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.2 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3672 B] Get:77 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [52.1 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libjs-json all 0~20221030+~1.0.8-1 [20.0 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libjs-lunr all 2.3.9~dfsg-2 [76.6 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libjs-modernizr all 3.13.0-0.1 [191 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [41.7 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [32.1 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 liblua5.4-0 amd64 5.4.6-3+b2 [147 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get:99 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Get:127 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.20-1 [102 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.20-1 [16.0 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 node-bootstrap-sass all 3.4.3-2 [186 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 node-html5shiv all 3.7.3+dfsg-5 [13.2 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 node-normalize.css all 8.0.1-5 [12.7 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get:134 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-cran-base64enc amd64 0.1-3-3 [27.9 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.4-1 [1712 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 r-cran-htmltools amd64 0.5.8.1-1 [378 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 r-cran-evaluate all 1.0.0-1 [112 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 r-cran-xfun amd64 0.49+dfsg-1 [546 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 r-cran-highr all 0.11+dfsg-1 [38.3 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-cran-knitr all 1.48+dfsg-1 [912 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.1 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.3-1 [1342 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.7.0-1 [157 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-cran-fs amd64 1.6.4+dfsg-1 [247 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.5.1-1 [105 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-rappdirs amd64 0.3.3-1 [47.4 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-sass amd64 0.4.9+dfsg-1 [965 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-bslib all 0.7.0+dfsg-1 [4365 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-cran-fontawesome all 0.5.2-1 [1286 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-tinytex all 0.53-1 [146 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.13-1-1 [2074 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-cran-later amd64 1.3.2+dfsg-1 [118 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-cran-promises amd64 1.3.0+dfsg-1 [284 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [493 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-cran-sourcetools amd64 0.1.7-1-1 [45.9 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.2-1 [165 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-cran-commonmark amd64 1.9.1-1 [119 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-shiny all 1.9.1+dfsg-1 [3126 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1474 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-cran-bookdown all 0.41+dfsg-1 [1404 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:177 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get:179 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 texlive-bibtex-extra all 2024.20241115-1 [80.0 MB] Get:181 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocversion all 3.19.1-1 [10.9 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [453 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 248 MB in 3s (75.2 MB/s) Selecting previously unselected package perl-modules-5.40. (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 ... 5158 files and directories currently installed.) Preparing to unpack .../000-perl-modules-5.40_5.40.0-7_all.deb ... Unpacking perl-modules-5.40 (5.40.0-7) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../001-libgdbm6t64_1.24-2_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.24-2) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../002-libgdbm-compat4t64_1.24-2_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.24-2) ... Selecting previously unselected package libperl5.40:amd64. Preparing to unpack .../003-libperl5.40_5.40.0-7_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-7) ... Selecting previously unselected package perl. Preparing to unpack .../004-perl_5.40.0-7_amd64.deb ... Unpacking perl (5.40.0-7) ... Selecting previously unselected package readline-common. Preparing to unpack .../005-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../007-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../008-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package ucf. Preparing to unpack .../009-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 .../010-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../011-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../012-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../013-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../014-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../015-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../016-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../017-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../018-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../019-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package fonts-glyphicons-halflings. Preparing to unpack .../020-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... Selecting previously unselected package fonts-lmodern. Preparing to unpack .../021-fonts-lmodern_2.005-1_all.deb ... Unpacking fonts-lmodern (2.005-1) ... Selecting previously unselected package fonts-mathjax. Preparing to unpack .../022-fonts-mathjax_2.7.9+dfsg-1_all.deb ... Unpacking fonts-mathjax (2.7.9+dfsg-1) ... Selecting previously unselected package javascript-common. Preparing to unpack .../023-javascript-common_11+nmu1_all.deb ... Unpacking javascript-common (11+nmu1) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../024-libatomic1_14.2.0-8_amd64.deb ... Unpacking libatomic1:amd64 (14.2.0-8) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../025-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package liblatex-tounicode-perl. Preparing to unpack .../026-liblatex-tounicode-perl_0.55-1_all.deb ... Unpacking liblatex-tounicode-perl (0.55-1) ... Selecting previously unselected package libbibtex-parser-perl. Preparing to unpack .../027-libbibtex-parser-perl_1.05+dfsg-1_all.deb ... Unpacking libbibtex-parser-perl (1.05+dfsg-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../028-libblas3_3.12.0-3+b1_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3+b1) ... Selecting previously unselected package libpixman-1-0:amd64. Preparing to unpack .../029-libpixman-1-0_0.44.0-3_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.44.0-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../030-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../102-libsm6_2%3a1.2.4-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.4-1) ... Selecting previously unselected package libsynctex2:amd64. 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Setting up r-cran-knitr (1.48+dfsg-1) ... Setting up r-cran-cachem (1.1.0-1) ... Setting up r-cran-sass (0.4.9+dfsg-1) ... Setting up r-cran-fontawesome (0.5.2-1) ... Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... Setting up texlive-bibtex-extra (2024.20241115-1) ... Setting up r-cran-memoise (2.0.1-1) ... Setting up r-cran-promises (1.3.0+dfsg-1) ... Setting up r-cran-httpuv (1.6.15+dfsg-1) ... Setting up r-cran-bslib (0.7.0+dfsg-1) ... Setting up r-cran-shiny (1.9.1+dfsg-1) ... Setting up r-cran-rmarkdown (2.28+dfsg-1) ... Setting up r-cran-bookdown (0.41+dfsg-1) ... Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. 0m35.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-y', 'install', 'r-bioc-biocstyle'] 0m35.1s INFO: Running scripts post_install 0m35.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_install_exceptions'] 0m35.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/post_install_exceptions'] 0m35.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m36.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m36.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmppfzi933f to sid 0m36.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m36.0s INFO: Running scripts pre_distupgrade 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', 'update'] 0m37.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7343 kB] Fetched 17.6 MB in 1s (11.8 MB/s) Reading package lists... 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', 'update'] 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-yf', 'dist-upgrade'] 0m40.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: r-bioc-biocstyle The following packages will be upgraded: apt base-files libapt-pkg6.0t64 libblas3 libc-bin libc6 libglib2.0-0t64 liblapack3 libpcre2-8-0 libperl5.40 libseccomp2 libzzip-0-13t64 perl perl-base perl-modules-5.40 r-cran-commonmark r-cran-knitr 17 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Need to get 20.7 MB of archives. After this operation, 139 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-4 [2804 kB] Get:2 http://deb.debian.org/debian sid/main amd64 base-files amd64 13.6 [72.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:4 http://deb.debian.org/debian sid/main amd64 perl amd64 5.40.0-8 [267 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.40.0-8 [1675 kB] Get:6 http://deb.debian.org/debian sid/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.14 [1103 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB] Get:9 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.14 [1395 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-4 [626 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:14 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get:16 http://deb.debian.org/debian sid/main amd64 r-cran-commonmark amd64 1.9.2-1 [122 kB] Get:17 http://deb.debian.org/debian sid/main amd64 r-cran-knitr all 1.49+dfsg-1 [861 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.7 MB in 0s (184 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31546 files and directories currently installed.) Preparing to unpack .../libc6_2.40-4_amd64.deb ... Unpacking libc6:amd64 (2.40-4) over (2.40-3) ... Setting up libc6:amd64 (2.40-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31546 files and directories currently installed.) Preparing to unpack .../base-files_13.6_amd64.deb ... Unpacking base-files (13.6) over (13.5) ... Setting up base-files (13.6) ... Updating /root/.profile to current default. (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 ... 31546 files and directories currently installed.) Preparing to unpack .../libperl5.40_5.40.0-8_amd64.deb ... Unpacking libperl5.40:amd64 (5.40.0-8) over (5.40.0-7) ... Preparing to unpack .../perl_5.40.0-8_amd64.deb ... Unpacking perl (5.40.0-8) over (5.40.0-7) ... Preparing to unpack .../perl-base_5.40.0-8_amd64.deb ... Unpacking perl-base (5.40.0-8) over (5.40.0-7) ... Setting up perl-base (5.40.0-8) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31546 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2) over (2.5.5-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-2) ... (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 ... 31545 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.14_amd64.deb ... Unpacking apt (2.9.14) over (2.9.10) ... Setting up apt (2.9.14) ... (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 ... 31542 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-4_amd64.deb ... Unpacking libc-bin (2.40-4) over (2.40-3) ... Setting up libc-bin (2.40-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31542 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.44-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.44-4) over (10.42-4+b2) ... Setting up libpcre2-8-0:amd64 (10.44-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 31541 files and directories currently installed.) Preparing to unpack .../0-libblas3_3.12.0-4_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-4) over (3.12.0-3+b1) ... Preparing to unpack .../1-libglib2.0-0t64_2.82.2-3_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.2-2) ... Preparing to unpack .../2-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) over (3.12.0-3+b1) ... Preparing to unpack .../3-libzzip-0-13t64_0.13.72+dfsg.1-1.3_amd64.deb ... Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) over (0.13.72+dfsg.1-1.2+b1) ... Preparing to unpack .../4-r-cran-commonmark_1.9.2-1_amd64.deb ... Unpacking r-cran-commonmark (1.9.2-1) over (1.9.1-1) ... Preparing to unpack .../5-r-cran-knitr_1.49+dfsg-1_all.deb ... Unpacking r-cran-knitr (1.49+dfsg-1) over (1.48+dfsg-1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:amd64 (3.12.0-4) ... Setting up libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.3) ... Setting up r-cran-knitr (1.49+dfsg-1) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up r-cran-commonmark (1.9.2-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up perl (5.40.0-8) ... Processing triggers for libc-bin (2.40-4) ... 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-yf', 'dist-upgrade'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.7s DUMP: b0bc141b8cd6d788b659dec670729469 - 0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m40.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-biocstyle'] 0m40.8s DUMP: Package: r-bioc-biocstyle Version: 2.34.0+dfsg-1 Installed-Size: 637 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-cran-bookdown, r-cran-knitr (>= 1.30), r-cran-rmarkdown (>= 1.2), r-cran-yaml, r-cran-biocmanager, texlive-bibtex-extra, xdg-utils, r-bioc-biocversion (>= 3.19.1), r-bioc-biocgenerics (>= 0.50.0) Suggests: r-cran-runit, r-cran-htmltools Description-en: standard styles for vignettes and other Bioconductor documents Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality. Description-md5: 3039a52b9b0668021ed645f7222b1fde Homepage: https://bioconductor.org/packages/BiocStyle/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-biocstyle/r-bioc-biocstyle_2.34.0+dfsg-1_all.deb Size: 452448 MD5sum: 6f4e648de063436a28307c0dd732929c SHA256: 9e632947f96c6469bc68c08f6febd554b41fe2c4a5d0f532d5b31ab8938c657b 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-biocstyle'] 0m40.8s INFO: apt-cache knows about the following packages: r-bioc-biocstyle 0m40.8s INFO: Running scripts pre_install 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_database-server'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_database-server'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_exceptions'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_exceptions'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_extras'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_extras'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy'] 0m40.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m40.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy'] 0m40.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy', 'r-bioc-biocstyle'] 0m40.9s DUMP: r-bioc-biocstyle: Installed: 2.32.1+dfsg-1 Candidate: 2.34.0+dfsg-1 Version table: 2.34.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages *** 2.32.1+dfsg-1 100 100 /var/lib/dpkg/status 0m40.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-cache', 'policy', 'r-bioc-biocstyle'] 0m40.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-y', 'install', 'r-bioc-biocstyle'] 0m41.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-biocstyle : Depends: r-api-bioc-3.20 but it is not installable E: Unable to correct problems, you have held broken packages. 0m41.1s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmppfzi933f', 'apt-get', '-y', 'install', 'r-bioc-biocstyle'] Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-biocstyle : Depends: r-api-bioc-3.20 but it is not installable E: Unable to correct problems, you have held broken packages. 0m42.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/shm'] 0m42.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/shm'] 0m42.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/console'] 0m42.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/console'] 0m42.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/ptmx'] 0m42.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/ptmx'] 0m42.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts'] 0m42.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/dev/pts'] 0m42.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/proc'] 0m42.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppfzi933f/proc'] 0m42.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m42.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppfzi933f'] 0m42.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppfzi933f 0m42.4s ERROR: piuparts run ends. ret=1 End: 2024-11-26 15:17:18 GMT