Start: 2025-04-09 17:26:31 GMT
Package: r-bioc-structuralvariantannotation
Version: 1.22.0+ds-2
Installed-Size: 1297
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Architecture: all
Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-genomicranges, r-bioc-rtracklayer, r-bioc-variantannotation, r-bioc-biocgenerics, r-cran-assertthat, r-bioc-biostrings, r-bioc-pwalign, 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_1.22.0+ds-2_all.deb
Size: 401032
MD5sum: 02f3afd5f64221b4d8fa82a4e5edf468
SHA256: 39cb0fad90aeb0f32a9d187750aa5f4fa3d74c95c1c2cb7bbcea5aa9f0873d30
Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.22.0+ds-2
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile.
0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ
0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong.
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: piuparts version 1.5.2~202503162239~1.5.1-10-g345d5865 starting up.
0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --install-remove-install --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-others --scriptsdir /etc/piuparts/scripts-leftovers --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt r-bioc-structuralvariantannotation=1.22.0+ds-2
0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64
0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpvaoa3wu7
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvaoa3wu7
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz']
0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/proc']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/proc']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/ptmx']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/ptmx']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/console']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/console']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/shm']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/shm']
0m0.4s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
0m0.4s DEBUG: Created policy-rc.d and chmodded it.
0m0.4s DEBUG: Created resolv.conf.
0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpvaoa3wu7/tmp/scripts/
0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-leftovers to /srv/piuparts.debian.org/tmp/tmpvaoa3wu7/tmp/scripts/
0m0.4s INFO: Running scripts post_chroot_unpack
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'update']
0m3.1s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7417 kB]
Fetched 17.8 MB in 2s (9158 kB/s)
Reading package lists...
0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'update']
0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-yf', 'dist-upgrade']
0m4.6s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
The following packages will be upgraded:
bash coreutils
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 4512 kB of archives.
After this operation, 179 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-2 [1500 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB]
Fetched 4512 kB in 0s (41.9 MB/s)
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Preparing to unpack .../bash_5.2.37-2_amd64.deb ...
Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ...
Setting up bash (5.2.37-2) ...
update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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(Reading database ... 4925 files and directories currently installed.)
Preparing to unpack .../coreutils_9.7-1_amd64.deb ...
Unpacking coreutils (9.7-1) over (9.6-2) ...
Setting up coreutils (9.7-1) ...
Processing triggers for debianutils (5.21) ...
0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-yf', 'dist-upgrade']
0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m5.2s DUMP:
31e44ff00e610efb534d9d62a0a21228 -
0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m5.2s INFO: Running scripts post_setup
0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_dummy_users']
0m5.8s 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
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_dummy_users']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_fake-essential']
0m7.6s DUMP:
*** Adding fake essential packages ***
Reading package lists...
Building dependency tree...
Reading state information...
init-system-helpers is already the newest version (1.68).
The following additional packages will be installed:
libncursesw6 libproc2-0 libtext-charwidth-perl libtext-wrapi18n-perl procps
sensible-utils ucf
Suggested packages:
dbconfig-mysql | dbconfig-pgsql | dbconfig-sqlite3 | dbconfig-no-thanks
Recommended packages:
libgpm2 psmisc linux-sysctl-defaults
The following NEW packages will be installed:
dbconfig-common libncursesw6 libproc2-0 libtext-charwidth-perl
libtext-wrapi18n-perl procps sensible-utils ucf
0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
Need to get 1757 kB of archives.
After this operation, 4947 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get:6 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get:7 http://deb.debian.org/debian sid/main amd64 ucf all 3.0051 [42.8 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 dbconfig-common all 2.0.24 [592 kB]
Preconfiguring packages ...
Fetched 1757 kB in 0s (24.8 MB/s)
Selecting previously unselected package libncursesw6:amd64.
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(Reading database ... 4925 files and directories currently installed.)
Preparing to unpack .../0-libncursesw6_6.5+20250216-2_amd64.deb ...
Unpacking libncursesw6:amd64 (6.5+20250216-2) ...
Selecting previously unselected package libproc2-0:amd64.
Preparing to unpack .../1-libproc2-0_2%3a4.0.4-7_amd64.deb ...
Unpacking libproc2-0:amd64 (2:4.0.4-7) ...
Selecting previously unselected package procps.
Preparing to unpack .../2-procps_2%3a4.0.4-7_amd64.deb ...
Unpacking procps (2:4.0.4-7) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../3-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libtext-charwidth-perl:amd64.
Preparing to unpack .../4-libtext-charwidth-perl_0.04-11+b4_amd64.deb ...
Unpacking libtext-charwidth-perl:amd64 (0.04-11+b4) ...
Selecting previously unselected package libtext-wrapi18n-perl.
Preparing to unpack .../5-libtext-wrapi18n-perl_0.06-10_all.deb ...
Unpacking libtext-wrapi18n-perl (0.06-10) ...
Selecting previously unselected package ucf.
Preparing to unpack .../6-ucf_3.0051_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0051) ...
Selecting previously unselected package dbconfig-common.
Preparing to unpack .../7-dbconfig-common_2.0.24_all.deb ...
Unpacking dbconfig-common (2.0.24) ...
Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ...
Setting up libtext-wrapi18n-perl (0.06-10) ...
Setting up libproc2-0:amd64 (2:4.0.4-7) ...
Setting up libncursesw6:amd64 (6.5+20250216-2) ...
Setting up sensible-utils (0.0.24) ...
Setting up procps (2:4.0.4-7) ...
Setting up ucf (3.0051) ...
Setting up dbconfig-common (2.0.24) ...
Creating config file /etc/dbconfig-common/config with new version
Processing triggers for libc-bin (2.41-6) ...
0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_fake-essential']
0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_forbid_home']
0m7.6s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_forbid_home']
0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.7s 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'
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_force-unsafe-io']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_minimize']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_minimize']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_squeeze-backports']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_squeeze-backports']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_zz_backports']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_setup_zz_backports']
0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
0m7.7s DEBUG: Recording chroot state
0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m8.2s DUMP:
install ok installed apt apt 3.0.0
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.7
install ok installed bash bash 5.2.37-2
install ok installed bsdutils bsdutils 1:2.41-3
install ok installed coreutils coreutils 9.7-1
install ok installed dash dash 0.5.12-12
install ok installed dbconfig-common dbconfig-common 2.0.24
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-3
install ok installed dpkg dpkg 1.22.18
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblkid1:amd64 libblkid1 2.41-3
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 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-4
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.8.1-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.41-3
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7
install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3
install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2
install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsystemd0:amd64 libsystemd0 257.5-2
install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4
install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.5-2
install ok installed libuuid1:amd64 libuuid1 2.41-3
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed login login 1:4.16.0-2+really2.41-3
install ok installed login.defs login.defs 1:4.17.4-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.41-3
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1
install ok installed passwd passwd 1:4.17.4-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed procps procps 2:4.0.4-7
install ok installed sed sed 4.9-2
install ok installed sensible-utils sensible-utils 0.0.24
install ok installed sqv sqv 1.3.0-1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025b-1
install ok installed ucf ucf 3.0051
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.41-3
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-divert', '--list']
0m8.2s DUMP:
local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged
local diversion of /home to /home.distrib
diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-divert', '--list']
0m8.2s INFO: Running scripts is_testable
0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/is_testable_uninstallable']
0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/is_testable_uninstallable']
0m8.2s INFO: apt-cache does not know about any of the requested packages
0m8.2s INFO: Running scripts pre_test
0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_test_exceptions']
0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_test_exceptions']
0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_test_root_password']
0m8.3s DUMP:
New password: Retype new password: passwd: password updated successfully
0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_test_root_password']
0m8.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m9.4s DEBUG: No broken symlinks as far as we can find.
0m9.4s INFO: Running scripts pre_install
0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m10.4s DUMP:
Package: r-bioc-structuralvariantannotation
Version: 1.22.0+ds-2
Installed-Size: 1297
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Architecture: all
Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-genomicranges, r-bioc-rtracklayer, r-bioc-variantannotation, r-bioc-biocgenerics, r-cran-assertthat, r-bioc-biostrings, r-bioc-pwalign, 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-en: Variant annotations for structural variants
StructuralVariantAnnotation contains useful helper
functions for dealing with structural variants in VCF format.
The packages contains functions for parsing VCFs from a number
of popular callers as well as functions for dealing with
breakpoints involving two separate genomic loci encoded as
GRanges objects.
Description-md5: da0d30e1c2fddfc05ec9f7a5a97d4001
Homepage: https://bioconductor.org/packages/StructuralVariantAnnotation/
Section: gnu-r
Priority: optional
Filename: pool/main/r/r-bioc-structuralvariantannotation/r-bioc-structuralvariantannotation_1.22.0+ds-2_all.deb
Size: 401032
MD5sum: 02f3afd5f64221b4d8fa82a4e5edf468
SHA256: 39cb0fad90aeb0f32a9d187750aa5f4fa3d74c95c1c2cb7bbcea5aa9f0873d30
0m10.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m10.4s DEBUG: metapackage:
Package: piuparts-depends-dummy
Version: 0.invalid.0
Architecture: all
Maintainer: piuparts developers team <piuparts-devel@alioth-lists.debian.net>
Depends: r-api-4.0, r-api-bioc-3.20, r-bioc-genomicranges, r-bioc-rtracklayer, r-bioc-variantannotation, r-bioc-biocgenerics, r-cran-assertthat, r-bioc-biostrings, r-bioc-pwalign, r-cran-stringr, r-cran-dplyr, r-cran-rlang, r-bioc-genomicfeatures, r-bioc-iranges, r-bioc-s4vectors, r-bioc-summarizedexperiment, r-bioc-genomeinfodb
Description: Dummy package to satisfy dependencies - created by piuparts
This package was created automatically by piuparts and can safely be removed
0m10.4s DEBUG: Starting command: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp73hap5pw/piuparts-depends-dummy']
0m10.5s DUMP:
dpkg-deb: warning: not checking contents of control area
dpkg-deb: building an unknown package in '/srv/piuparts.debian.org/tmp/tmp73hap5pw/piuparts-depends-dummy.deb'.
0m10.5s DEBUG: Command ok: ['dpkg-deb', '-b', '-Zgzip', '--nocheck', '/srv/piuparts.debian.org/tmp/tmp73hap5pw/piuparts-depends-dummy']
0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt']
0m10.5s DUMP:
3.0.0
0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-f', '${Version}\n', '-W', 'apt']
0m10.5s DEBUG: Copying /srv/piuparts.debian.org/tmp/tmp73hap5pw/piuparts-depends-dummy.deb to /srv/piuparts.debian.org/tmp/tmpvaoa3wu7/tmp
0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb']
0m41.2s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
ca-certificates fontconfig fontconfig-config fonts-dejavu-core
fonts-dejavu-mono libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev
libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev
libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1
libfreetype6 libfribidi0 libgcc-14-dev libgfortran5 libglib2.0-0t64
libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2
liblerc4 liblsan0 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0
libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2
libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev
libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl
r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics
r-bioc-biocio r-bioc-biocparallel 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-pwalign
r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays
r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment
r-bioc-ucsc.utils r-bioc-variantannotation r-bioc-xvector r-bioc-zlibbioc
r-cran-abind 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-dplyr r-cran-fansi r-cran-fastmap r-cran-formatr r-cran-futile.logger
r-cran-futile.options r-cran-generics r-cran-glue r-cran-httr
r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
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-plogr r-cran-png
r-cran-r6 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-yaml readline-common rpcsvc-proto unzip x11-common
xdg-utils zip zlib1g-dev
Suggested packages:
libboost-doc libboost1.83-doc libboost-atomic1.83-dev
libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev
libboost-contract1.83-dev libboost-coroutine1.83-dev
libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
libboost-numpy1.83-dev libboost-program-options1.83-dev
libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev
libboost-serialization1.83-dev libboost-stacktrace1.83-dev
libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
libc-devtools glibc-doc manpages-dev low-memory-monitor gnutls-bin krb5-doc
krb5-user libstdc++-14-doc tcl8.6 tk8.6 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-bioc-golubesets
r-bioc-limma r-bioc-hdf5array r-bioc-affy r-bioc-deseq2 r-bioc-annotate
r-cran-testthat r-cran-rmarkdown r-cran-foreach r-cran-bbmisc
r-cran-doparallel r-bioc-shortread r-cran-batchtools r-cran-data.table
r-cran-covr r-cran-biocmanager r-bioc-genefilter r-cran-lobstr
r-bioc-delayedmatrixstats r-cran-r.utils r-bioc-edger r-bioc-txdbmaker
r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz
r-bioc-annotationhub r-bioc-dexseq r-cran-digest r-bioc-sparsematrixstats
r-bioc-experimenthub r-bioc-rhdf5 r-bioc-singlecellexperiment
r-cran-rmariadb r-bioc-snpstats r-cran-ggplot2 r-cran-magick r-cran-rmysql
r-cran-rcpp r-cran-rmpi r-cran-rlecuyer readline-doc
Recommended packages:
manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs
krb5-locales libldap-common publicsuffix libsasl2-modules r-recommended
r-base-dev r-doc-html r-cran-testthat r-cran-roxygen2 r-cran-knitr
r-cran-markdown r-cran-rmarkdown r-cran-ff r-cran-microbenchmark
r-cran-callr r-cran-covr r-cran-digest 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-brio r-cran-decor r-cran-desc r-cran-ggplot2
r-cran-lobstr r-cran-mockery r-cran-progress r-cran-scales r-cran-rcpp
r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-broom
r-cran-dbplyr r-cran-purrr r-cran-rmysql r-cran-rpostgresql r-cran-tidyr
r-cran-unitizer r-cran-shiny r-cran-testit r-cran-survival r-cran-pkgload
r-cran-waldo r-cran-jpeg r-cran-readr r-cran-xml2 r-cran-r.rsp r-cran-sf
r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-r.devices
r-cran-sodium r-cran-diagrammer r-cran-formattable r-cran-lubridate
r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-vdiffr
r-cran-runit r-cran-fs r-cran-usethis r-cran-dbitest r-cran-gert r-cran-gh
r-cran-hms r-cran-rvest r-cran-evaluate r-cran-here r-cran-pkgbuild
r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
ca-certificates fontconfig fontconfig-config fonts-dejavu-core
fonts-dejavu-mono libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev
libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev
libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1
libfreetype6 libfribidi0 libgcc-14-dev libgfortran5 libglib2.0-0t64
libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2
liblerc4 liblsan0 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0
libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2
libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev
libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl
piuparts-depends-dummy r-base-core r-bioc-annotationdbi r-bioc-biobase
r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel 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-pwalign r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation
r-bioc-xvector r-bioc-zlibbioc r-cran-abind 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-dplyr r-cran-fansi r-cran-fastmap r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue
r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
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-plogr r-cran-png
r-cran-r6 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-yaml readline-common rpcsvc-proto unzip x11-common
xdg-utils zip zlib1g-dev
0 upgraded, 186 newly installed, 0 to remove and 0 not upgraded.
Need to get 194 MB/194 MB of archives.
After this operation, 570 MB of additional disk space will be used.
Get:1 /tmp/piuparts-depends-dummy.deb piuparts-depends-dummy all 0.invalid.0 [766 B]
Get:2 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.0-1 [1491 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20241223 [164 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.7.1-1 [108 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14.2.0-19 [2725 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-19 [9308 B]
Get:16 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-19 [137 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14.2.0-19 [26.0 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14.2.0-19 [1204 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14.2.0-19 [2460 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14.2.0-19 [1074 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14.2.0-19 [1488 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-19 [145 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libgcc-14-dev amd64 14.2.0-19 [2672 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.41-6 [57.0 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.21-1 [2542 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.41-6 [1988 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 libstdc++-14-dev amd64 14.2.0-19 [2376 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB]
Get:32 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B]
Get:33 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:35 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.12-1 [343 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get:42 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB]
Get:43 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get:47 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-5 [9316 B]
Get:48 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get:49 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.3-2 [477 kB]
Get:51 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB]
Get:52 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.13.0-1 [381 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get:67 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get:68 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB]
Get:69 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.84.1-1 [1514 kB]
Get:70 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get:71 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB]
Get:72 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+24 [217 kB]
Get:73 http://deb.debian.org/debian sid/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get:74 http://deb.debian.org/debian sid/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get:75 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get:76 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get:77 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get:78 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get:79 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get:80 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get:81 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB]
Get:82 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB]
Get:83 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB]
Get:84 http://deb.debian.org/debian sid/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB]
Get:85 http://deb.debian.org/debian sid/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB]
Get:86 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:87 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get:88 http://deb.debian.org/debian sid/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB]
Get:89 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get:90 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get:91 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.7.0-3 [346 kB]
Get:92 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB]
Get:93 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB]
Get:94 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get:95 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get:96 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get:97 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB]
Get:98 http://deb.debian.org/debian sid/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get:99 http://deb.debian.org/debian sid/main amd64 zip amd64 3.0-14 [233 kB]
Get:100 http://deb.debian.org/debian sid/main amd64 unzip amd64 6.0-29 [173 kB]
Get:101 http://deb.debian.org/debian sid/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get:102 http://deb.debian.org/debian sid/main amd64 r-base-core amd64 4.4.3-1+b1 [28.3 MB]
Get:103 http://deb.debian.org/debian sid/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB]
Get:104 http://deb.debian.org/debian sid/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB]
Get:105 http://deb.debian.org/debian sid/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB]
Get:106 http://deb.debian.org/debian sid/main amd64 r-bioc-iranges amd64 2.40.1-2 [2309 kB]
Get:107 http://deb.debian.org/debian sid/main amd64 r-cran-dbi all 1.2.3-1 [852 kB]
Get:108 http://deb.debian.org/debian sid/main amd64 r-cran-bit amd64 4.6.0+dfsg-1 [455 kB]
Get:109 http://deb.debian.org/debian sid/main amd64 r-cran-bit64 amd64 4.6.0-1-1 [481 kB]
Get:110 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.5-1 [1712 kB]
Get:111 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.4-1 [1370 kB]
Get:112 http://deb.debian.org/debian sid/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB]
Get:113 http://deb.debian.org/debian sid/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
Get:114 http://deb.debian.org/debian sid/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB]
Get:115 http://deb.debian.org/debian sid/main amd64 r-cran-blob all 1.2.4-1 [49.6 kB]
Get:116 http://deb.debian.org/debian sid/main amd64 r-cran-fastmap amd64 1.2.0-1 [72.2 kB]
Get:117 http://deb.debian.org/debian sid/main amd64 r-cran-cachem amd64 1.1.0-1 [73.9 kB]
Get:118 http://deb.debian.org/debian sid/main amd64 r-cran-memoise all 2.0.1-1 [53.8 kB]
Get:119 http://deb.debian.org/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get:120 http://deb.debian.org/debian sid/main amd64 r-cran-plogr all 0.2.0-3 [14.9 kB]
Get:121 http://deb.debian.org/debian sid/main amd64 r-cran-cpp11 all 0.5.2-1 [226 kB]
Get:122 http://deb.debian.org/debian sid/main amd64 r-cran-rsqlite amd64 2.3.9-1 [1216 kB]
Get:123 http://deb.debian.org/debian sid/main amd64 r-cran-curl amd64 6.2.1+dfsg-1 [195 kB]
Get:124 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [445 kB]
Get:125 http://deb.debian.org/debian sid/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB]
Get:126 http://deb.debian.org/debian sid/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB]
Get:127 http://deb.debian.org/debian sid/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB]
Get:128 http://deb.debian.org/debian sid/main amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [402 kB]
Get:129 http://deb.debian.org/debian sid/main amd64 r-cran-r6 all 2.6.1-1 [106 kB]
Get:130 http://deb.debian.org/debian sid/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
Get:131 http://deb.debian.org/debian sid/main amd64 r-cran-png amd64 0.1-8-1+b1 [41.5 kB]
Get:132 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get:133 http://deb.debian.org/debian sid/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B]
Get:134 http://deb.debian.org/debian sid/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
Get:135 http://deb.debian.org/debian sid/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB]
Get:136 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
Get:137 http://deb.debian.org/debian sid/main amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3848 kB]
Get:138 http://deb.debian.org/debian sid/main amd64 r-cran-crayon all 1.5.3-1 [165 kB]
Get:139 http://deb.debian.org/debian sid/main amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.4 MB]
Get:140 http://deb.debian.org/debian sid/main amd64 r-bioc-keggrest all 1.46.0+dfsg-2 [184 kB]
Get:141 http://deb.debian.org/debian sid/main amd64 r-bioc-annotationdbi all 1.68.0-2 [4703 kB]
Get:142 http://deb.debian.org/debian sid/main amd64 r-bioc-biocio all 1.16.0+dfsg-2 [210 kB]
Get:143 http://deb.debian.org/debian sid/main amd64 r-cran-formatr all 1.14-2 [152 kB]
Get:144 http://deb.debian.org/debian sid/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:145 http://deb.debian.org/debian sid/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:146 http://deb.debian.org/debian sid/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:147 http://deb.debian.org/debian sid/main amd64 r-cran-snow all 1:0.4.4-2 [98.9 kB]
Get:148 http://deb.debian.org/debian sid/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB]
Get:149 http://deb.debian.org/debian sid/main amd64 r-cran-bh all 1.84.0-1 [5912 B]
Get:150 http://deb.debian.org/debian sid/main amd64 r-bioc-biocparallel amd64 1.40.0-2 [1326 kB]
Get:151 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2092 kB]
Get:152 http://deb.debian.org/debian sid/main amd64 r-cran-xml amd64 3.99-0.18-1 [1762 kB]
Get:153 http://deb.debian.org/debian sid/main amd64 r-cran-bitops amd64 1.0-9-1 [30.7 kB]
Get:154 http://deb.debian.org/debian sid/main amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1335 kB]
Get:155 http://deb.debian.org/debian sid/main amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3600 kB]
Get:156 http://deb.debian.org/debian sid/main amd64 r-cran-matrixstats amd64 1.5.0-1 [502 kB]
Get:157 http://deb.debian.org/debian sid/main amd64 r-bioc-matrixgenerics all 1.18.1-1 [449 kB]
Get:158 http://deb.debian.org/debian sid/main amd64 r-cran-lattice amd64 0.22-7-1 [1418 kB]
Get:159 http://deb.debian.org/debian sid/main amd64 r-cran-matrix amd64 1.7-3-1 [4048 kB]
Get:160 http://deb.debian.org/debian sid/main amd64 r-cran-abind all 1.4-8-1 [68.1 kB]
Get:161 http://deb.debian.org/debian sid/main amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [702 kB]
Get:162 http://deb.debian.org/debian sid/main amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1372 kB]
Get:163 http://deb.debian.org/debian sid/main amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2076 kB]
Get:164 http://deb.debian.org/debian sid/main amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1116 kB]
Get:165 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2161 kB]
Get:166 http://deb.debian.org/debian sid/main amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [799 kB]
Get:167 http://deb.debian.org/debian sid/main amd64 r-cran-rjson amd64 0.2.23-1 [100.0 kB]
Get:168 http://deb.debian.org/debian sid/main amd64 r-cran-yaml amd64 2.3.10-1 [108 kB]
Get:169 http://deb.debian.org/debian sid/main amd64 r-cran-restfulr amd64 0.0.15-1 [382 kB]
Get:170 http://deb.debian.org/debian sid/main amd64 r-bioc-rtracklayer amd64 1.66.0-2 [5213 kB]
Get:171 http://deb.debian.org/debian sid/main amd64 r-bioc-bsgenome all 1.74.0-2 [7011 kB]
Get:172 http://deb.debian.org/debian sid/main amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [930 kB]
Get:173 http://deb.debian.org/debian sid/main amd64 r-bioc-pwalign amd64 1.2.0-2 [755 kB]
Get:174 http://deb.debian.org/debian sid/main amd64 r-bioc-variantannotation amd64 1.52.0-2 [3549 kB]
Get:175 http://deb.debian.org/debian sid/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB]
Get:176 http://deb.debian.org/debian sid/main amd64 r-cran-generics all 0.1.3-1 [81.4 kB]
Get:177 http://deb.debian.org/debian sid/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get:178 http://deb.debian.org/debian sid/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB]
Get:179 http://deb.debian.org/debian sid/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
Get:180 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.6-1 [629 kB]
Get:181 http://deb.debian.org/debian sid/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB]
Get:182 http://deb.debian.org/debian sid/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB]
Get:183 http://deb.debian.org/debian sid/main amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [223 kB]
Get:184 http://deb.debian.org/debian sid/main amd64 r-cran-dplyr amd64 1.1.4-4 [1543 kB]
Get:185 http://deb.debian.org/debian sid/main amd64 r-cran-stringi amd64 1.8.4-1+b1 [896 kB]
Get:186 http://deb.debian.org/debian sid/main amd64 r-cran-stringr all 1.5.1-1 [296 kB]
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Setting up r-cran-stringi (1.8.4-1+b1) ...
Setting up r-cran-cpp11 (0.5.2-1) ...
Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up r-cran-matrix (1.7-3-1) ...
Setting up r-cran-cachem (1.1.0-1) ...
Setting up r-bioc-iranges (2.40.1-2) ...
Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
Setting up r-cran-restfulr (0.0.15-1) ...
Setting up r-cran-vctrs (0.6.5-1) ...
Setting up r-cran-pillar (1.10.1+dfsg-1) ...
Setting up r-cran-openssl (2.3.2+dfsg-1) ...
Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
Setting up r-cran-stringr (1.5.1-1) ...
Setting up r-bioc-biocparallel (1.40.0-2) ...
Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
Setting up r-cran-tibble (3.2.1+dfsg-3) ...
Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
Setting up r-cran-httr (1.4.7+dfsg-1) ...
Setting up r-cran-memoise (2.0.1-1) ...
Setting up r-cran-blob (1.2.4-1) ...
Setting up r-bioc-xvector (0.46.0-2) ...
Setting up r-cran-dplyr (1.1.4-4) ...
Setting up r-cran-rsqlite (2.3.9-1) ...
Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ...
Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
Setting up r-bioc-pwalign (1.2.0-2) ...
Setting up r-bioc-keggrest (1.46.0+dfsg-2) ...
Setting up r-bioc-annotationdbi (1.68.0-2) ...
Setting up r-bioc-genomicalignments (1.42.0-2) ...
Setting up r-bioc-rtracklayer (1.66.0-2) ...
Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
Setting up r-bioc-bsgenome (1.74.0-2) ...
Setting up r-bioc-variantannotation (1.52.0-2) ...
Setting up piuparts-depends-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.41-6) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', '--allow-downgrades', 'install', './tmp/piuparts-depends-dummy.deb']
0m41.2s INFO: Installation of ['./tmp/piuparts-depends-dummy.deb'] ok
0m41.2s DEBUG: Removing /srv/piuparts.debian.org/tmp/tmpvaoa3wu7/./tmp/piuparts-depends-dummy.deb
0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy']
0m41.2s DUMP:
piuparts-depends-dummy install ok installed
0m41.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-f', '${Package} ${Status}\n', '-W', 'piuparts-depends-dummy']
0m41.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m41.3s DUMP:
(Reading database ... 36778 files and directories currently installed.)
Removing piuparts-depends-dummy (0.invalid.0) ...
0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
0m41.3s DEBUG: Recording chroot state
0m42.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m44.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m46.8s DEBUG: No broken symlinks as far as we can find.
0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m47.5s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m47.6s DUMP:
r-bioc-structuralvariantannotation:
Installed: (none)
Candidate: 1.22.0+ds-2
Version table:
1.22.0+ds-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
0m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m48.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Suggested packages:
r-cran-ggplot2 r-cran-devtools r-cran-testthat r-cran-roxygen2
r-cran-rmarkdown r-cran-tidyverse r-cran-knitr r-bioc-ggbio
r-bioc-biovizbase
The following NEW packages will be installed:
r-bioc-structuralvariantannotation
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 401 kB of archives.
After this operation, 1328 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 r-bioc-structuralvariantannotation all 1.22.0+ds-2 [401 kB]
Fetched 401 kB in 0s (2051 kB/s)
Selecting previously unselected package r-bioc-structuralvariantannotation.
(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 36778 files and directories currently installed.)
Preparing to unpack .../r-bioc-structuralvariantannotation_1.22.0+ds-2_all.deb ...
Unpacking r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
Setting up r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m48.8s INFO: Running scripts post_install
0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m48.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'systemd-tmpfiles', '--cat-config']
0m48.8s DUMP:
chroot: failed to run command 'systemd-tmpfiles': No such file or directory
0m48.8s DEBUG: Command failed (status=127), but ignoring error: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'systemd-tmpfiles', '--cat-config']
0m48.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'remove', 'r-bioc-structuralvariantannotation']
0m49.6s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libasan8
libatomic1 libblas3 libboost-dev libboost1.83-dev libbrotli1 libc-dev-bin
libc6-dev libcairo2 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1
libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0
libgcc-14-dev libgfortran5 libglib2.0-0t64 libgnutls30t64 libgomp1
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhwasan0 libice6 libicu76
libitm1 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack3 libldap2 liblerc4 liblsan0 libnghttp2-14
libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64
libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2
libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev
libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
libtirpc3t64 libtk8.6 libtsan2 libubsan1 libwebp7 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev r-base-core
r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio
r-bioc-biocparallel 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-pwalign r-bioc-rhtslib r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation
r-bioc-xvector r-bioc-zlibbioc r-cran-abind 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-dplyr r-cran-fansi r-cran-fastmap r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue
r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
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-plogr r-cran-png
r-cran-r6 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-yaml readline-common rpcsvc-proto unzip x11-common
xdg-utils zip zlib1g-dev
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
r-bioc-structuralvariantannotation
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 1328 kB disk space will be freed.
(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 36841 files and directories currently installed.)
Removing r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'remove', 'r-bioc-structuralvariantannotation']
0m49.6s INFO: Reinstalling after remove
0m49.6s INFO: Running scripts pre_install
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m49.7s 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:
0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m49.7s DUMP:
r-bioc-structuralvariantannotation:
Installed: (none)
Candidate: 1.22.0+ds-2
Version table:
1.22.0+ds-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m50.7s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Suggested packages:
r-cran-ggplot2 r-cran-devtools r-cran-testthat r-cran-roxygen2
r-cran-rmarkdown r-cran-tidyverse r-cran-knitr r-bioc-ggbio
r-bioc-biovizbase
The following NEW packages will be installed:
r-bioc-structuralvariantannotation
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/401 kB of archives.
After this operation, 1328 kB of additional disk space will be used.
Selecting previously unselected package r-bioc-structuralvariantannotation.
(Reading database ...
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(Reading database ... 10%
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(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 45%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 36778 files and directories currently installed.)
Preparing to unpack .../r-bioc-structuralvariantannotation_1.22.0+ds-2_all.deb ...
Unpacking r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
Setting up r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
0m50.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m50.7s INFO: Running scripts post_install
0m50.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m50.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m50.7s INFO: Running scripts pre_install
0m50.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_database-server']
0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_exceptions']
0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_extras']
0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture']
0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m50.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m50.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m50.9s 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:
0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy']
0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m50.9s DUMP:
r-bioc-structuralvariantannotation:
Installed: 1.22.0+ds-2
Candidate: 1.22.0+ds-2
Version table:
*** 1.22.0+ds-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m50.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-cache', 'policy', 'r-bioc-structuralvariantannotation']
0m50.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', '--reinstall', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m51.9s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded.
Need to get 0 B/401 kB of archives.
After this operation, 0 B of additional disk space will be used.
(Reading database ...
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(Reading database ... 35%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 36841 files and directories currently installed.)
Preparing to unpack .../r-bioc-structuralvariantannotation_1.22.0+ds-2_all.deb ...
Unpacking r-bioc-structuralvariantannotation (1.22.0+ds-2) over (1.22.0+ds-2) ...
Setting up r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', '-y', 'install', '--reinstall', 'r-bioc-structuralvariantannotation=1.22.0+ds-2']
0m51.9s INFO: Running scripts post_install
0m51.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m52.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_install_exceptions']
0m52.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m53.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
0m56.4s DEBUG: No broken symlinks as far as we can find.
0m58.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', '-ac', '--ignore-obsolete']
1m1.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', '-ac', '--ignore-obsolete']
1m1.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
1m1.4s DUMP:
0.15.6
1m1.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
1m1.4s INFO: Running adequate version 0.15.6 now.
1m1.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'r-bioc-structuralvariantannotation']
1m1.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'r-bioc-structuralvariantannotation']
1m1.5s INFO: Running scripts pre_remove
1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
1m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
1m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
1m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
1m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_50_find_bad_permissions']
1m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_50_find_bad_permissions']
1m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_50_find_missing_copyright']
1m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_50_find_missing_copyright']
1m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_exceptions']
1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_exceptions']
1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_preseed_cleanup']
1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/pre_remove_preseed_cleanup']
1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
1m6.0s DUMP:
install ok installed apt apt 3.0.0
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.7
install ok installed bash bash 5.2.37-2
install ok installed bsdutils bsdutils 1:2.41-3
install ok installed ca-certificates ca-certificates 20241223
install ok installed coreutils coreutils 9.7-1
install ok installed dash dash 0.5.12-12
install ok installed dbconfig-common dbconfig-common 2.0.24
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-3
install ok installed dpkg dpkg 1.22.18
install ok installed findutils findutils 4.10.0-3
install ok installed fontconfig fontconfig 2.15.0-2.3
install ok installed fontconfig-config fontconfig-config 2.15.0-2.3
install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8
install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0
install ok installed libasan8:amd64 libasan8 14.2.0-19
install ok installed libatomic1:amd64 libatomic1 14.2.0-19
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblas3:amd64 libblas3 3.12.1-2
install ok installed libblkid1:amd64 libblkid1 2.41-3
install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2
install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-4.2
install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7
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 2.41-6
install ok installed libc-dev-bin libc-dev-bin 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libc6-dev:amd64 libc6-dev 2.41-6
install ok installed libcairo2:amd64 libcairo2 1.18.4-1+b1
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-4
install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1
install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.38-1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libcurl4t64:amd64 libcurl4t64 8.13.0-1
install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.278
install ok installed libdeflate0:amd64 libdeflate0 1.23-1+b1
install ok installed libexpat1:amd64 libexpat1 2.7.1-1
install ok installed libffi8:amd64 libffi8 3.4.7-1
install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-2.3
install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1
install ok installed libfribidi0:amd64 libfribidi0 1.0.16-1
install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-19
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgfortran5:amd64 libgfortran5 14.2.0-19
install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.84.1-1
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.9-2
install ok installed libgomp1:amd64 libgomp1 14.2.0-19
install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1
install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5
install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.2.0-1+b1
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed libhwasan0:amd64 libhwasan0 14.2.0-19
install ok installed libice6:amd64 libice6 2:1.1.1-1
install ok installed libicu76:amd64 libicu76 76.1-3
install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2
install ok installed libitm1:amd64 libitm1 14.2.0-19
install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2
install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3.1
install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5
install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-5
install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5
install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5
install ok installed liblapack3:amd64 liblapack3 3.12.1-2
install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-3
install ok installed libldap2:amd64 libldap2 2.6.9+dfsg-2
install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5
install ok installed liblsan0:amd64 liblsan0 14.2.0-19
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.8.1-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.41-3
install ok installed libncursesw6:amd64 libncursesw6 6.5+20250216-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1
install ok installed libnghttp3-9:amd64 libnghttp3-9 1.8.0-1
install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.56.3-1
install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.56.3-1
install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.56.3-1
install ok installed libpaper-utils libpaper-utils 2.2.5-0.3+b2
install ok installed libpaper2:amd64 libpaper2 2.2.5-0.3+b2
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3
install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.47-1.1
install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-7
install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1
install ok installed libquadmath0:amd64 libquadmath0 14.2.0-19
install ok installed libreadline8t64:amd64 libreadline8t64 8.2-6
install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5
install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9
install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9
install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsharpyuv0:amd64 libsharpyuv0 1.5.0-0.1
install ok installed libsm6:amd64 libsm6 2:1.2.6-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.41-3
install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-2
install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1
install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1
install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-19
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsystemd0:amd64 libsystemd0 257.5-2
install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2
install ok installed libtcl8.6:amd64 libtcl8.6 8.6.16+dfsg-1
install ok installed libtext-charwidth-perl:amd64 libtext-charwidth-perl 0.04-11+b4
install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-10
install ok installed libthai-data libthai-data 0.1.29-2
install ok installed libthai0:amd64 libthai0 0.1.29-2+b1
install ok installed libtiff6:amd64 libtiff6 4.7.0-3
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libtirpc-common libtirpc-common 1.3.6+ds-1
install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.6+ds-1
install ok installed libtk8.6:amd64 libtk8.6 8.6.16-1
install ok installed libtsan2:amd64 libtsan2 14.2.0-19
install ok installed libubsan1:amd64 libubsan1 14.2.0-19
install ok installed libudev1:amd64 libudev1 257.5-2
install ok installed libunistring5:amd64 libunistring5 1.3-2
install ok installed libuuid1:amd64 libuuid1 2.41-3
install ok installed libwebp7:amd64 libwebp7 1.5.0-0.1
install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1
install ok installed libx11-data libx11-data 2:1.8.12-1
install ok installed libxau6:amd64 libxau6 1:1.0.11-1
install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1
install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1
install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1
install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1
install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3
install ok installed libxft2:amd64 libxft2 2.3.6-1+b4
install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.4
install ok installed libxrender1:amd64 libxrender1 1:0.9.12-1
install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b3
install ok installed libxt6t64:amd64 libxt6t64 1:1.2.1-1.2+b2
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed linux-libc-dev linux-libc-dev 6.12.21-1
install ok installed login login 1:4.16.0-2+really2.41-3
install ok installed login.defs login.defs 1:4.17.4-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.41-3
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl openssl 3.5.0-1
install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1
install ok installed passwd passwd 1:4.17.4-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed procps procps 2:4.0.4-7
install ok installed r-base-core r-base-core 4.4.3-1+b1
install ok installed r-bioc-annotationdbi r-bioc-annotationdbi 1.68.0-2
install ok installed r-bioc-biobase r-bioc-biobase 2.66.0-2
install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.52.0-2
install ok installed r-bioc-biocio r-bioc-biocio 1.16.0+dfsg-2
install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.40.0-2
install ok installed r-bioc-biostrings r-bioc-biostrings 2.74.1+dfsg-2
install ok installed r-bioc-bsgenome r-bioc-bsgenome 1.74.0-2
install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.32.0+dfsg-2
install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.42.3+dfsg-1
install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.13-2
install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.42.0-2
install ok installed r-bioc-genomicfeatures r-bioc-genomicfeatures 1.58.0+dfsg-2
install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.58.0+dfsg-2
install ok installed r-bioc-iranges r-bioc-iranges 2.40.1-2
install ok installed r-bioc-keggrest r-bioc-keggrest 1.46.0+dfsg-2
install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.18.1-1
install ok installed r-bioc-pwalign r-bioc-pwalign 1.2.0-2
install ok installed r-bioc-rhtslib r-bioc-rhtslib 3.2.0+dfsg-2
install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.22.0+dfsg-2
install ok installed r-bioc-rtracklayer r-bioc-rtracklayer 1.66.0-2
install ok installed r-bioc-s4arrays r-bioc-s4arrays 1.6.0+dfsg-2
install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.44.0+dfsg-2
install ok installed r-bioc-sparsearray r-bioc-sparsearray 1.6.2+dfsg-2
install ok installed r-bioc-structuralvariantannotation r-bioc-structuralvariantannotation 1.22.0+ds-2
install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.36.0+dfsg-2
install ok installed r-bioc-ucsc.utils r-bioc-ucsc.utils 1.2.0+ds-2
install ok installed r-bioc-variantannotation r-bioc-variantannotation 1.52.0-2
install ok installed r-bioc-xvector r-bioc-xvector 0.46.0-2
install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.52.0+dfsg-2
install ok installed r-cran-abind r-cran-abind 1.4-8-1
install ok installed r-cran-askpass r-cran-askpass 1.2.1-1
install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2
install ok installed r-cran-bh r-cran-bh 1.84.0-1
install ok installed r-cran-bit r-cran-bit 4.6.0+dfsg-1
install ok installed r-cran-bit64 r-cran-bit64 4.6.0-1-1
install ok installed r-cran-bitops r-cran-bitops 1.0-9-1
install ok installed r-cran-blob r-cran-blob 1.2.4-1
install ok installed r-cran-cachem r-cran-cachem 1.1.0-1
install ok installed r-cran-cli r-cran-cli 3.6.4-1
install ok installed r-cran-codetools r-cran-codetools 0.2-20-1
install ok installed r-cran-cpp11 r-cran-cpp11 0.5.2-1
install ok installed r-cran-crayon r-cran-crayon 1.5.3-1
install ok installed r-cran-curl r-cran-curl 6.2.1+dfsg-1
install ok installed r-cran-dbi r-cran-dbi 1.2.3-1
install ok installed r-cran-dplyr r-cran-dplyr 1.1.4-4
install ok installed r-cran-fansi r-cran-fansi 1.0.6-1
install ok installed r-cran-fastmap r-cran-fastmap 1.2.0-1
install ok installed r-cran-formatr r-cran-formatr 1.14-2
install ok installed r-cran-futile.logger r-cran-futile.logger 1.4.3-4
install ok installed r-cran-futile.options r-cran-futile.options 1.0.1-3
install ok installed r-cran-generics r-cran-generics 0.1.3-1
install ok installed r-cran-glue r-cran-glue 1.8.0-1
install ok installed r-cran-httr r-cran-httr 1.4.7+dfsg-1
install ok installed r-cran-jsonlite r-cran-jsonlite 1.9.1+dfsg-1
install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2
install ok installed r-cran-lattice r-cran-lattice 0.22-7-1
install ok installed r-cran-lifecycle r-cran-lifecycle 1.0.4+dfsg-1
install ok installed r-cran-magrittr r-cran-magrittr 2.0.3-1
install ok installed r-cran-matrix r-cran-matrix 1.7-3-1
install ok installed r-cran-matrixstats r-cran-matrixstats 1.5.0-1
install ok installed r-cran-memoise r-cran-memoise 2.0.1-1
install ok installed r-cran-mime r-cran-mime 0.12-2
install ok installed r-cran-openssl r-cran-openssl 2.3.2+dfsg-1
install ok installed r-cran-pillar r-cran-pillar 1.10.1+dfsg-1
install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2
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+b1
install ok installed r-cran-r6 r-cran-r6 2.6.1-1
install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.16+dfsg-1
install ok installed r-cran-restfulr r-cran-restfulr 0.0.15-1
install ok installed r-cran-rjson r-cran-rjson 0.2.23-1
install ok installed r-cran-rlang r-cran-rlang 1.1.5-1
install ok installed r-cran-rsqlite r-cran-rsqlite 2.3.9-1
install ok installed r-cran-snow r-cran-snow 1:0.4.4-2
install ok installed r-cran-stringi r-cran-stringi 1.8.4-1+b1
install ok installed r-cran-stringr r-cran-stringr 1.5.1-1
install ok installed r-cran-sys r-cran-sys 3.4.3-1
install ok installed r-cran-tibble r-cran-tibble 3.2.1+dfsg-3
install ok installed r-cran-tidyselect r-cran-tidyselect 1.2.1+dfsg-1
install ok installed r-cran-utf8 r-cran-utf8 1.2.4-1
install ok installed r-cran-vctrs r-cran-vctrs 0.6.5-1
install ok installed r-cran-withr r-cran-withr 3.0.2+dfsg-1
install ok installed r-cran-xml r-cran-xml 3.99-0.18-1
install ok installed r-cran-yaml r-cran-yaml 2.3.10-1
install ok installed readline-common readline-common 8.2-6
install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1
install ok installed sed sed 4.9-2
install ok installed sensible-utils sensible-utils 0.0.24
install ok installed sqv sqv 1.3.0-1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025b-1
install ok installed ucf ucf 3.0051
install ok installed unzip unzip 6.0-29
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.41-3
install ok installed x11-common x11-common 1:7.7+24
install ok installed xdg-utils xdg-utils 1.2.1-2
install ok installed zip zip 3.0-14
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1
1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', '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-dplyr', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', '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-plogr', 'r-cran-png', 'r-cran-r6', '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-yaml', 'readline-common', 'rpcsvc-proto', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-structuralvariantannotation']
1m9.2s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
ca-certificates fontconfig fontconfig-config fonts-dejavu-core
fonts-dejavu-mono libasan8 libatomic1 libblas3 libboost-dev libboost1.83-dev
libbrotli1 libc-dev-bin libc6-dev libcairo2 libcom-err2 libcrypt-dev
libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1
libfreetype6 libfribidi0 libgcc-14-dev libgfortran5 libglib2.0-0t64
libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libhwasan0 libice6 libicu76 libidn2-0 libitm1 libjbig0 libjpeg62-turbo
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2
liblerc4 liblsan0 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0
libpng16-16t64 libpsl5t64 libquadmath0 libreadline8t64 librtmp1 libsasl2-2
libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libstdc++-14-dev
libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
libtirpc3t64 libtk8.6 libtsan2 libubsan1 libunistring5 libwebp7 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev openssl
r-base-core r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics
r-bioc-biocio r-bioc-biocparallel 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-pwalign
r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays
r-bioc-s4vectors r-bioc-sparsearray r-bioc-structuralvariantannotation
r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation
r-bioc-xvector r-bioc-zlibbioc r-cran-abind 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-dplyr r-cran-fansi r-cran-fastmap r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue
r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
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-plogr r-cran-png
r-cran-r6 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-yaml readline-common rpcsvc-proto unzip x11-common
xdg-utils zip zlib1g-dev
0 upgraded, 0 newly installed, 186 to remove and 0 not upgraded.
After this operation, 571 MB disk space will be freed.
(Reading database ...
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(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 ... 36841 files and directories currently installed.)
Removing r-bioc-structuralvariantannotation (1.22.0+ds-2) ...
Removing r-bioc-variantannotation (1.52.0-2) ...
Removing r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
Removing r-bioc-bsgenome (1.74.0-2) ...
Removing r-bioc-pwalign (1.2.0-2) ...
Removing r-bioc-annotationdbi (1.68.0-2) ...
Removing r-bioc-keggrest (1.46.0+dfsg-2) ...
Removing r-cran-stringr (1.5.1-1) ...
Removing r-cran-stringi (1.8.4-1+b1) ...
Removing r-cran-png (0.1-8-1+b1) ...
Removing r-cran-assertthat (0.2.1-2) ...
Removing r-cran-rsqlite (2.3.9-1) ...
Removing r-cran-bit64 (4.6.0-1-1) ...
Removing r-cran-bit (4.6.0+dfsg-1) ...
Removing r-cran-blob (1.2.4-1) ...
Removing r-cran-memoise (2.0.1-1) ...
Removing r-cran-cachem (1.1.0-1) ...
Removing r-cran-dplyr (1.1.4-4) ...
Removing r-cran-tidyselect (1.2.1+dfsg-1) ...
Removing r-cran-tibble (3.2.1+dfsg-3) ...
Removing r-cran-pillar (1.10.1+dfsg-1) ...
Removing r-cran-dbi (1.2.3-1) ...
Removing r-cran-fansi (1.0.6-1) ...
Removing r-cran-fastmap (1.2.0-1) ...
Removing r-cran-generics (0.1.3-1) ...
Removing r-cran-magrittr (2.0.3-1) ...
Removing r-cran-pkgconfig (2.0.3-2) ...
Removing r-cran-plogr (0.2.0-3) ...
Removing r-cran-utf8 (1.2.4-1) ...
Removing r-cran-withr (3.0.2+dfsg-1) ...
Removing r-bioc-rtracklayer (1.66.0-2) ...
Removing r-bioc-genomicalignments (1.42.0-2) ...
Removing r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
Removing r-bioc-delayedarray (0.32.0+dfsg-2) ...
Removing r-bioc-sparsearray (1.6.2+dfsg-2) ...
Removing r-bioc-s4arrays (1.6.0+dfsg-2) ...
Removing r-cran-abind (1.4-8-1) ...
Removing r-bioc-rsamtools (2.22.0+dfsg-2) ...
Removing r-bioc-biocparallel (1.40.0-2) ...
Removing r-cran-snow (1:0.4.4-2) ...
Removing r-cran-restfulr (0.0.15-1) ...
Removing r-cran-yaml (2.3.10-1) ...
Removing r-cran-bh (1.84.0-1) ...
Removing libboost-dev:amd64 (1.83.0.2+b2) ...
Removing libboost1.83-dev:amd64 (1.83.0-4.2) ...
Removing libstdc++-14-dev:amd64 (14.2.0-19) ...
Removing libgcc-14-dev:amd64 (14.2.0-19) ...
Removing libasan8:amd64 (14.2.0-19) ...
Removing r-cran-rcurl (1.98-1.16+dfsg-1) ...
Removing r-bioc-biostrings (2.74.1+dfsg-2) ...
Removing r-bioc-genomicranges (1.58.0+dfsg-2) ...
Removing r-bioc-xvector (0.46.0-2) ...
Removing r-bioc-rhtslib (3.2.0+dfsg-2) ...
Removing r-bioc-zlibbioc (1.52.0+dfsg-2) ...
Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Removing libc6-dev:amd64 (2.41-6) ...
Removing libc-dev-bin (2.41-6) ...
Removing libcrypt-dev:amd64 (1:4.4.38-1) ...
Removing libhwasan0:amd64 (14.2.0-19) ...
Removing libitm1:amd64 (14.2.0-19) ...
Removing liblsan0:amd64 (14.2.0-19) ...
Removing libquadmath0:amd64 (14.2.0-19) ...
Removing libtsan2:amd64 (14.2.0-19) ...
Removing libubsan1:amd64 (14.2.0-19) ...
Removing r-cran-xml (3.99-0.18-1) ...
Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.4) ...
Removing linux-libc-dev (6.12.21-1) ...
Removing r-bioc-biobase (2.66.0-2) ...
Removing r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
Removing r-bioc-ucsc.utils (1.2.0+ds-2) ...
Removing r-bioc-iranges (2.40.1-2) ...
Removing r-bioc-biocio (1.16.0+dfsg-2) ...
Removing r-bioc-matrixgenerics (1.18.1-1) ...
Removing r-bioc-genomeinfodbdata (1.2.13-2) ...
Removing r-cran-httr (1.4.7+dfsg-1) ...
Removing r-cran-openssl (2.3.2+dfsg-1) ...
Removing r-cran-askpass (1.2.1-1) ...
Removing r-cran-bitops (1.0-9-1) ...
Removing r-cran-vctrs (0.6.5-1) ...
Removing r-cran-codetools (0.2-20-1) ...
Removing r-cran-cpp11 (0.5.2-1) ...
Removing r-cran-crayon (1.5.3-1) ...
Removing r-cran-curl (6.2.1+dfsg-1) ...
Removing r-cran-futile.logger (1.4.3-4) ...
Removing r-cran-lambda.r (1.2.4-2) ...
Removing r-cran-formatr (1.14-2) ...
Removing r-cran-futile.options (1.0.1-3) ...
Removing r-cran-lifecycle (1.0.4+dfsg-1) ...
Removing r-cran-glue (1.8.0-1) ...
Removing r-cran-jsonlite (1.9.1+dfsg-1) ...
Removing r-cran-matrixstats (1.5.0-1) ...
Removing r-cran-mime (0.12-2) ...
Removing r-cran-r6 (2.6.1-1) ...
Removing r-cran-rjson (0.2.23-1) ...
Removing r-cran-rlang (1.1.5-1) ...
Removing r-cran-sys (3.4.3-1) ...
Removing rpcsvc-proto (1.4.3-1) ...
Removing r-cran-matrix (1.7-3-1) ...
Removing r-bioc-s4vectors (0.44.0+dfsg-2) ...
Removing r-bioc-biocgenerics (0.52.0-2) ...
Removing r-cran-cli (3.6.4-1) ...
Removing r-cran-lattice (0.22-7-1) ...
Removing r-base-core (4.4.3-1+b1) ...
Removing ca-certificates (20241223) ...
Removing dangling symlinks from /etc/ssl/certs... done.
Removing libpangocairo-1.0-0:amd64 (1.56.3-1) ...
Removing libpangoft2-1.0-0:amd64 (1.56.3-1) ...
Removing libpango-1.0-0:amd64 (1.56.3-1) ...
Removing fontconfig (2.15.0-2.3) ...
Removing libtk8.6:amd64 (8.6.16-1) ...
Removing libxft2:amd64 (2.3.6-1+b4) ...
Removing libcairo2:amd64 (1.18.4-1+b1) ...
Removing libfontconfig1:amd64 (2.15.0-2.3) ...
Removing fontconfig-config (2.15.0-2.3) ...
Removing fonts-dejavu-core (2.37-8) ...
Removing fonts-dejavu-mono (2.37-8) ...
Removing libharfbuzz0b:amd64 (10.2.0-1+b1) ...
Removing libglib2.0-0t64:amd64 (2.84.1-1) ...
Removing libatomic1:amd64 (14.2.0-19) ...
Removing liblapack3:amd64 (3.12.1-2) ...
Removing libblas3:amd64 (3.12.1-2) ...
Removing libfreetype6:amd64 (2.13.3+dfsg-1) ...
Removing libcurl4t64:amd64 (8.13.0-1) ...
Removing libbrotli1:amd64 (1.1.0-2+b7) ...
Removing libtirpc3t64:amd64 (1.3.6+ds-1) ...
Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Removing libgssapi-krb5-2:amd64 (1.21.3-5) ...
Removing libkrb5-3:amd64 (1.21.3-5) ...
Removing libcom-err2:amd64 (1.47.2-1+b1) ...
Removing libthai0:amd64 (0.1.29-2+b1) ...
Removing libdatrie1:amd64 (0.2.13-3+b1) ...
Removing libtiff6:amd64 (4.7.0-3) ...
Removing libdeflate0:amd64 (1.23-1+b1) ...
Removing libexpat1:amd64 (2.7.1-1) ...
Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Removing libgnutls30t64:amd64 (3.8.9-2) ...
Removing libp11-kit0:amd64 (0.25.5-3) ...
Removing libffi8:amd64 (3.4.7-1) ...
Removing libfribidi0:amd64 (1.0.16-1) ...
Removing libgfortran5:amd64 (14.2.0-19) ...
Removing libgomp1:amd64 (14.2.0-19) ...
Removing libgraphite2-3:amd64 (1.3.14-2+b1) ...
Removing libxt6t64:amd64 (1:1.2.1-1.2+b2) ...
Removing libsm6:amd64 (2:1.2.6-1) ...
Removing libice6:amd64 (2:1.1.1-1) ...
Removing libicu76:amd64 (76.1-3) ...
Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ...
Removing libidn2-0:amd64 (2.3.8-2) ...
Removing libjbig0:amd64 (2.1-6.1+b2) ...
Removing libjpeg62-turbo:amd64 (1:2.1.5-3.1) ...
Removing libk5crypto3:amd64 (1.21.3-5) ...
Removing libkeyutils1:amd64 (1.6.3-5) ...
Removing libkrb5support0:amd64 (1.21.3-5) ...
Removing libldap2:amd64 (2.6.9+dfsg-2) ...
Removing liblerc4:amd64 (4.0.0+ds-5) ...
Removing libnghttp2-14:amd64 (1.64.0-1) ...
Removing libnghttp3-9:amd64 (1.8.0-1) ...
Removing libpaper-utils (2.2.5-0.3+b2) ...
Removing libpaper2:amd64 (2.2.5-0.3+b2) ...
Removing libpixman-1-0:amd64 (0.44.0-3) ...
Removing libpng16-16t64:amd64 (1.6.47-1.1) ...
Removing libreadline8t64:amd64 (8.2-6) ...
Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ...
Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ...
Removing libwebp7:amd64 (1.5.0-0.1) ...
Removing libsharpyuv0:amd64 (1.5.0-0.1) ...
Removing libssh2-1t64:amd64 (1.11.1-1) ...
Removing libtasn1-6:amd64 (4.20.0-2) ...
Removing libtcl8.6:amd64 (8.6.16+dfsg-1) ...
Removing libthai-data (0.1.29-2) ...
Removing libtirpc-common (1.3.6+ds-1) ...
Removing libunistring5:amd64 (1.3-2) ...
Removing libxss1:amd64 (1:1.2.3-1+b3) ...
Removing libxrender1:amd64 (1:0.9.12-1) ...
Removing libxcb-shm0:amd64 (1.17.0-2+b1) ...
Removing libxcb-render0:amd64 (1.17.0-2+b1) ...
Removing libxext6:amd64 (2:1.3.4-1+b3) ...
Removing openssl (3.5.0-1) ...
Removing readline-common (8.2-6) ...
Removing unzip (6.0-29) ...
Removing x11-common (1:7.7+24) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of stop.
Removing xdg-utils (1.2.1-2) ...
Removing zip (3.0-14) ...
Removing libx11-6:amd64 (2:1.8.12-1) ...
Removing libx11-data (2:1.8.12-1) ...
Removing libxcb1:amd64 (1.17.0-2+b1) ...
Removing libxau6:amd64 (1:1.0.11-1) ...
Removing libxdmcp6:amd64 (1:1.1.5-1) ...
Processing triggers for libc-bin (2.41-6) ...
1m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'remove', '--allow-remove-essential', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', '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-dplyr', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', '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-plogr', 'r-cran-png', 'r-cran-r6', '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-yaml', 'readline-common', 'rpcsvc-proto', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-bioc-structuralvariantannotation']
1m9.2s INFO: Running scripts post_remove
1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_remove_cleanup']
1m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_remove_cleanup']
1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_remove_exceptions']
1m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_remove_exceptions']
1m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', '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-dplyr', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', '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-plogr', 'r-cran-png', 'r-cran-r6', '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-yaml', 'readline-common', 'rpcsvc-proto', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64']
1m9.7s DUMP:
(Reading database ... 5519 files and directories currently installed.)
Purging configuration files for ca-certificates (20241223) ...
Removing dangling symlinks from /etc/ssl/certs... done.
Purging configuration files for fontconfig (2.15.0-2.3) ...
Purging configuration files for fontconfig-config (2.15.0-2.3) ...
Purging configuration files for fonts-dejavu-core (2.37-8) ...
Purging configuration files for fonts-dejavu-mono (2.37-8) ...
dpkg: warning: ignoring request to remove libasan8 which isn't installed
dpkg: warning: ignoring request to remove libatomic1 which isn't installed
dpkg: warning: ignoring request to remove libblas3 which isn't installed
dpkg: warning: ignoring request to remove libboost-dev which isn't installed
dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed
dpkg: warning: ignoring request to remove libbrotli1 which isn't installed
dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed
dpkg: warning: ignoring request to remove libc6-dev which isn't installed
dpkg: warning: ignoring request to remove libcairo2 which isn't installed
dpkg: warning: ignoring request to remove libcom-err2 which isn't installed
Purging configuration files for libcrypt-dev:amd64 (1:4.4.38-1) ...
dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed
dpkg: warning: ignoring request to remove libdatrie1 which isn't installed
dpkg: warning: ignoring request to remove libdeflate0 which isn't installed
dpkg: warning: ignoring request to remove libexpat1 which isn't installed
dpkg: warning: ignoring request to remove libffi8 which isn't installed
dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed
dpkg: warning: ignoring request to remove libfreetype6 which isn't installed
dpkg: warning: ignoring request to remove libfribidi0 which isn't installed
dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed
dpkg: warning: ignoring request to remove libgfortran5 which isn't installed
Purging configuration files for libglib2.0-0t64:amd64 (2.84.1-1) ...
dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed
dpkg: warning: ignoring request to remove libgomp1 which isn't installed
dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed
Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ...
dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed
dpkg: warning: ignoring request to remove libhwasan0 which isn't installed
dpkg: warning: ignoring request to remove libice6 which isn't installed
dpkg: warning: ignoring request to remove libicu76 which isn't installed
dpkg: warning: ignoring request to remove libidn2-0 which isn't installed
dpkg: warning: ignoring request to remove libitm1 which isn't installed
dpkg: warning: ignoring request to remove libjbig0 which isn't installed
dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed
dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed
dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed
dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed
dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed
dpkg: warning: ignoring request to remove liblapack3 which isn't installed
dpkg: warning: ignoring request to remove libldap2 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 libnghttp3-9 which isn't installed
dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed
dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed
dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed
dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed
dpkg: warning: ignoring request to remove libpaper-utils which isn't installed
Purging configuration files for libpaper2:amd64 (2.2.5-0.3+b2) ...
dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed
dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed
dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed
dpkg: warning: ignoring request to remove libquadmath0 which isn't installed
Purging configuration files for libreadline8t64:amd64 (8.2-6) ...
dpkg: warning: ignoring request to remove librtmp1 which isn't installed
dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed
dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed
dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed
dpkg: warning: ignoring request to remove libsm6 which isn't installed
dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed
dpkg: warning: ignoring request to remove libstdc++-14-dev which isn't installed
dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed
dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed
dpkg: warning: ignoring request to remove libthai-data which isn't installed
dpkg: warning: ignoring request to remove libthai0 which isn't installed
dpkg: warning: ignoring request to remove libtiff6 which isn't installed
Purging configuration files for libtirpc-common (1.3.6+ds-1) ...
Purging configuration files for libtirpc3t64:amd64 (1.3.6+ds-1) ...
dpkg: warning: ignoring request to remove libtk8.6 which isn't installed
dpkg: warning: ignoring request to remove libtsan2 which isn't installed
dpkg: warning: ignoring request to remove libubsan1 which isn't installed
dpkg: warning: ignoring request to remove libunistring5 which isn't installed
dpkg: warning: ignoring request to remove libwebp7 which isn't installed
dpkg: warning: ignoring request to remove libx11-6 which isn't installed
dpkg: warning: ignoring request to remove libx11-data which isn't installed
dpkg: warning: ignoring request to remove libxau6 which isn't installed
dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed
dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed
dpkg: warning: ignoring request to remove libxcb1 which isn't installed
dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed
dpkg: warning: ignoring request to remove libxext6 which isn't installed
dpkg: warning: ignoring request to remove libxft2 which isn't installed
dpkg: warning: ignoring request to remove libxml2 which isn't installed
dpkg: warning: ignoring request to remove libxrender1 which isn't installed
dpkg: warning: ignoring request to remove libxss1 which isn't installed
dpkg: warning: ignoring request to remove libxt6t64 which isn't installed
dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed
Purging configuration files for openssl (3.5.0-1) ...
Purging configuration files for r-base-core (4.4.3-1+b1) ...
dpkg: warning: ignoring request to remove r-bioc-annotationdbi which isn't installed
dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed
dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed
dpkg: warning: ignoring request to remove r-bioc-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-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-pwalign which isn't installed
dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed
dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed
dpkg: warning: ignoring request to remove r-bioc-rtracklayer which isn't installed
dpkg: warning: ignoring request to remove r-bioc-s4arrays which isn't installed
dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed
dpkg: warning: ignoring request to remove r-bioc-sparsearray which isn't installed
dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed
dpkg: warning: ignoring request to remove r-bioc-ucsc.utils 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-abind which isn't installed
dpkg: warning: ignoring request to remove r-cran-askpass which isn't installed
dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed
dpkg: warning: ignoring request to remove r-cran-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-dplyr 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-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-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-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-plogr which isn't installed
dpkg: warning: ignoring request to remove r-cran-png which isn't installed
dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed
dpkg: warning: ignoring request to remove r-cran-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-yaml which isn't installed
Purging configuration files for readline-common (8.2-6) ...
dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed
dpkg: warning: ignoring request to remove unzip which isn't installed
Purging configuration files for x11-common (1:7.7+24) ...
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
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libasan8:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcom-err2:amd64', 'libcrypt-dev:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libffi8:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-14-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu76:amd64', 'libidn2-0:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap2:amd64', 'liblerc4:amd64', 'liblsan0:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libp11-kit0:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper2:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libpsl5t64:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1t64:amd64', 'libstdc++-14-dev:amd64', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libunistring5:amd64', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6t64:amd64', 'linux-libc-dev', 'openssl', 'r-base-core', 'r-bioc-annotationdbi', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocio', 'r-bioc-biocparallel', '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-pwalign', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-rtracklayer', 'r-bioc-s4arrays', 'r-bioc-s4vectors', 'r-bioc-sparsearray', 'r-bioc-summarizedexperiment', 'r-bioc-ucsc.utils', 'r-bioc-variantannotation', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-abind', '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-dplyr', 'r-cran-fansi', 'r-cran-fastmap', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-glue', 'r-cran-httr', 'r-cran-jsonlite', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lifecycle', '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-plogr', 'r-cran-png', 'r-cran-r6', '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-yaml', 'readline-common', 'rpcsvc-proto', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64']
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation']
1m9.7s DUMP:
dpkg: warning: ignoring request to remove r-bioc-structuralvariantannotation which isn't installed
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', 'r-bioc-structuralvariantannotation']
1m9.7s INFO: Running scripts post_purge
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_purge_exceptions']
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_purge_exceptions']
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_purge_manual_cleanup']
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_purge_manual_cleanup']
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', '--pending']
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--purge', '--pending']
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--remove', '--pending']
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg', '--remove', '--pending']
1m9.7s INFO: Running scripts post_test
1m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_test_exceptions']
1m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'tmp/scripts/post_test_exceptions']
1m9.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
1m10.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
1m10.5s DEBUG: No broken symlinks as far as we can find.
1m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-divert', '--list']
1m10.5s DUMP:
local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged
local diversion of /home to /home.distrib
diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
1m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'dpkg-divert', '--list']
1m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
1m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7', 'apt-get', 'clean']
1m10.5s DEBUG: Recording chroot state
1m12.1s INFO: PASS: Installation and purging test.
1m12.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/shm']
1m12.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/shm']
1m12.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/console']
1m12.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/console']
1m12.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/ptmx']
1m12.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/ptmx']
1m12.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts']
1m12.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/dev/pts']
1m12.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/proc']
1m12.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7/proc']
1m12.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
1m12.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvaoa3wu7']
1m12.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvaoa3wu7
1m12.7s INFO: PASS: All tests.
1m12.7s INFO: piuparts run ends.
ret=0
End: 2025-04-09 17:27:44 GMT