Start: 2024-09-12 05:02:30 GMT [bullseye] Package: r-cran-shazam Version: 1.0.2-1 Installed-Size: 2565 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.2-1), r-api-4.0, r-cran-ggplot2 (>= 3.2.0), r-cran-alakazam (>= 1.0.2), r-cran-ape, r-cran-diptest, r-cran-doparallel, r-cran-dplyr (>= 0.8.1), r-cran-foreach, r-cran-igraph, r-cran-iterators, r-cran-kedd, r-cran-kernsmooth, r-cran-lazyeval, r-cran-mass, r-cran-progress, r-cran-rlang, r-cran-scales, r-cran-seqinr, r-cran-stringi (>= 1.1.3), r-cran-tidyr, r-cran-tidyselect Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat Description: Immunoglobulin Somatic Hypermutation Analysis Homepage: https://cran.r-project.org/package=shazam Description-md5: 34fd8fba9274dcd56ee399bba24b4182 Section: science Priority: optional Filename: pool/main/r/r-cran-shazam/r-cran-shazam_1.0.2-1_all.deb Size: 2142920 MD5sum: f5e5933513faeeea8d3feb3752e08251 SHA256: 51a4e9e772676540721be0c7e7f66c126085cab65bd951d4d5473f3df8d4144a [bullseye-next] Package: r-cran-shazam Version: 1.0.2-1 Installed-Size: 2565 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.2-1), r-api-4.0, r-cran-ggplot2 (>= 3.2.0), r-cran-alakazam (>= 1.0.2), r-cran-ape, r-cran-diptest, r-cran-doparallel, r-cran-dplyr (>= 0.8.1), r-cran-foreach, r-cran-igraph, r-cran-iterators, r-cran-kedd, r-cran-kernsmooth, r-cran-lazyeval, r-cran-mass, r-cran-progress, r-cran-rlang, r-cran-scales, r-cran-seqinr, r-cran-stringi (>= 1.1.3), r-cran-tidyr, r-cran-tidyselect Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat Description: Immunoglobulin Somatic Hypermutation Analysis Homepage: https://cran.r-project.org/package=shazam Description-md5: 34fd8fba9274dcd56ee399bba24b4182 Section: science Priority: optional Filename: pool/main/r/r-cran-shazam/r-cran-shazam_1.0.2-1_all.deb Size: 2142920 MD5sum: f5e5933513faeeea8d3feb3752e08251 SHA256: 51a4e9e772676540721be0c7e7f66c126085cab65bd951d4d5473f3df8d4144a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt r-cran-shazam=1.0.2-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201135~1.4.3-10-g39df1906 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt r-cran-shazam=1.0.2-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfgp2lo_q 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfgp2lo_q 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfgp2lo_q/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'update'] 0m2.2s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [8066 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6235 kB] Fetched 14.4 MB in 2s (8893 kB/s) Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4431 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 base-files amd64 11.1+deb11u11 [70.2 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libc6 amd64 2.31-13+deb11u11 [2823 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libc-bin amd64 2.31-13+deb11u11 [829 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libk5crypto3 amd64 1.18.3-6+deb11u5 [114 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libkrb5support0 amd64 1.18.3-6+deb11u5 [65.7 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libkrb5-3 amd64 1.18.3-6+deb11u5 [363 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libgssapi-krb5-2 amd64 1.18.3-6+deb11u5 [166 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4431 kB in 0s (47.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../base-files_11.1+deb11u11_amd64.deb ... Unpacking base-files (11.1+deb11u11) over (11.1+deb11u10) ... Setting up base-files (11.1+deb11u11) ... Installing new version of config file /etc/debian_version ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libc6_2.31-13+deb11u11_amd64.deb ... Unpacking libc6:amd64 (2.31-13+deb11u11) over (2.31-13+deb11u10) ... Setting up libc6:amd64 (2.31-13+deb11u11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-13+deb11u11_amd64.deb ... Unpacking libc-bin (2.31-13+deb11u11) over (2.31-13+deb11u10) ... Setting up libc-bin (2.31-13+deb11u11) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libk5crypto3_1.18.3-6+deb11u5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.18.3-6+deb11u5) over (1.18.3-6+deb11u4) ... Setting up libk5crypto3:amd64 (1.18.3-6+deb11u5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libkrb5support0_1.18.3-6+deb11u5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.18.3-6+deb11u5) over (1.18.3-6+deb11u4) ... Setting up libkrb5support0:amd64 (1.18.3-6+deb11u5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libkrb5-3_1.18.3-6+deb11u5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.18.3-6+deb11u5) over (1.18.3-6+deb11u4) ... Setting up libkrb5-3:amd64 (1.18.3-6+deb11u5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6670 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.18.3-6+deb11u5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.18.3-6+deb11u5) over (1.18.3-6+deb11u4) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-6+deb11u5) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: f58ca9ba0b3223edf5b7797c101a5448 - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s 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' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u11 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u5 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u5 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u5 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u5 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'show', '--no-all-versions', 'r-cran-shazam'] 0m4.2s DUMP: Package: r-cran-shazam Version: 1.0.2-1 Installed-Size: 2565 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.2-1), r-api-4.0, r-cran-ggplot2 (>= 3.2.0), r-cran-alakazam (>= 1.0.2), r-cran-ape, r-cran-diptest, r-cran-doparallel, r-cran-dplyr (>= 0.8.1), r-cran-foreach, r-cran-igraph, r-cran-iterators, r-cran-kedd, r-cran-kernsmooth, r-cran-lazyeval, r-cran-mass, r-cran-progress, r-cran-rlang, r-cran-scales, r-cran-seqinr, r-cran-stringi (>= 1.1.3), r-cran-tidyr, r-cran-tidyselect Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat Description-en: Immunoglobulin Somatic Hypermutation Analysis Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires. . SHazaM is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides tools for advanced analysis of somatic hypermutation (SHM) in immunoglobulin (Ig) sequences. Shazam focuses on the following analysis topics: . * Quantification of mutational load SHazaM includes methods for determine the rate of observed and expected mutations under various criteria. Mutational profiling criteria include rates under SHM targeting models, mutations specific to CDR and FWR regions, and physicochemical property dependent substitution rates. * Statistical models of SHM targeting patterns Models of SHM may be divided into two independent components: 1) a mutability model that defines where mutations occur and 2) a nucleotide substitution model that defines the resulting mutation. Collectively these two components define an SHM targeting model. SHazaM provides empirically derived SHM 5-mer context mutation models for both humans and mice, as well tools to build SHM targeting models from data. * Analysis of selection pressure using BASELINe The Bayesian Estimation of Antigen-driven Selection in Ig Sequences (BASELINe) method is a novel method for quantifying antigen-driven selection in high-throughput Ig sequence data. BASELINe uses SHM targeting models can be used to estimate the null distribution of expected mutation frequencies, and provide measures of selection pressure informed by known AID targeting biases. * Model-dependent distance calculations SHazaM provides methods to compute evolutionary distances between sequences or set of sequences based on SHM targeting models. This information is particularly useful in understanding and defining clonal relationships. Description-md5: 34fd8fba9274dcd56ee399bba24b4182 Homepage: https://cran.r-project.org/package=shazam Section: science Priority: optional Filename: pool/main/r/r-cran-shazam/r-cran-shazam_1.0.2-1_all.deb Size: 2142920 MD5sum: f5e5933513faeeea8d3feb3752e08251 SHA256: 51a4e9e772676540721be0c7e7f66c126085cab65bd951d4d5473f3df8d4144a 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'show', '--no-all-versions', 'r-cran-shazam'] 0m4.2s INFO: apt-cache knows about the following packages: r-cran-shazam 0m4.2s INFO: Running scripts pre_install 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m4.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m4.2s DUMP: r-cran-shazam: Installed: (none) Candidate: 1.0.2-1 Version table: 1.0.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam'] 0m52.4s 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 libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler openssl r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-ade4 r-cran-airr r-cran-alakazam r-cran-ape r-cran-assertthat r-cran-bh r-cran-bitops r-cran-brio r-cran-callr r-cran-cli r-cran-clipr r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-diptest r-cran-doparallel r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-foreach r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-hms r-cran-igraph r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kedd r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pixmap r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-segmented r-cran-seqinr r-cran-snow r-cran-sp r-cran-stringi r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-yaml readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc manpages-dev libstdc++-10-doc tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-all r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-bbmisc r-bioc-variantannotation r-bioc-shortread r-bioc-biocstyle r-cran-knitr r-cran-data.table r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-hdf5array r-bioc-genefilter r-bioc-delayedmatrixstats r-cran-runit r-bioc-rtracklayer r-bioc-edger r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-sparsematrixstats r-bioc-graph r-bioc-rhdf5 r-cran-rmarkdown r-cran-adegraphics r-cran-adephylo r-cran-deldir r-cran-spdep r-cran-waveslim r-cran-gee r-cran-expm clustalw muscle phyml t-coffee r-cran-covr r-cran-htmlwidgets r-cran-prettycode r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-png r-cran-jpeg r-cran-viridis r-cran-bench r-cran-broom r-cran-dbi r-cran-rmysql r-cran-rpostgresql r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-lubridate r-cran-rgl r-cran-magick r-cran-httr r-cran-curl r-cran-plyr r-cran-getopt r-cran-base64enc r-cran-bit64 r-cran-inline r-cran-xml r-cran-dichromat r-cran-rmpi r-cran-rsprng r-cran-rlecuyer r-cran-rgdal r-cran-mockery r-cran-usethis r-cran-blob r-cran-formattable r-cran-htmltools r-cran-zeallot readline-doc Recommended packages: manpages manpages-dev libc-devtools libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules r-recommended r-base-dev r-doc-html r-cran-runit r-cran-batchjobs r-cran-batchtools r-cran-rmpi r-bioc-shortread r-bioc-annotate r-cran-cliapp r-cran-mockery r-cran-decor r-cran-knitr r-cran-caret r-cran-mlbench r-cran-rpart r-cran-data.table r-cran-rsqlite r-cran-bit64 r-cran-dbplyr r-cran-testit r-cran-survival r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2 r-cran-lubridate r-cran-curl r-cran-rmarkdown r-cran-mockr r-cran-dbi 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 libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler openssl r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-ade4 r-cran-airr r-cran-alakazam r-cran-ape r-cran-assertthat r-cran-bh r-cran-bitops r-cran-brio r-cran-callr r-cran-cli r-cran-clipr r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-diptest r-cran-doparallel r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-foreach r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-hms r-cran-igraph r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kedd r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pixmap r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-segmented r-cran-seqinr r-cran-shazam r-cran-snow r-cran-sp r-cran-stringi r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-yaml readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 197 newly installed, 0 to remove and 0 not upgraded. Need to get 192 MB of archives. After this operation, 527 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libasan6 amd64 10.2.1-6 [2065 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libatomic1 amd64 10.2.1-6 [9008 B] Get:17 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libitm1 amd64 10.2.1-6 [25.8 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 liblsan0 amd64 10.2.1-6 [828 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libtsan0 amd64 10.2.1-6 [2000 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libubsan1 amd64 10.2.1-6 [777 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libgcc-10-dev amd64 10.2.1-6 [2328 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libc-dev-bin amd64 2.31-13+deb11u11 [276 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 linux-libc-dev amd64 5.10.223-1 [1756 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libtirpc-dev amd64 1.3.1-1+deb11u1 [191 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libc6-dev amd64 2.31-13+deb11u11 [2361 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:34 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2+deb11u1 [156 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u13 [347 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u4 [1377 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:88 http://deb.debian.org/debian bullseye/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 littler all 0.3.12-1 [15.6 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biobase amd64 2.50.0-1 [2229 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 r-cran-formatr all 1.7-2 [151 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 r-cran-lambda.r all 1.2.4-2 [118 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.options all 1.0.1-3 [20.0 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 r-cran-futile.logger all 1.4.3-4 [98.4 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 r-cran-snow all 1:0.4.3-2 [109 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 r-cran-bh all 1.74.0-1 [5196 B] Get:98 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocparallel amd64 1.24.1-1 [1143 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 r-bioc-s4vectors amd64 0.28.1-1 [2027 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 r-bioc-iranges amd64 2.24.1-1 [2202 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 r-bioc-zlibbioc all 1.36.0+dfsg-1 [8824 B] Get:103 http://deb.debian.org/debian bullseye/main amd64 r-bioc-xvector amd64 0.30.0-1 [620 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 r-cran-crayon all 1.4.0-1 [143 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biostrings amd64 2.58.0-1 [14.2 MB] Get:106 http://deb.debian.org/debian bullseye/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrix amd64 1.3-2-1 [3604 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 r-cran-matrixstats amd64 0.58.0-3 [664 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 r-bioc-matrixgenerics all 1.2.1-4 [288 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 r-bioc-delayedarray amd64 0.16.1+dfsg-1 [1798 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 r-cran-bitops amd64 1.0-6-5 [23.6 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcurl amd64 1.98-1.2-1+b1 [787 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodbdata all 1.2.4-1 [10.7 MB] Get:114 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomeinfodb all 1.26.2-2 [3905 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicranges amd64 1.42.0+dfsg-1 [1856 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 r-bioc-summarizedexperiment all 1.20.0+dfsg-1 [1955 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rhtslib amd64 1.22.0+dfsg-1 [1024 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 r-bioc-rsamtools amd64 2.6.0-1 [3659 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 r-bioc-genomicalignments amd64 1.26.0-1 [2196 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 r-cran-mass amd64 7.3-53.1-1 [1115 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 r-cran-pixmap all 0.4-12-1 [201 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 r-cran-sp amd64 1:1.4-5-1 [1793 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 r-cran-rlang amd64 0.4.10-1 [1176 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 r-cran-vctrs amd64 0.3.6-1 [1107 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 r-cran-hms all 1.0.0-1 [102 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 r-cran-r6 all 2.5.0-1 [104 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 r-cran-progress all 1.2.2-2 [88.9 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 r-cran-ade4 amd64 1.7-16-1 [5098 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 r-cran-cli all 2.3.0-1 [480 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 r-cran-clipr all 0.7.1-1 [50.7 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 r-cran-fansi amd64 0.4.2-1 [345 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 r-cran-magrittr amd64 2.0.1-1 [198 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 r-cran-pillar all 1.4.7-1 [227 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 r-cran-tibble amd64 3.0.6+dfsg-1 [416 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 r-cran-cpp11 all 0.2.6-1 [144 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcpp amd64 1.0.6-1 [2035 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 r-cran-readr amd64 1.4.0-1 [753 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 r-cran-stringi amd64 1.5.3-1 [729 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 r-cran-yaml amd64 2.2.1-1+b1 [104 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 r-cran-airr all 1.3.0-2 [366 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 r-cran-brio amd64 1.1.1-1 [31.7 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 r-cran-ps amd64 1.5.0-1 [277 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 r-cran-processx amd64 3.4.5-1 [295 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 r-cran-jsonlite amd64 1.7.2+dfsg-1 [447 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 r-cran-withr all 2.4.1-1 [210 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 r-cran-rstudioapi all 0.13-1 [262 kB] Get:162 http://deb.debian.org/debian bullseye/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 r-cran-diffobj amd64 0.3.2-1 [1069 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 r-cran-testthat amd64 3.0.1-1 [1451 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 r-cran-isoband amd64 0.2.3-2 [2085 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 r-cran-nlme amd64 3.1.152-1 [2241 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 r-cran-mgcv amd64 1.8-34-1 [2998 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 r-cran-colorspace amd64 2.0-0+dfsg-1 [1684 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:176 http://deb.debian.org/debian bullseye/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:178 http://deb.debian.org/debian bullseye/main amd64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get:179 http://deb.debian.org/debian bullseye/main amd64 r-cran-ape amd64 5.4-1-1 [2208 kB] Get:180 http://deb.debian.org/debian bullseye/main amd64 r-cran-generics all 0.1.0-1 [73.5 kB] Get:181 http://deb.debian.org/debian bullseye/main amd64 r-cran-purrr amd64 0.3.4-1+b1 [398 kB] Get:182 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyselect amd64 1.1.0+dfsg-1 [192 kB] Get:183 http://deb.debian.org/debian bullseye/main amd64 r-cran-dplyr amd64 1.0.4-1 [1143 kB] Get:184 http://deb.debian.org/debian bullseye/main amd64 r-cran-igraph amd64 1.2.6-1 [3521 kB] Get:185 http://deb.debian.org/debian bullseye/main amd64 r-cran-lazyeval amd64 0.2.2-1+b1 [142 kB] Get:186 http://deb.debian.org/debian bullseye/main amd64 r-cran-segmented all 1.3-1-1 [521 kB] Get:187 http://deb.debian.org/debian bullseye/main amd64 r-cran-seqinr amd64 4.2-5-1 [3991 kB] Get:188 http://deb.debian.org/debian bullseye/main amd64 r-cran-tidyr amd64 1.1.2-1 [786 kB] Get:189 http://deb.debian.org/debian bullseye/main amd64 r-cran-alakazam amd64 1.1.0-1+b1 [2544 kB] Get:190 http://deb.debian.org/debian bullseye/main amd64 r-cran-codetools all 0.2-18-1 [91.8 kB] Get:191 http://deb.debian.org/debian bullseye/main amd64 r-cran-diptest amd64 0.75-7-2 [356 kB] Get:192 http://deb.debian.org/debian bullseye/main amd64 r-cran-iterators all 1.0.13-1 [329 kB] Get:193 http://deb.debian.org/debian bullseye/main amd64 r-cran-foreach all 1.5.1-1 [120 kB] Get:194 http://deb.debian.org/debian bullseye/main amd64 r-cran-doparallel all 1.0.16-1 [61.3 kB] Get:195 http://deb.debian.org/debian bullseye/main amd64 r-cran-kedd all 1.0.3-2 [846 kB] Get:196 http://deb.debian.org/debian bullseye/main amd64 r-cran-kernsmooth amd64 2.23-18-1 [91.1 kB] Get:197 http://deb.debian.org/debian bullseye/main amd64 r-cran-shazam all 1.0.2-1 [2143 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 192 MB in 31s (6113 kB/s) 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Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libdatrie1:amd64 (0.2.13-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1+deb11u4) ... No schema files found: doing nothing. Setting up unzip (6.0-26+deb11u1) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up linux-libc-dev:amd64 (5.10.223-1) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libasan6:amd64 (10.2.1-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up zip (3.0-12) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libtirpc-dev:amd64 (1.3.1-1+deb11u1) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libatomic1:amd64 (10.2.1-6) ... Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libubsan1:amd64 (10.2.1-6) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up sensible-utils (0.0.14) ... Setting up libcrypt-dev:amd64 (1:4.4.18-4) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:amd64 (1.9.0-2+deb11u1) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up libc-dev-bin (2.31-13+deb11u11) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblsan0:amd64 (10.2.1-6) ... Setting up libitm1:amd64 (10.2.1-6) ... Setting up libtsan0:amd64 (10.2.1-6) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libgcc-10-dev:amd64 (10.2.1-6) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up ucf (3.0043) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u13) ... Setting up libc6-dev:amd64 (2.31-13+deb11u11) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libstdc++-10-dev:amd64 (10.2.1-6) ... Setting up libboost1.74-dev:amd64 (1.74.0-9) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up r-cran-bh (1.74.0-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-futile.options (1.0.1-3) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up r-cran-formatr (1.7-2) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up r-cran-pixmap (0.4-12-1) ... Setting up r-cran-lazyeval (0.2.2-1+b1) ... Setting up r-cran-clipr (0.7.1-1) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up r-bioc-genomeinfodbdata (1.2.4-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-codetools (0.2-18-1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-diptest (0.75-7-2) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-matrixstats (0.58.0-3) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-bioc-matrixgenerics (1.2.1-4) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-generics (0.1.0-1) ... Setting up r-cran-iterators (1.0.13-1) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-ape (5.4-1-1) ... Setting up r-cran-yaml (2.2.1-1+b1) ... Setting up r-cran-lambda.r (1.2.4-2) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-foreach (1.5.1-1) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-snow (1:0.4.3-2) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-bitops (1.0-6-5) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-bioc-zlibbioc (1.36.0+dfsg-1) ... Setting up r-bioc-biobase (2.50.0-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-sp (1:1.4-5-1) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-kedd (1.0.3-2) ... Setting up r-cran-stringi (1.5.3-1) ... Setting up r-cran-cpp11 (0.2.6-1) ... Setting up r-cran-segmented (1.3-1-1) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-bioc-s4vectors (0.28.1-1) ... Setting up r-cran-futile.logger (1.4.3-4) ... Setting up r-cran-purrr (0.3.4-1+b1) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-doparallel (1.0.16-1) ... Setting up r-cran-kernsmooth (2.23-18-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-bioc-iranges (2.24.1-1) ... Setting up r-cran-rcurl (1.98-1.2-1+b1) ... Setting up r-bioc-delayedarray (0.16.1+dfsg-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-bioc-biocparallel (1.24.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-bioc-rhtslib (1.22.0+dfsg-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-igraph (1.2.6-1) ... Setting up r-bioc-genomeinfodb (1.26.2-2) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-bioc-xvector (0.30.0-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-bioc-genomicranges (1.42.0+dfsg-1) ... Setting up r-bioc-biostrings (2.58.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-tidyselect (1.1.0+dfsg-1) ... Setting up r-cran-hms (1.0.0-1) ... Setting up r-bioc-rsamtools (2.6.0-1) ... Setting up r-cran-dplyr (1.0.4-1) ... Setting up r-cran-progress (1.2.2-2) ... Setting up r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-ade4 (1.7-16-1) ... Setting up r-cran-readr (1.4.0-1) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-tidyr (1.1.2-1) ... Setting up r-bioc-genomicalignments (1.26.0-1) ... Setting up r-cran-seqinr (4.2-5-1) ... Setting up r-cran-airr (1.3.0-2) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up r-cran-alakazam (1.1.0-1+b1) ... Setting up r-cran-shazam (1.0.2-1) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam'] 0m52.4s INFO: Running scripts post_install 0m52.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m52.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m52.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m53.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m53.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpfgp2lo_q to bullseye-next 0m53.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m53.6s INFO: Running scripts pre_distupgrade 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_exceptions'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_exceptions'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m53.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m53.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'update'] 0m54.4s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Get:2 http://security.debian.org bullseye-security InRelease [27.2 kB] Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://security.debian.org bullseye-security/main amd64 Packages [289 kB] Get:5 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:6 http://security.debian.org bullseye-security/main Translation-en [185 kB] Get:7 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:8 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Fetched 629 kB in 0s (1380 kB/s) Reading package lists... 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'update'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-yf', 'dist-upgrade'] 0m55.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libgnutls30 libsystemd0 libudev1 libxml2 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2578 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://security.debian.org bullseye-security/main amd64 libsystemd0 amd64 247.3-7+deb11u6 [377 kB] Get:2 http://security.debian.org bullseye-security/main amd64 libgnutls30 amd64 3.7.1-5+deb11u6 [1340 kB] Get:3 http://security.debian.org bullseye-security/main amd64 libudev1 amd64 247.3-7+deb11u6 [169 kB] Get:4 http://security.debian.org bullseye-security/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u5 [693 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2578 kB in 0s (29.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37240 files and directories currently installed.) Preparing to unpack .../libsystemd0_247.3-7+deb11u6_amd64.deb ... Unpacking libsystemd0:amd64 (247.3-7+deb11u6) over (247.3-7+deb11u5) ... Setting up libsystemd0:amd64 (247.3-7+deb11u6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37240 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u6_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u6) over (3.7.1-5+deb11u5) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37240 files and directories currently installed.) Preparing to unpack .../libudev1_247.3-7+deb11u6_amd64.deb ... Unpacking libudev1:amd64 (247.3-7+deb11u6) over (247.3-7+deb11u5) ... Setting up libudev1:amd64 (247.3-7+deb11u6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37240 files and directories currently installed.) Preparing to unpack .../libxml2_2.9.10+dfsg-6.7+deb11u5_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u5) over (2.9.10+dfsg-6.7+deb11u4) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u5) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-yf', 'dist-upgrade'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.3s DUMP: 1832fa8ddea5c8356fdd0be892028ffe - 0m55.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m55.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'show', '--no-all-versions', 'r-cran-shazam'] 0m55.4s DUMP: Package: r-cran-shazam Version: 1.0.2-1 Installed-Size: 2565 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-base-core (>= 4.0.2-1), r-api-4.0, r-cran-ggplot2 (>= 3.2.0), r-cran-alakazam (>= 1.0.2), r-cran-ape, r-cran-diptest, r-cran-doparallel, r-cran-dplyr (>= 0.8.1), r-cran-foreach, r-cran-igraph, r-cran-iterators, r-cran-kedd, r-cran-kernsmooth, r-cran-lazyeval, r-cran-mass, r-cran-progress, r-cran-rlang, r-cran-scales, r-cran-seqinr, r-cran-stringi (>= 1.1.3), r-cran-tidyr, r-cran-tidyselect Suggests: r-cran-knitr, r-cran-rmarkdown, r-cran-testthat Description-en: Immunoglobulin Somatic Hypermutation Analysis Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires. . SHazaM is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides tools for advanced analysis of somatic hypermutation (SHM) in immunoglobulin (Ig) sequences. Shazam focuses on the following analysis topics: . * Quantification of mutational load SHazaM includes methods for determine the rate of observed and expected mutations under various criteria. Mutational profiling criteria include rates under SHM targeting models, mutations specific to CDR and FWR regions, and physicochemical property dependent substitution rates. * Statistical models of SHM targeting patterns Models of SHM may be divided into two independent components: 1) a mutability model that defines where mutations occur and 2) a nucleotide substitution model that defines the resulting mutation. Collectively these two components define an SHM targeting model. SHazaM provides empirically derived SHM 5-mer context mutation models for both humans and mice, as well tools to build SHM targeting models from data. * Analysis of selection pressure using BASELINe The Bayesian Estimation of Antigen-driven Selection in Ig Sequences (BASELINe) method is a novel method for quantifying antigen-driven selection in high-throughput Ig sequence data. BASELINe uses SHM targeting models can be used to estimate the null distribution of expected mutation frequencies, and provide measures of selection pressure informed by known AID targeting biases. * Model-dependent distance calculations SHazaM provides methods to compute evolutionary distances between sequences or set of sequences based on SHM targeting models. This information is particularly useful in understanding and defining clonal relationships. Description-md5: 34fd8fba9274dcd56ee399bba24b4182 Homepage: https://cran.r-project.org/package=shazam Section: science Priority: optional Filename: pool/main/r/r-cran-shazam/r-cran-shazam_1.0.2-1_all.deb Size: 2142920 MD5sum: f5e5933513faeeea8d3feb3752e08251 SHA256: 51a4e9e772676540721be0c7e7f66c126085cab65bd951d4d5473f3df8d4144a 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'show', '--no-all-versions', 'r-cran-shazam'] 0m55.4s INFO: apt-cache knows about the following packages: r-cran-shazam 0m55.4s INFO: Running scripts pre_install 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m55.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m55.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m55.5s DUMP: r-cran-shazam: Installed: 1.0.2-1 Candidate: 1.0.2-1 Version table: *** 1.0.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m55.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m55.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam'] 0m55.7s DUMP: Reading package lists... Building dependency tree... Reading state information... r-cran-shazam is already the newest version (1.0.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam'] 0m55.7s INFO: Running scripts post_install 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m55.7s INFO: Running scripts post_distupgrade 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_exceptions'] 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m55.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_distupgrade_zz_backports'] 0m55.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m56.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m56.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m57.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m57.9s INFO: Running scripts pre_install 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_database-server'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_exceptions'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_extras'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m58.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.11,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m58.0s DUMP: r-cran-shazam: Installed: 1.0.2-1 Candidate: 1.0.2-1 Version table: *** 1.0.2-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-cache', 'policy', 'r-cran-shazam'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam=1.0.2-1'] 0m58.2s DUMP: Reading package lists... Building dependency tree... Reading state information... r-cran-shazam is already the newest version (1.0.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', '-y', 'install', 'r-cran-shazam=1.0.2-1'] 0m58.2s INFO: Running scripts post_install 0m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_install_exceptions'] 0m58.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m59.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 0m59.5s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m59.5s INFO: /bin converted to /usr/bin by /usr merge 0m59.5s INFO: /lib converted to /usr/lib by /usr merge 0m59.5s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m59.5s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m59.5s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m59.5s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m59.5s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m59.5s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m59.5s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m59.5s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m59.5s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m59.5s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m59.5s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m59.5s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m59.5s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m59.5s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m59.5s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m59.5s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m59.5s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m59.5s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m59.5s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m59.5s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m59.5s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m59.5s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m59.5s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m59.5s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m59.5s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m59.5s INFO: /sbin converted to /usr/sbin by /usr merge 1m0.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', '-ac', '--ignore-obsolete'] 1m2.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', '-ac', '--ignore-obsolete'] 1m2.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m2.8s DUMP: 0.15.6 1m2.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m2.8s INFO: Running adequate version 0.15.6 now. 1m2.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'r-cran-shazam'] 1m2.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'r-cran-shazam'] 1m2.8s INFO: Running scripts pre_remove 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_exceptions'] 1m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/pre_remove_exceptions'] 1m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m5.9s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u11 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2 install ok installed ca-certificates ca-certificates 20210119 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig fontconfig 2.13.1-4.2 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libasan6:amd64 libasan6 10.2.1-6 install ok installed libatomic1:amd64 libatomic1 10.2.1-6 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libboost-dev:amd64 libboost-dev 1.74.0.3 install ok installed libboost1.74-dev:amd64 libboost1.74-dev 1.74.0-9 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbsd0:amd64 libbsd0 0.11.3-1+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u11 install ok installed libc-dev-bin libc-dev-bin 2.31-13+deb11u11 install ok installed libc6:amd64 libc6 2.31-13+deb11u11 install ok installed libc6-dev:amd64 libc6-dev 2.31-13+deb11u11 install ok installed libcairo2:amd64 libcairo2 1.16.0-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.18-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcurl4:amd64 libcurl4 7.74.0-1.3+deb11u13 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1+deb11u1 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2+deb11u1 install ok installed libgcc-10-dev:amd64 libgcc-10-dev 10.2.1-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgfortran5:amd64 libgfortran5 10.2.1-6 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.8-1+deb11u4 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u6 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libitm1:amd64 libitm1 10.2.1-6 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u5 install ok installed liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblsan0:amd64 liblsan0 10.2.1-6 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmd0:amd64 libmd0 1.0.3-3 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1+deb11u1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.46.2-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.46.2-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.46.2-3 install ok installed libpaper-utils libpaper-utils 1.1.28+b1 install ok installed libpaper1:amd64 libpaper1 1.1.28+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.40.0-1.1~deb11u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libquadmath0:amd64 libquadmath0 10.2.1-6 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2+deb11u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++-10-dev:amd64 libstdc++-10-dev 10.2.1-6 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u6 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.11+dfsg-1 install ok installed libthai-data libthai-data 0.1.28-3 install ok installed libthai0:amd64 libthai0 0.1.28-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u5 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libtk8.6:amd64 libtk8.6 8.6.11-2 install ok installed libtsan0:amd64 libtsan0 10.2.1-6 install ok installed libubsan1:amd64 libubsan1 10.2.1-6 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u6 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libx11-6:amd64 libx11-6 2:1.7.2-1+deb11u2 install ok installed libx11-data libx11-data 2:1.7.2-1+deb11u2 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.14-3 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.14-3 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1.1 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxml2:amd64 libxml2 2.9.10+dfsg-6.7+deb11u5 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.0-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed linux-libc-dev:amd64 linux-libc-dev 5.10.223-1 install ok installed littler littler 0.3.12-1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed openssl openssl 1.1.1w-0+deb11u1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed r-base-core r-base-core 4.0.4-1 install ok installed r-bioc-biobase r-bioc-biobase 2.50.0-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.36.0-1 install ok installed r-bioc-biocparallel r-bioc-biocparallel 1.24.1-1 install ok installed r-bioc-biostrings r-bioc-biostrings 2.58.0-1 install ok installed r-bioc-delayedarray r-bioc-delayedarray 0.16.1+dfsg-1 install ok installed r-bioc-genomeinfodb r-bioc-genomeinfodb 1.26.2-2 install ok installed r-bioc-genomeinfodbdata r-bioc-genomeinfodbdata 1.2.4-1 install ok installed r-bioc-genomicalignments r-bioc-genomicalignments 1.26.0-1 install ok installed r-bioc-genomicranges r-bioc-genomicranges 1.42.0+dfsg-1 install ok installed r-bioc-iranges r-bioc-iranges 2.24.1-1 install ok installed r-bioc-matrixgenerics r-bioc-matrixgenerics 1.2.1-4 install ok installed r-bioc-rhtslib r-bioc-rhtslib 1.22.0+dfsg-1 install ok installed r-bioc-rsamtools r-bioc-rsamtools 2.6.0-1 install ok installed r-bioc-s4vectors r-bioc-s4vectors 0.28.1-1 install ok installed r-bioc-summarizedexperiment r-bioc-summarizedexperiment 1.20.0+dfsg-1 install ok installed r-bioc-xvector r-bioc-xvector 0.30.0-1 install ok installed r-bioc-zlibbioc r-bioc-zlibbioc 1.36.0+dfsg-1 install ok installed r-cran-ade4 r-cran-ade4 1.7-16-1 install ok installed r-cran-airr r-cran-airr 1.3.0-2 install ok installed r-cran-alakazam r-cran-alakazam 1.1.0-1+b1 install ok installed r-cran-ape r-cran-ape 5.4-1-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.1-2 install ok installed r-cran-bh r-cran-bh 1.74.0-1 install ok installed r-cran-bitops r-cran-bitops 1.0-6-5 install ok installed r-cran-brio r-cran-brio 1.1.1-1 install ok installed r-cran-callr r-cran-callr 3.5.1-1 install ok installed r-cran-cli r-cran-cli 2.3.0-1 install ok installed r-cran-clipr r-cran-clipr 0.7.1-1 install ok installed r-cran-codetools r-cran-codetools 0.2-18-1 install ok installed r-cran-colorspace r-cran-colorspace 2.0-0+dfsg-1 install ok installed r-cran-cpp11 r-cran-cpp11 0.2.6-1 install ok installed r-cran-crayon r-cran-crayon 1.4.0-1 install ok installed r-cran-desc r-cran-desc 1.2.0-3 install ok installed r-cran-diffobj r-cran-diffobj 0.3.2-1 install ok installed r-cran-digest r-cran-digest 0.6.27-1 install ok installed r-cran-diptest r-cran-diptest 0.75-7-2 install ok installed r-cran-doparallel r-cran-doparallel 1.0.16-1 install ok installed r-cran-dplyr r-cran-dplyr 1.0.4-1 install ok installed r-cran-ellipsis r-cran-ellipsis 0.3.1-1 install ok installed r-cran-evaluate r-cran-evaluate 0.14-2 install ok installed r-cran-fansi r-cran-fansi 0.4.2-1 install ok installed r-cran-farver r-cran-farver 2.0.3-1+b1 install ok installed r-cran-foreach r-cran-foreach 1.5.1-1 install ok installed r-cran-formatr r-cran-formatr 1.7-2 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 0.1.0-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.3.3+dfsg-1 install ok installed r-cran-glue r-cran-glue 1.4.2-1 install ok installed r-cran-gtable r-cran-gtable 0.3.0+dfsg-2 install ok installed r-cran-hms r-cran-hms 1.0.0-1 install ok installed r-cran-igraph r-cran-igraph 1.2.6-1 install ok installed r-cran-isoband r-cran-isoband 0.2.3-2 install ok installed r-cran-iterators r-cran-iterators 1.0.13-1 install ok installed r-cran-jsonlite r-cran-jsonlite 1.7.2+dfsg-1 install ok installed r-cran-kedd r-cran-kedd 1.0.3-2 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-18-1 install ok installed r-cran-labeling r-cran-labeling 0.4.2-1 install ok installed r-cran-lambda.r r-cran-lambda.r 1.2.4-2 install ok installed r-cran-lattice r-cran-lattice 0.20-41-1+b1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.2-1+b1 install ok installed r-cran-lifecycle r-cran-lifecycle 0.2.0-2 install ok installed r-cran-littler r-cran-littler 0.3.12-1 install ok installed r-cran-magrittr r-cran-magrittr 2.0.1-1 install ok installed r-cran-mass r-cran-mass 7.3-53.1-1 install ok installed r-cran-matrix r-cran-matrix 1.3-2-1 install ok installed r-cran-matrixstats r-cran-matrixstats 0.58.0-3 install ok installed r-cran-mgcv r-cran-mgcv 1.8-34-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-2 install ok installed r-cran-nlme r-cran-nlme 3.1.152-1 install ok installed r-cran-pillar r-cran-pillar 1.4.7-1 install ok installed r-cran-pixmap r-cran-pixmap 0.4-12-1 install ok installed r-cran-pkgbuild r-cran-pkgbuild 1.2.0-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.3-2 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.2.1-1 install ok installed r-cran-pkgload r-cran-pkgload 1.1.0-1 install ok installed r-cran-praise r-cran-praise 1.0.0-4 install ok installed r-cran-prettyunits r-cran-prettyunits 1.1.1-2 install ok installed r-cran-processx r-cran-processx 3.4.5-1 install ok installed r-cran-progress r-cran-progress 1.2.2-2 install ok installed r-cran-ps r-cran-ps 1.5.0-1 install ok installed r-cran-purrr r-cran-purrr 0.3.4-1+b1 install ok installed r-cran-r6 r-cran-r6 2.5.0-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-3 install ok installed r-cran-rcpp r-cran-rcpp 1.0.6-1 install ok installed r-cran-rcurl r-cran-rcurl 1.98-1.2-1+b1 install ok installed r-cran-readr r-cran-readr 1.4.0-1 install ok installed r-cran-rematch2 r-cran-rematch2 2.1.2-2 install ok installed r-cran-rlang r-cran-rlang 0.4.10-1 install ok installed r-cran-rprojroot r-cran-rprojroot 2.0.2-1 install ok installed r-cran-rstudioapi r-cran-rstudioapi 0.13-1 install ok installed r-cran-scales r-cran-scales 1.1.1-1 install ok installed r-cran-segmented r-cran-segmented 1.3-1-1 install ok installed r-cran-seqinr r-cran-seqinr 4.2-5-1 install ok installed r-cran-shazam r-cran-shazam 1.0.2-1 install ok installed r-cran-snow r-cran-snow 1:0.4.3-2 install ok installed r-cran-sp r-cran-sp 1:1.4-5-1 install ok installed r-cran-stringi r-cran-stringi 1.5.3-1 install ok installed r-cran-testthat r-cran-testthat 3.0.1-1 install ok installed r-cran-tibble r-cran-tibble 3.0.6+dfsg-1 install ok installed r-cran-tidyr r-cran-tidyr 1.1.2-1 install ok installed r-cran-tidyselect r-cran-tidyselect 1.1.0+dfsg-1 install ok installed r-cran-utf8 r-cran-utf8 1.1.4-2 install ok installed r-cran-vctrs r-cran-vctrs 0.3.6-1 install ok installed r-cran-viridislite r-cran-viridislite 0.3.0-4 install ok installed r-cran-waldo r-cran-waldo 0.2.3-2 install ok installed r-cran-withr r-cran-withr 2.4.1-1 install ok installed r-cran-yaml r-cran-yaml 2.2.1-1+b1 install ok installed readline-common readline-common 8.1-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.14 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed ucf ucf 3.0043 install ok installed unzip unzip 6.0-26+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u2 install ok installed x11-common x11-common 1:7.7+22 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-12 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.11.dfsg-2+deb11u2 1m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan6:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu67:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'liblsan0:amd64', 'libmd0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libstdc++-10-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'linux-libc-dev:amd64', 'littler', 'openssl', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-ade4', 'r-cran-airr', 'r-cran-alakazam', 'r-cran-ape', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bitops', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-clipr', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-diptest', 'r-cran-doparallel', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-hms', 'r-cran-igraph', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', 'r-cran-kedd', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pixmap', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-segmented', 'r-cran-seqinr', 'r-cran-snow', 'r-cran-sp', 'r-cran-stringi', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-yaml', 'readline-common', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-cran-shazam'] 1m7.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libasan6 libatomic1 libblas3 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo2 libcrypt-dev libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgcc-10-dev libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libice6 libicu67 libitm1 libjbig0 libjpeg62-turbo liblapack3 libldap-2.4-2 liblsan0 libmd0 libnghttp2-14 libnsl-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libstdc++-10-dev libtcl8.6 libthai-data libthai0 libtiff5 libtirpc-dev libtk8.6 libtsan0 libubsan1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 linux-libc-dev littler openssl r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-ade4 r-cran-airr r-cran-alakazam r-cran-ape r-cran-assertthat r-cran-bh r-cran-bitops r-cran-brio r-cran-callr r-cran-cli r-cran-clipr r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest r-cran-diptest r-cran-doparallel r-cran-dplyr r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-foreach r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-hms r-cran-igraph r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-kedd r-cran-kernsmooth r-cran-labeling r-cran-lambda.r r-cran-lattice r-cran-lazyeval r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pixmap r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress r-cran-ps r-cran-purrr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-readr r-cran-rematch2 r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-segmented r-cran-seqinr r-cran-shazam r-cran-snow r-cran-sp r-cran-stringi r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo r-cran-withr r-cran-yaml readline-common sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 197 to remove and 0 not upgraded. After this operation, 527 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 37240 files and directories currently installed.) Removing r-cran-shazam (1.0.2-1) ... Removing r-cran-alakazam (1.1.0-1+b1) ... Removing r-bioc-genomicalignments (1.26.0-1) ... Removing r-bioc-rsamtools (2.6.0-1) ... Removing r-bioc-biocparallel (1.24.1-1) ... Removing r-cran-snow (1:0.4.3-2) ... Removing r-cran-igraph (1.2.6-1) ... Removing r-bioc-summarizedexperiment (1.20.0+dfsg-1) ... Removing r-cran-airr (1.3.0-2) ... Removing r-cran-readr (1.4.0-1) ... Removing r-cran-ggplot2 (3.3.3+dfsg-1) ... Removing r-cran-scales (1.1.1-1) ... Removing r-cran-rcolorbrewer (1.1-2-3) ... Removing r-cran-bh (1.74.0-1) ... Removing libboost-dev:amd64 (1.74.0.3) ... Removing libboost1.74-dev:amd64 (1.74.0-9) ... Removing libstdc++-10-dev:amd64 (10.2.1-6) ... Removing libgcc-10-dev:amd64 (10.2.1-6) ... Removing libasan6:amd64 (10.2.1-6) ... Removing libatomic1:amd64 (10.2.1-6) ... Removing r-cran-mgcv (1.8-34-1) ... Removing r-cran-ape (5.4-1-1) ... Removing r-cran-seqinr (4.2-5-1) ... Removing r-cran-ade4 (1.7-16-1) ... Removing r-cran-kernsmooth (2.23-18-1) ... Removing r-bioc-genomicranges (1.42.0+dfsg-1) ... Removing r-bioc-genomeinfodb (1.26.2-2) ... Removing r-cran-rcurl (1.98-1.2-1+b1) ... Removing r-bioc-rhtslib (1.22.0+dfsg-1) ... Removing r-bioc-biostrings (2.58.0-1) ... Removing r-bioc-xvector (0.30.0-1) ... Removing r-bioc-zlibbioc (1.36.0+dfsg-1) ... Removing zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Removing libc6-dev:amd64 (2.31-13+deb11u11) ... Removing libc-dev-bin (2.31-13+deb11u11) ... Removing libcrypt-dev:amd64 (1:4.4.18-4) ... Removing libxml2:amd64 (2.9.10+dfsg-6.7+deb11u5) ... Removing r-cran-stringi (1.5.3-1) ... Removing libitm1:amd64 (10.2.1-6) ... Removing liblsan0:amd64 (10.2.1-6) ... Removing libnsl-dev:amd64 (1.3.0-2) ... Removing libtirpc-dev:amd64 (1.3.1-1+deb11u1) ... Removing libtsan0:amd64 (10.2.1-6) ... Removing libubsan1:amd64 (10.2.1-6) ... Removing linux-libc-dev:amd64 (5.10.223-1) ... Removing littler (0.3.12-1) ... Removing r-bioc-biobase (2.50.0-1) ... Removing r-bioc-delayedarray (0.16.1+dfsg-1) ... Removing r-bioc-iranges (2.24.1-1) ... Removing r-bioc-s4vectors (0.28.1-1) ... Removing r-bioc-matrixgenerics (1.2.1-4) ... Removing r-bioc-biocgenerics (0.36.0-1) ... Removing r-bioc-genomeinfodbdata (1.2.4-1) ... Removing r-cran-isoband (0.2.3-2) ... Removing r-cran-testthat (3.0.1-1) ... Removing r-cran-pkgload (1.1.0-1) ... Removing r-cran-waldo (0.2.3-2) ... Removing r-cran-bitops (1.0-6-5) ... Removing r-cran-brio (1.1.1-1) ... Removing r-cran-pkgbuild (1.2.0-1) ... Removing r-cran-callr (3.5.1-1) ... Removing r-cran-clipr (0.7.1-1) ... Removing r-cran-doparallel (1.0.16-1) ... Removing r-cran-foreach (1.5.1-1) ... Removing r-cran-codetools (0.2-18-1) ... Removing r-cran-munsell (0.5.0-2) ... Removing r-cran-colorspace (2.0-0+dfsg-1) ... Removing r-cran-tidyr (1.1.2-1) ... Removing r-cran-cpp11 (0.2.6-1) ... Removing r-cran-rematch2 (2.1.2-2) ... Removing r-cran-dplyr (1.0.4-1) ... Removing r-cran-tibble (3.0.6+dfsg-1) ... Removing r-cran-pillar (1.4.7-1) ... Removing r-cran-progress (1.2.2-2) ... Removing r-cran-diffobj (0.3.2-1) ... Removing r-cran-tidyselect (1.1.0+dfsg-1) ... Removing r-cran-hms (1.0.0-1) ... Removing r-cran-vctrs (0.3.6-1) ... Removing r-cran-digest (0.6.27-1) ... Removing r-cran-diptest (0.75-7-2) ... Removing r-cran-ellipsis (0.3.1-1) ... Removing r-cran-evaluate (0.14-2) ... Removing r-cran-fansi (0.4.2-1) ... Removing r-cran-farver (2.0.3-1+b1) ... Removing r-cran-futile.logger (1.4.3-4) ... Removing r-cran-lambda.r (1.2.4-2) ... Removing r-cran-formatr (1.7-2) ... Removing r-cran-futile.options (1.0.1-3) ... Removing r-cran-generics (0.1.0-1) ... Removing r-cran-lifecycle (0.2.0-2) ... Removing r-cran-gtable (0.3.0+dfsg-2) ... Removing r-cran-iterators (1.0.13-1) ... Removing r-cran-jsonlite (1.7.2+dfsg-1) ... Removing r-cran-kedd (1.0.3-2) ... Removing r-cran-labeling (0.4.2-1) ... Removing r-cran-sp (1:1.4-5-1) ... Removing r-cran-nlme (3.1.152-1) ... Removing r-cran-lazyeval (0.2.2-1+b1) ... Removing r-cran-purrr (0.3.4-1+b1) ... Removing r-cran-magrittr (2.0.1-1) ... Removing r-cran-mass (7.3-53.1-1) ... Removing r-cran-matrixstats (0.58.0-3) ... Removing r-cran-pixmap (0.4-12-1) ... Removing r-cran-pkgconfig (2.0.3-2) ... Removing r-cran-praise (1.0.0-4) ... Removing r-cran-prettyunits (1.1.1-2) ... Removing r-cran-processx (3.4.5-1) ... Removing r-cran-ps (1.5.0-1) ... Removing r-cran-rlang (0.4.10-1) ... Removing r-cran-rstudioapi (0.13-1) ... Removing r-cran-segmented (1.3-1-1) ... Removing r-cran-utf8 (1.1.4-2) ... Removing r-cran-viridislite (0.3.0-4) ... Removing r-cran-withr (2.4.1-1) ... Removing r-cran-yaml (2.2.1-1+b1) ... Removing r-cran-matrix (1.3-2-1) ... Removing r-cran-rcpp (1.0.6-1) ... Removing r-cran-desc (1.2.0-3) ... Removing r-cran-cli (2.3.0-1) ... Removing r-cran-assertthat (0.2.1-2) ... Removing r-cran-crayon (1.4.0-1) ... Removing r-cran-glue (1.4.2-1) ... Removing r-cran-lattice (0.20-41-1+b1) ... Removing r-cran-littler (0.3.12-1) ... Removing r-cran-pkgkitten (0.2.1-1) ... Removing r-cran-r6 (2.5.0-1) ... Removing r-cran-rprojroot (2.0.2-1) ... Removing r-base-core (4.0.4-1) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.46.2-3) ... Removing libpangoft2-1.0-0:amd64 (1.46.2-3) ... Removing libpango-1.0-0:amd64 (1.46.2-3) ... Removing fontconfig (2.13.1-4.2) ... Removing libtk8.6:amd64 (8.6.11-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-5) ... Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing fonts-dejavu-core (2.37-2) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing libcurl4:amd64 (7.74.0-1.3+deb11u13) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libxt6:amd64 (1:1.2.0-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.14-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libthai0:amd64 (0.1.28-3) ... Removing libdatrie1:amd64 (0.2.13-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u5) ... Removing libdeflate0:amd64 (1.7-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libfribidi0:amd64 (1.0.8-2+deb11u1) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing libglib2.0-0:amd64 (2.66.8-1+deb11u4) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libnghttp2-14:amd64 (1.43.0-1+deb11u1) ... Removing libpaper-utils (1.1.28+b1) ... Removing libpaper1:amd64 (1.1.28+b1) ... Removing libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing libreadline8:amd64 (8.1-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libssh2-1:amd64 (1.9.0-2+deb11u1) ... Removing libtcl8.6:amd64 (8.6.11+dfsg-1) ... Removing libthai-data (0.1.28-3) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.14-3) ... Removing libxext6:amd64 (2:1.3.3-1.1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing openssl (1.1.1w-0+deb11u1) ... Removing readline-common (8.1-1) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.14) ... Removing unzip (6.0-26+deb11u1) ... Removing x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-12) ... Removing libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.3-1+deb11u1) ... Removing libmd0:amd64 (1.0.3-3) ... Removing libx11-data (2:1.7.2-1+deb11u2) ... Removing libxau6:amd64 (1:1.0.9-1) ... Processing triggers for libc-bin (2.31-13+deb11u11) ... 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan6:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu67:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'liblsan0:amd64', 'libmd0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libstdc++-10-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'linux-libc-dev:amd64', 'littler', 'openssl', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-ade4', 'r-cran-airr', 'r-cran-alakazam', 'r-cran-ape', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bitops', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-clipr', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-diptest', 'r-cran-doparallel', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-hms', 'r-cran-igraph', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', 'r-cran-kedd', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pixmap', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-segmented', 'r-cran-seqinr', 'r-cran-snow', 'r-cran-sp', 'r-cran-stringi', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-yaml', 'readline-common', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64', 'r-cran-shazam'] 1m7.4s INFO: Running scripts post_remove 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_remove_exceptions'] 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_remove_exceptions'] 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan6:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu67:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'liblsan0:amd64', 'libmd0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libstdc++-10-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'linux-libc-dev:amd64', 'littler', 'openssl', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-ade4', 'r-cran-airr', 'r-cran-alakazam', 'r-cran-ape', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bitops', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-clipr', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-diptest', 'r-cran-doparallel', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-hms', 'r-cran-igraph', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', 'r-cran-kedd', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pixmap', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-segmented', 'r-cran-seqinr', 'r-cran-snow', 'r-cran-sp', 'r-cran-stringi', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-yaml', 'readline-common', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m7.8s DUMP: (Reading database ... 6723 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.13.1-4.2) ... Purging configuration files for fontconfig-config (2.13.1-4.2) ... Purging configuration files for fonts-dejavu-core (2.37-2) ... dpkg: warning: while removing fonts-dejavu-core, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: ignoring request to remove libasan6 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-dev which isn't installed dpkg: warning: ignoring request to remove libboost1.74-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcrypt-dev which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgcc-10-dev which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.66.8-1+deb11u4) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu67 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 liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove libmd0 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.28+b1) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libstdc++-10-dev which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtirpc-dev which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan0 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed Purging configuration files for openssl (1.1.1w-0+deb11u1) ... Purging configuration files for r-base-core (4.0.4-1) ... dpkg: warning: ignoring request to remove r-bioc-biobase which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-biocparallel which isn't installed dpkg: warning: ignoring request to remove r-bioc-biostrings which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-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-matrixgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-rhtslib which isn't installed dpkg: warning: ignoring request to remove r-bioc-rsamtools which isn't installed dpkg: warning: ignoring request to remove r-bioc-s4vectors which isn't installed dpkg: warning: ignoring request to remove r-bioc-summarizedexperiment which isn't installed dpkg: warning: ignoring request to remove r-bioc-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-ade4 which isn't installed dpkg: warning: ignoring request to remove r-cran-airr which isn't installed dpkg: warning: ignoring request to remove r-cran-alakazam which isn't installed dpkg: warning: ignoring request to remove r-cran-ape 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-bitops which isn't installed dpkg: warning: ignoring request to remove r-cran-brio which isn't installed dpkg: warning: ignoring request to remove r-cran-callr 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-clipr 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-colorspace 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-desc which isn't installed dpkg: warning: ignoring request to remove r-cran-diffobj which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-diptest which isn't installed dpkg: warning: ignoring request to remove r-cran-doparallel which isn't installed dpkg: warning: ignoring request to remove r-cran-dplyr which isn't installed dpkg: warning: ignoring request to remove r-cran-ellipsis which isn't installed dpkg: warning: ignoring request to remove r-cran-evaluate 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-farver which isn't installed dpkg: warning: ignoring request to remove r-cran-foreach 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-ggplot2 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-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-hms which isn't installed dpkg: warning: ignoring request to remove r-cran-igraph which isn't installed dpkg: warning: ignoring request to remove r-cran-isoband which isn't installed dpkg: warning: ignoring request to remove r-cran-iterators 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-kedd which isn't installed dpkg: warning: ignoring request to remove r-cran-kernsmooth which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling 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-lazyeval which isn't installed dpkg: warning: ignoring request to remove r-cran-lifecycle which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass 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-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pixmap which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgbuild which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgload which isn't installed dpkg: warning: ignoring request to remove r-cran-praise which isn't installed dpkg: warning: ignoring request to remove r-cran-prettyunits which isn't installed dpkg: warning: ignoring request to remove r-cran-processx which isn't installed dpkg: warning: ignoring request to remove r-cran-progress which isn't installed dpkg: warning: ignoring request to remove r-cran-ps which isn't installed dpkg: warning: ignoring request to remove r-cran-purrr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed Purging configuration files for r-cran-rcurl (1.98-1.2-1+b1) ... dpkg: warning: ignoring request to remove r-cran-readr which isn't installed dpkg: warning: ignoring request to remove r-cran-rematch2 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-rprojroot which isn't installed dpkg: warning: ignoring request to remove r-cran-rstudioapi which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-segmented which isn't installed dpkg: warning: ignoring request to remove r-cran-seqinr 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-sp 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-testthat 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-tidyr 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-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-waldo 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-yaml which isn't installed Purging configuration files for readline-common (8.1-1) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed Purging configuration files for ucf (3.0043) ... Purging configuration files for unzip (6.0-26+deb11u1) ... Purging configuration files for x11-common (1:7.7+22) ... 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 1m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'libasan6:amd64', 'libatomic1:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost1.74-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo2:amd64', 'libcrypt-dev:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgcc-10-dev:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libice6:amd64', 'libicu67:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'libldap-2.4-2:amd64', 'liblsan0:amd64', 'libmd0:amd64', 'libnghttp2-14:amd64', 'libnsl-dev:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libstdc++-10-dev:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtirpc-dev:amd64', 'libtk8.6:amd64', 'libtsan0:amd64', 'libubsan1:amd64', 'libwebp6:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'linux-libc-dev:amd64', 'littler', 'openssl', 'r-base-core', 'r-bioc-biobase', 'r-bioc-biocgenerics', 'r-bioc-biocparallel', 'r-bioc-biostrings', 'r-bioc-delayedarray', 'r-bioc-genomeinfodb', 'r-bioc-genomeinfodbdata', 'r-bioc-genomicalignments', 'r-bioc-genomicranges', 'r-bioc-iranges', 'r-bioc-matrixgenerics', 'r-bioc-rhtslib', 'r-bioc-rsamtools', 'r-bioc-s4vectors', 'r-bioc-summarizedexperiment', 'r-bioc-xvector', 'r-bioc-zlibbioc', 'r-cran-ade4', 'r-cran-airr', 'r-cran-alakazam', 'r-cran-ape', 'r-cran-assertthat', 'r-cran-bh', 'r-cran-bitops', 'r-cran-brio', 'r-cran-callr', 'r-cran-cli', 'r-cran-clipr', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-cpp11', 'r-cran-crayon', 'r-cran-desc', 'r-cran-diffobj', 'r-cran-digest', 'r-cran-diptest', 'r-cran-doparallel', 'r-cran-dplyr', 'r-cran-ellipsis', 'r-cran-evaluate', 'r-cran-fansi', 'r-cran-farver', 'r-cran-foreach', 'r-cran-formatr', 'r-cran-futile.logger', 'r-cran-futile.options', 'r-cran-generics', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-hms', 'r-cran-igraph', 'r-cran-isoband', 'r-cran-iterators', 'r-cran-jsonlite', 'r-cran-kedd', 'r-cran-kernsmooth', 'r-cran-labeling', 'r-cran-lambda.r', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-lifecycle', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-matrixstats', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pixmap', 'r-cran-pkgbuild', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-pkgload', 'r-cran-praise', 'r-cran-prettyunits', 'r-cran-processx', 'r-cran-progress', 'r-cran-ps', 'r-cran-purrr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-rcurl', 'r-cran-readr', 'r-cran-rematch2', 'r-cran-rlang', 'r-cran-rprojroot', 'r-cran-rstudioapi', 'r-cran-scales', 'r-cran-segmented', 'r-cran-seqinr', 'r-cran-snow', 'r-cran-sp', 'r-cran-stringi', 'r-cran-testthat', 'r-cran-tibble', 'r-cran-tidyr', 'r-cran-tidyselect', 'r-cran-utf8', 'r-cran-vctrs', 'r-cran-viridislite', 'r-cran-waldo', 'r-cran-withr', 'r-cran-yaml', 'readline-common', 'sensible-utils', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'zlib1g-dev:amd64'] 1m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', 'r-cran-shazam'] 1m7.9s DUMP: dpkg: warning: ignoring request to remove r-cran-shazam which isn't installed 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', 'r-cran-shazam'] 1m7.9s INFO: Running scripts post_purge 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_purge_exceptions'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_purge_exceptions'] 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', '--pending'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--purge', '--pending'] 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--remove', '--pending'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg', '--remove', '--pending'] 1m7.9s INFO: Running scripts post_test 1m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_test_exceptions'] 1m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'tmp/scripts/post_test_exceptions'] 1m7.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 1m8.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-divert', '--list'] 1m8.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'dpkg-divert', '--list'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'clean'] 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q', 'apt-get', 'clean'] 1m8.2s DEBUG: Recording chroot state 1m8.5s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-dejavu-core /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned 1m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/shm'] 1m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/shm'] 1m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/console'] 1m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/console'] 1m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/ptmx'] 1m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/ptmx'] 1m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts'] 1m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/dev/pts'] 1m8.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/proc'] 1m8.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q/proc'] 1m8.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 1m8.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfgp2lo_q'] 1m8.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfgp2lo_q 1m8.9s INFO: PASS: Upgrading between Debian distributions. 1m8.9s INFO: PASS: All tests. 1m8.9s INFO: piuparts run ends. ret=0 End: 2024-09-12 05:03:39 GMT