Start: 2025-12-26 15:49:08 GMT [stable] Package: r-bioc-phyloseq Version: 1.50.0+dfsg-2 Installed-Size: 3134 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5) Suggests: r-bioc-biocstyle (>= 2.4), r-bioc-deseq2 (>= 1.16.1), r-bioc-genefilter (>= 1.58), r-cran-knitr (>= 1.16), r-cran-magrittr (>= 1.5), r-bioc-metagenomeseq (>= 1.14), r-cran-rmarkdown (>= 1.6), r-cran-testthat (>= 1.0.2) Description: GNU R handling and analysis of high-throughput microbiome census data Homepage: https://bioconductor.org/packages/phyloseq/ Description-md5: ce1efdc42d4cdfd64fc0152b75e33d3f Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-phyloseq/r-bioc-phyloseq_1.50.0+dfsg-2_all.deb Size: 2255164 MD5sum: c8cb3240eb4b3a83221df416408191e2 SHA256: 2806dacca7b4be8488bb2ae0a0f24d85e39e39e24cc634437fb56ba4f95d27a6 [testing] [sid] Package: r-bioc-phyloseq Version: 1.54.0+dfsg-1 Installed-Size: 3135 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.22, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5) Suggests: r-cran-magrittr (>= 1.5) Description: GNU R handling and analysis of high-throughput microbiome census data Homepage: https://bioconductor.org/packages/phyloseq/ Description-md5: ce1efdc42d4cdfd64fc0152b75e33d3f Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-phyloseq/r-bioc-phyloseq_1.54.0+dfsg-1_all.deb Size: 2256488 MD5sum: 4e7e168735cea23448120d0102d4e17c SHA256: dd238c4a9d0430f90b137959a7e162b5f6f7a09d4614b43100d19c48dab1bfe4 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt r-bioc-phyloseq=1.54.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.6.1~202508211944~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt r-bioc-phyloseq=1.54.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 6.1.0-41-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.158-1 (2025-11-09) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpztnuszbj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpztnuszbj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpztnuszbj/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m1.4s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s DUMP: 58256853ebd2bd549527b330c2592235 - 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s INFO: Running scripts post_setup 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_dummy_users'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', '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/tmpztnuszbj', 'tmp/scripts/post_setup_forbid_home'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', '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/tmpztnuszbj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_setup_zz_backports'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8+deb13u2 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69~deb13u1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1~deb13u1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1~deb13u1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.9-1~deb13u1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.9-1~deb13u1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1~deb13u1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4+deb13u1 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m3.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m4.3s DUMP: Package: r-bioc-phyloseq Version: 1.50.0+dfsg-2 Installed-Size: 3134 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.20, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5) Suggests: r-bioc-biocstyle (>= 2.4), r-bioc-deseq2 (>= 1.16.1), r-bioc-genefilter (>= 1.58), r-cran-knitr (>= 1.16), r-cran-magrittr (>= 1.5), r-bioc-metagenomeseq (>= 1.14), r-cran-rmarkdown (>= 1.6), r-cran-testthat (>= 1.0.2) Description-en: GNU R handling and analysis of high-throughput microbiome census data The Bioconductor module phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Description-md5: ce1efdc42d4cdfd64fc0152b75e33d3f Homepage: https://bioconductor.org/packages/phyloseq/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-phyloseq/r-bioc-phyloseq_1.50.0+dfsg-2_all.deb Size: 2255164 MD5sum: c8cb3240eb4b3a83221df416408191e2 SHA256: 2806dacca7b4be8488bb2ae0a0f24d85e39e39e24cc634437fb56ba4f95d27a6 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m4.3s INFO: apt-cache knows about the following packages: r-bioc-phyloseq 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_database-server'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.2,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy', 'r-bioc-phyloseq'] 0m4.5s DUMP: r-bioc-phyloseq: Installed: (none) Candidate: 1.50.0+dfsg-2 Version table: 1.50.0+dfsg-2 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy', 'r-bioc-phyloseq'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-y', 'install', 'r-bioc-phyloseq'] 0m24.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 libatomic1 libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcolamd3 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libglpk40 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu76 libidn2-0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 liblerc4 libltdl7 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libsuitesparseconfig7 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler openssl procps r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biomformat r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-multtest r-bioc-s4vectors r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-ade4 r-cran-ape r-cran-askpass r-cran-cli r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-digest r-cran-fansi r-cran-farver r-cran-foreach r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-httr r-cran-igraph r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-permute r-cran-pillar r-cran-pixmap r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-sp r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-vegan r-cran-viridislite r-cran-withr readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: libc-devtools glibc-doc manpages-dev low-memory-monitor libiodbc2-dev default-libmysqlclient-dev gnutls-bin krb5-doc krb5-user tcl8.6 tk8.6 elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-all r-cran-runit r-bioc-golubesets r-bioc-biocstyle r-cran-knitr r-bioc-limma r-bioc-s4arrays r-bioc-sparsearray r-bioc-delayedarray r-bioc-hdf5array r-bioc-genomicranges r-bioc-pwalign r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-testthat r-cran-rmarkdown r-bioc-bsgenome r-bioc-genomicfeatures r-cran-covr r-cran-r.utils r-bioc-genomicalignments r-cran-snow r-bioc-genefilter r-bioc-metagenomeseq r-bioc-summarizedexperiment r-bioc-shortread r-bioc-graph r-cran-dbi r-cran-rmariadb r-cran-adegraphics r-cran-adephylo r-cran-deldir r-cran-spdep r-cran-waveslim r-cran-progress r-cran-doparallel r-cran-gee r-cran-expm r-cran-xml2 clustalw muscle phyml t-coffee r-cran-magick r-cran-sf r-cran-getopt r-cran-bookdown r-cran-sessioninfo r-cran-inline readline-doc Recommended packages: manpages manpages-dev libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules psmisc linux-sysctl-defaults r-recommended r-base-dev r-doc-html r-cran-phangorn r-cran-testthat r-cran-callr r-cran-covr r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-bench r-cran-brio r-cran-decor r-cran-desc r-cran-lobstr r-cran-mockery r-cran-progress r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils r-cran-bit64 r-cran-bit r-cran-r.utils r-cran-xts r-cran-zoo r-cran-yaml r-cran-markdown r-cran-unitizer r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-dbi r-cran-rsqlite r-cran-waldo r-cran-readr r-cran-rgl r-cran-r.rsp r-cran-lintr r-cran-tidyverse r-cran-sodium r-cran-diagrammer r-cran-formattable r-cran-lubridate r-cran-nanotime r-cran-palmerpenguins r-cran-units r-cran-abind r-cran-doparallel r-cran-itertools r-cran-fs r-cran-usethis r-cran-dichromat r-cran-hms r-cran-gstat r-cran-deldir r-cran-terra r-cran-raster r-cran-blob r-cran-evaluate r-cran-here r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-generics r-cran-pkgdown r-cran-zeallot libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 libatomic1 libblas3 libbrotli1 libc-dev-bin libc6-dev libcairo2 libcolamd3 libcom-err2 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libexpat1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libglpk40 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu76 libidn2-0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap2 liblerc4 libltdl7 libncursesw6 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1t64 libsuitesparseconfig7 libtasn1-6 libtcl8.6 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libunistring5 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler openssl procps r-base-core r-bioc-biobase r-bioc-biocgenerics r-bioc-biomformat r-bioc-biostrings r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-multtest r-bioc-phyloseq r-bioc-s4vectors r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-ade4 r-cran-ape r-cran-askpass r-cran-cli r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-digest r-cran-fansi r-cran-farver r-cran-foreach r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-httr r-cran-igraph r-cran-isoband r-cran-iterators r-cran-jsonlite r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme r-cran-openssl r-cran-permute r-cran-pillar r-cran-pixmap r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rcpparmadillo r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-sp r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-vegan r-cran-viridislite r-cran-withr readline-common rpcsvc-proto sensible-utils ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 176 newly installed, 0 to remove and 0 not upgraded. Need to get 179 MB of archives. After this operation, 348 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5+20250216-2 [135 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.5.4-1~deb13u1 [1495 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20250419 [162 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B] Get:10 http://deb.debian.org/debian trixie/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:11 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0052 [43.3 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.48-1 [282 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2.3 [318 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2.3 [392 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2.3 [463 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-19 [137 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libsuitesparseconfig7 amd64 1:7.10.1+dfsg-1 [32.3 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libamd3 amd64 1:7.10.1+dfsg-1 [49.2 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-19 [9308 B] Get:24 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.1-6 [160 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.41-12 [58.2 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.12.57-1 [2692 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.41-12 [1991 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libcolamd3 amd64 1:7.10.1+dfsg-1 [41.0 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:46 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.14.1-2+deb13u2 [391 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.84.4-3~deb13u1 [1519 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.5.4-4 [416 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libglpk40 amd64 5.0-1+b2 [401 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24+deb13u1 [217 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.1-6 [2447 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:79 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.3-1 [226 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [55.6 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [35.7 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 libpaper2 amd64 2.2.5-0.3+b2 [16.7 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 2.2.5-0.3+b2 [16.5 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.7.0-3+deb13u1 [346 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.6+ds-1 [11.0 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.6+ds-1 [83.3 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1+deb13u2 [698 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-15 [235 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-29 [173 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.5.0-3 [28.6 MB] Get:103 http://deb.debian.org/debian trixie/main amd64 r-cran-littler amd64 0.3.21-1 [107 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 littler all 0.3.21-1 [16.9 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 r-bioc-biocgenerics all 0.52.0-2 [627 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 r-bioc-biobase amd64 2.66.0-2 [2316 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgkitten all 0.2.4-1 [29.1 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpp amd64 1.0.14-1 [2080 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 r-cran-plyr amd64 1.8.9-1 [832 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [445 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 r-cran-lattice amd64 0.22-7-1 [1418 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 r-cran-matrix amd64 1.7-3-1 [4048 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 r-bioc-biomformat all 1.34.0+dfsg-2 [231 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2061 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 r-bioc-iranges amd64 2.40.1-3 [2310 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [9968 B] Get:118 http://deb.debian.org/debian trixie/main amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 r-cran-curl amd64 6.2.1+dfsg-1 [195 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 r-cran-mime amd64 0.12-2 [35.6 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 r-cran-sys amd64 3.4.3-1 [44.4 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 r-cran-askpass amd64 1.2.1-1 [24.2 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [402 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 r-cran-r6 all 2.6.1-1 [106 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.3 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] Get:128 http://deb.debian.org/debian trixie/main amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3848 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 r-cran-crayon all 1.5.3-1 [165 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.4 MB] Get:131 http://deb.debian.org/debian trixie/main amd64 r-cran-survival amd64 3.8-3-1 [8265 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 r-cran-mass amd64 7.3-65-1 [1113 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 r-bioc-multtest amd64 2.62.0-2 [843 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 r-cran-pixmap all 0.4-13-1 [211 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 r-cran-sp amd64 1:2.2-0+dfsg-1 [1445 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 r-cran-rcpparmadillo amd64 14.4.2-1-1 [869 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 r-cran-ade4 amd64 1.7-23-1 [5403 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 r-cran-nlme amd64 3.1.168-1 [2329 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 r-cran-digest amd64 0.6.37-1 [206 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 r-cran-ape amd64 5.8-1-1 [2910 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 r-cran-cluster amd64 2.1.8.1-1 [585 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2105 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 r-cran-codetools all 0.2-20-1 [91.1 kB] Get:144 http://deb.debian.org/debian trixie/main amd64 r-cran-iterators all 1.0.14-1 [337 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 r-cran-foreach all 1.5.2-1 [122 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 r-cran-cli amd64 3.6.4-1 [1370 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 r-cran-glue amd64 1.8.0-1 [165 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 r-cran-rlang amd64 1.1.5-3 [1709 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 r-cran-gtable all 0.3.6+dfsg-1 [228 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 r-cran-mgcv amd64 1.9-3-1 [3378 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 r-cran-farver amd64 2.1.2-1 [1411 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 r-cran-labeling all 0.4.3-1 [62.4 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1716 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 r-cran-munsell all 0.5.1-1 [237 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 r-cran-viridislite all 0.4.2-2 [1299 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 r-cran-scales all 1.3.0-1 [677 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 r-cran-fansi amd64 1.0.6-2 [629 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 r-cran-utf8 amd64 1.2.4-1 [133 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 r-cran-vctrs amd64 0.6.5-1 [1375 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB] Get:165 http://deb.debian.org/debian trixie/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [425 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 r-cran-withr all 3.0.2+dfsg-1 [226 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3933 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 r-cran-cpp11 all 0.5.2-1 [226 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 r-cran-igraph amd64 2.1.4-1 [5138 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 r-cran-stringi amd64 1.8.4-1+b1 [896 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 r-cran-stringr all 1.5.1-1 [296 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 r-cran-reshape2 amd64 1.4.4-2 [114 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 r-cran-permute all 0.9-7-1 [225 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 r-cran-vegan amd64 2.6-10+dfsg-3 [3136 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 r-bioc-phyloseq all 1.50.0+dfsg-2 [2255 kB] Preconfiguring packages ... Fetched 179 MB in 3s (64.2 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4939 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../001-libncursesw6_6.5+20250216-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250216-2) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../086-libsharpyuv0_1.5.0-0.1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../087-libsm6_2%3a1.2.6-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.6-1) ... Selecting previously unselected package libtcl8.6:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.6+ds-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../093-libxft2_2.3.6-1+b4_amd64.deb ... Unpacking libxft2:amd64 (2.3.6-1+b4) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../094-libxss1_1%3a1.2.3-1+b3_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1+b3) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../095-libtk8.6_8.6.16-1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.16-1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../096-libxml2_2.12.7+dfsg+really2.9.14-2.1+deb13u2_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1+deb13u2) ... 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Preparing to unpack .../151-r-cran-mgcv_1.9-3-1_amd64.deb ... Unpacking r-cran-mgcv (1.9-3-1) ... Selecting previously unselected package r-cran-farver. Preparing to unpack .../152-r-cran-farver_2.1.2-1_amd64.deb ... Unpacking r-cran-farver (2.1.2-1) ... Selecting previously unselected package r-cran-labeling. Preparing to unpack .../153-r-cran-labeling_0.4.3-1_all.deb ... Unpacking r-cran-labeling (0.4.3-1) ... Selecting previously unselected package r-cran-colorspace. Preparing to unpack .../154-r-cran-colorspace_2.1-1+dfsg-1_amd64.deb ... Unpacking r-cran-colorspace (2.1-1+dfsg-1) ... Selecting previously unselected package r-cran-munsell. Preparing to unpack .../155-r-cran-munsell_0.5.1-1_all.deb ... Unpacking r-cran-munsell (0.5.1-1) ... Selecting previously unselected package r-cran-rcolorbrewer. Preparing to unpack .../156-r-cran-rcolorbrewer_1.1-3-1_all.deb ... Unpacking r-cran-rcolorbrewer (1.1-3-1) ... Selecting previously unselected package r-cran-viridislite. 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Preparing to unpack .../175-r-bioc-phyloseq_1.50.0+dfsg-2_all.deb ... Unpacking r-bioc-phyloseq (1.50.0+dfsg-2) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up libgraphite2-3:amd64 (1.3.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libtext-charwidth-perl:amd64 (0.04-11+b4) ... Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libtirpc-common (1.3.6+ds-1) ... Setting up unzip (6.0-29) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up x11-common (1:7.7+24+deb13u1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up linux-libc-dev (6.12.57-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up libgomp1:amd64 (14.2.0-19) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up zip (3.0-15) ... Setting up libblas3:amd64 (3.12.1-6) ... 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 rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.48-1) ... Setting up libatomic1:amd64 (14.2.0-19) ... Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.5+20250216-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libltdl7:amd64 (2.5.4-4) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up sensible-utils (0.0.25) ... Setting up libcrypt-dev:amd64 (1:4.4.38-1) ... Setting up libtiff6:amd64 (4.7.0-3+deb13u1) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libsuitesparseconfig7:amd64 (1:7.10.1+dfsg-1) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libicu76:amd64 (76.1-4) ... Setting up libpaper2:amd64 (2.2.5-0.3+b2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libc-dev-bin (2.41-12) ... Setting up openssl (3.5.4-1~deb13u1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1+deb13u2) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.1-6) ... 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 libamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libcolamd3:amd64 (1:7.10.1+dfsg-1) ... Setting up fontconfig-config (2.15.0-2.3) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libpaper-utils (2.2.5-0.3+b2) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.84.4-3~deb13u1) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libglpk40:amd64 (5.0-1+b2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up ucf (3.0052) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up libc6-dev:amd64 (2.41-12) ... Setting up libharfbuzz0b:amd64 (10.2.0-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.3) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up fontconfig (2.15.0-2.3) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up libtirpc3t64:amd64 (1.3.6+ds-1) ... Setting up libtk8.6:amd64 (8.6.16-1) ... Setting up libpango-1.0-0:amd64 (1.56.3-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libcairo2:amd64 (1.18.4-1+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... Setting up libcurl4t64:amd64 (8.14.1-2+deb13u2) ... Setting up r-base-core (4.5.0-3) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.5.3-1) ... Setting up r-cran-labeling (0.4.3-1) ... Setting up r-cran-lattice (0.22-7-1) ... Setting up r-cran-nlme (3.1.168-1) ... Setting up r-cran-farver (2.1.2-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up r-cran-pixmap (0.4-13-1) ... Setting up r-cran-cluster (2.1.8.1-1) ... Setting up r-cran-r6 (2.6.1-1) ... Setting up r-cran-pkgkitten (0.2.4-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-bioc-genomeinfodbdata (1.2.13-2) ... Setting up r-cran-littler (0.3.21-1) ... Setting up r-cran-permute (0.9-7-1) ... Setting up r-cran-rcpp (1.0.14-1) ... Setting up r-cran-curl (6.2.1+dfsg-1) ... Setting up r-cran-codetools (0.2-20-1) ... Setting up r-bioc-biocgenerics (0.52.0-2) ... Setting up r-cran-rlang (1.1.5-3) ... Setting up littler (0.3.21-1) ... Setting up r-cran-sys (3.4.3-1) ... Setting up r-cran-withr (3.0.2+dfsg-1) ... Setting up r-cran-mime (0.12-2) ... Setting up r-cran-iterators (1.0.14-1) ... Setting up r-cran-digest (0.6.37-1) ... Setting up r-cran-ape (5.8-1-1) ... Setting up r-cran-foreach (1.5.2-1) ... Setting up r-cran-fansi (1.0.6-2) ... Setting up r-cran-mass (7.3-65-1) ... Setting up r-cran-data.table (1.17.0+dfsg-1) ... Setting up r-cran-glue (1.8.0-1) ... Setting up r-cran-cli (3.6.4-1) ... Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ... Setting up r-cran-askpass (1.2.1-1) ... Setting up r-bioc-biobase (2.66.0-2) ... Setting up r-cran-jsonlite (1.9.1+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-sp (1:2.2-0+dfsg-1) ... Setting up r-cran-utf8 (1.2.4-1) ... Setting up r-cran-colorspace (2.1-1+dfsg-1) ... Setting up r-cran-stringi (1.8.4-1+b1) ... Setting up r-cran-cpp11 (0.5.2-1) ... Setting up r-cran-plyr (1.8.9-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1) ... Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.6+dfsg-1) ... Setting up r-cran-matrix (1.7-3-1) ... Setting up r-cran-mgcv (1.9-3-1) ... Setting up r-cran-rcpparmadillo (14.4.2-1-1) ... Setting up r-bioc-iranges (2.40.1-3) ... Setting up r-cran-vctrs (0.6.5-1) ... Setting up r-cran-pillar (1.10.1+dfsg-1) ... Setting up r-cran-openssl (2.3.2+dfsg-1) ... Setting up r-cran-stringr (1.5.1-1) ... Setting up r-bioc-biomformat (1.34.0+dfsg-2) ... Setting up r-cran-munsell (0.5.1-1) ... Setting up r-cran-tibble (3.2.1+dfsg-3) ... Setting up r-cran-survival (3.8-3-1) ... Setting up r-cran-igraph (2.1.4-1) ... Setting up r-cran-ade4 (1.7-23-1) ... Setting up r-cran-reshape2 (1.4.4-2) ... Setting up r-cran-httr (1.4.7+dfsg-1) ... Setting up r-cran-scales (1.3.0-1) ... Setting up r-cran-vegan (2.6-10+dfsg-3) ... Setting up r-bioc-xvector (0.46.0-2) ... Setting up r-bioc-multtest (2.62.0-2) ... Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ... Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ... Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ... Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... Setting up r-bioc-phyloseq (1.50.0+dfsg-2) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-y', 'install', 'r-bioc-phyloseq'] 0m24.1s INFO: Running scripts post_install 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_install_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_install_exceptions'] 0m24.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m25.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m25.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpztnuszbj to testing 0m25.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m25.1s INFO: Running scripts pre_distupgrade 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m26.7s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [137 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9659 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6439 kB] Fetched 16.2 MB in 1s (16.2 MB/s) Reading package lists... 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m44.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libxml2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: gcc-15-base libc-gconv-modules-extra libngtcp2-16 libngtcp2-crypto-ossl0 libxml2-16 The following packages will be upgraded: apt base-files base-passwd bash bsdutils diffutils fontconfig fontconfig-config gcc-14-base grep init-system-helpers libamd3 libapt-pkg7.0 libatomic1 libaudit-common libaudit1 libblas3 libblkid1 libbrotli1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcolamd3 libcom-err2 libcrypt-dev libcrypt1 libcurl4t64 libdatrie1 libdb5.3t64 libdebconfclient0 libexpat1 libffi8 libfontconfig1 libfribidi0 libgcc-s1 libgfortran5 libglib2.0-0t64 libglpk40 libgmp10 libgnutls30t64 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed6t64 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 liblastlog2-2 libltdl7 liblz4-1 liblzma5 libmount1 libncursesw6 libnettle8t64 libnghttp2-14 libnghttp3-9 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-8-0 libpixman-1-0 libpng16-16t64 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsuitesparseconfig7 libsystemd0 libtcl8.6 libtiff6 libtinfo6 libtk8.6 libudev1 libuuid1 libxt6t64 libzstd1 linux-libc-dev littler login login.defs mawk mount ncurses-base ncurses-bin openssl openssl-provider-legacy passwd perl-base r-base-core r-cran-curl r-cran-digest r-cran-igraph r-cran-littler r-cran-matrix r-cran-mgcv r-cran-rcpp r-cran-rcpparmadillo r-cran-scales readline-common sensible-utils sqv sysvinit-utils tzdata util-linux x11-common zlib1g zlib1g-dev 125 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 95.6 MB of archives. After this operation, 8766 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 libc-dev-bin amd64 2.42-6 [60.7 kB] Get:2 http://deb.debian.org/debian forky/main amd64 libcrypt1 amd64 1:4.5.1-1 [98.0 kB] Get:3 http://deb.debian.org/debian forky/main amd64 libcrypt-dev amd64 1:4.5.1-1 [128 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libc6-dev amd64 2.42-6 [2090 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libc-gconv-modules-extra amd64 2.42-6 [1123 kB] Get:6 http://deb.debian.org/debian forky/main amd64 libc6 amd64 2.42-6 [1889 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libc-bin amd64 2.42-6 [674 kB] Get:8 http://deb.debian.org/debian forky/main amd64 linux-libc-dev all 6.17.12-1 [2565 kB] Get:9 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-11 [53.9 kB] Get:10 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-11 [71.5 kB] Get:11 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:12 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-1 [1556 kB] Get:13 http://deb.debian.org/debian forky/main amd64 diffutils amd64 1:3.12-1 [405 kB] Get:14 http://deb.debian.org/debian forky/main amd64 grep amd64 3.12-1 [443 kB] Get:15 http://deb.debian.org/debian forky/main amd64 ncurses-bin amd64 6.5+20251123-1 [445 kB] Get:16 http://deb.debian.org/debian forky/main amd64 perl-base amd64 5.40.1-7 [1679 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.2-4 [38.7 kB] Get:18 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.41.2-4 [93.5 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.2-4 [174 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.2-4 [211 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.2-4 [145 kB] Get:22 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.2-4 [1163 kB] Get:23 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.2-4 [163 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libselinux1 amd64 3.9-4+b1 [86.1 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 259-1 [470 kB] Get:27 http://deb.debian.org/debian forky/main amd64 liblz4-1 amd64 1.10.0-6 [70.5 kB] Get:28 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-2 [310 kB] Get:29 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.4-1 [308 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-2 [308 kB] Get:31 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b2 [919 kB] Get:32 http://deb.debian.org/debian forky/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b2 [89.0 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Get:34 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-11 [736 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 259-1 [157 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.12 [1229 kB] Get:37 http://deb.debian.org/debian forky/main amd64 libdebconfclient0 amd64 0.282+b2 [11.2 kB] Get:38 http://deb.debian.org/debian forky/main amd64 base-passwd amd64 3.6.8 [54.6 kB] Get:39 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:40 http://deb.debian.org/debian forky/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:41 http://deb.debian.org/debian forky/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:42 http://deb.debian.org/debian forky/main amd64 sqv amd64 1.3.0-5 [648 kB] Get:43 http://deb.debian.org/debian forky/main amd64 libseccomp2 amd64 2.6.0-2+b1 [52.2 kB] Get:44 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.12 [1520 kB] Get:45 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:46 http://deb.debian.org/debian forky/main amd64 ncurses-base all 6.5+20251123-1 [277 kB] Get:47 http://deb.debian.org/debian forky/main amd64 sysvinit-utils amd64 3.15-6 [35.0 kB] Get:48 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:49 http://deb.debian.org/debian forky/main amd64 libcap-ng0 amd64 0.8.5-4+b2 [17.5 kB] Get:50 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.2-1+b1 [60.2 kB] Get:51 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.2-4 [105 kB] Get:52 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get:53 http://deb.debian.org/debian forky/main amd64 libcap2 amd64 1:2.75-10+b5 [28.8 kB] Get:54 http://deb.debian.org/debian forky/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-11 [710 kB] Get:55 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:56 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.2-4 [29.5 kB] Get:57 http://deb.debian.org/debian forky/main amd64 libncursesw6 amd64 6.5+20251123-1 [136 kB] Get:58 http://deb.debian.org/debian forky/main amd64 libtinfo6 amd64 6.5+20251123-1 [353 kB] Get:59 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-2 [211 kB] Get:60 http://deb.debian.org/debian forky/main amd64 mawk amd64 1.3.4.20250131-2 [142 kB] Get:61 http://deb.debian.org/debian forky/main amd64 libsemanage-common all 3.9-1 [7888 B] Get:62 http://deb.debian.org/debian forky/main amd64 libsepol2 amd64 3.9-2 [300 kB] Get:63 http://deb.debian.org/debian forky/main amd64 libsemanage2 amd64 3.9-1+b1 [96.9 kB] Get:64 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-2 [1286 kB] Get:65 http://deb.debian.org/debian forky/main amd64 tzdata all 2025c-3 [263 kB] Get:66 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get:67 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:68 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get:69 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get:70 http://deb.debian.org/debian forky/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get:71 http://deb.debian.org/debian forky/main amd64 libatomic1 amd64 15.2.0-11 [9532 B] Get:72 http://deb.debian.org/debian forky/main amd64 libgomp1 amd64 15.2.0-11 [140 kB] Get:73 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-11 [862 kB] Get:74 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-10 [52.4 kB] Get:75 http://deb.debian.org/debian forky/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [33.5 kB] Get:76 http://deb.debian.org/debian forky/main amd64 libamd3 amd64 1:7.12.1+dfsg-1 [50.5 kB] Get:77 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get:78 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b9 [304 kB] Get:79 http://deb.debian.org/debian forky/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [42.3 kB] Get:80 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b6 [25.0 kB] Get:81 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:82 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:83 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get:84 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:85 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:86 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:87 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get:88 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:89 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get:90 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-3 [26.1 kB] Get:91 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.10-1 [444 kB] Get:92 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.11-3 [1509 kB] Get:93 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:94 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.18.0~rc2-1 [412 kB] Get:95 http://deb.debian.org/debian forky/main amd64 libdatrie1 amd64 0.2.14-1 [39.6 kB] Get:96 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-5 [26.7 kB] Get:97 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.86.3-1 [1547 kB] Get:98 http://deb.debian.org/debian forky/main amd64 libltdl7 amd64 2.5.4-9 [416 kB] Get:99 http://deb.debian.org/debian forky/main amd64 libglpk40 amd64 5.0-2 [398 kB] Get:100 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-11 [76.7 kB] Get:101 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 12.2.0-1 [529 kB] Get:102 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get:103 http://deb.debian.org/debian forky/main amd64 libpangocairo-1.0-0 amd64 1.56.3-2 [38.1 kB] Get:104 http://deb.debian.org/debian forky/main amd64 libpangoft2-1.0-0 amd64 1.56.3-2 [62.0 kB] Get:105 http://deb.debian.org/debian forky/main amd64 libpango-1.0-0 amd64 1.56.3-2 [239 kB] Get:106 http://deb.debian.org/debian forky/main amd64 libpaper2 amd64 2.2.5-0.3+b3 [16.7 kB] Get:107 http://deb.debian.org/debian forky/main amd64 libpaper-utils amd64 2.2.5-0.3+b3 [16.5 kB] Get:108 http://deb.debian.org/debian forky/main amd64 libpixman-1-0 amd64 0.46.4-1 [259 kB] Get:109 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.53-1 [288 kB] Get:110 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get:111 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get:112 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get:113 http://deb.debian.org/debian forky/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get:114 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get:115 http://deb.debian.org/debian forky/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get:116 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:117 http://deb.debian.org/debian forky/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [208 kB] Get:118 http://deb.debian.org/debian forky/main amd64 r-base-core amd64 4.5.2-1 [28.6 MB] Get:119 http://deb.debian.org/debian forky/main amd64 r-cran-littler amd64 0.3.21-2 [93.2 kB] Get:120 http://deb.debian.org/debian forky/main amd64 littler all 0.3.21-2 [16.9 kB] Get:121 http://deb.debian.org/debian forky/main amd64 openssl amd64 3.5.4-1 [1496 kB] Get:122 http://deb.debian.org/debian forky/main amd64 r-cran-curl amd64 7.0.0+dfsg-1 [203 kB] Get:123 http://deb.debian.org/debian forky/main amd64 r-cran-digest amd64 0.6.39-1 [212 kB] Get:124 http://deb.debian.org/debian forky/main amd64 r-cran-matrix amd64 1.7-4-1 [4144 kB] Get:125 http://deb.debian.org/debian forky/main amd64 r-cran-igraph amd64 2.1.4-1+b1 [5136 kB] Get:126 http://deb.debian.org/debian forky/main amd64 r-cran-mgcv amd64 1.9-4-1 [3608 kB] Get:127 http://deb.debian.org/debian forky/main amd64 r-cran-rcpp amd64 1.1.0-1 [2114 kB] Get:128 http://deb.debian.org/debian forky/main amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [943 kB] Get:129 http://deb.debian.org/debian forky/main amd64 r-cran-scales all 1.4.0-1 [800 kB] Get:130 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+26 [217 kB] Preconfiguring packages ... Fetched 95.6 MB in 2s (46.2 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 ... 19920 files and directories currently installed.) Preparing to unpack .../libc-dev-bin_2.42-6_amd64.deb ... Unpacking libc-dev-bin (2.42-6) over (2.41-12) ... Preparing to unpack .../libcrypt1_1%3a4.5.1-1_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.5.1-1) over (1:4.4.38-1) ... Setting up libcrypt1:amd64 (1:4.5.1-1) ... (Reading database ... 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Installing new version of config file /etc/ld.so.conf.d/x86_64-linux-gnu.conf ... Setting up libc-bin (2.42-6) ... (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 ... 19927 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.17.12-1_all.deb ... Unpacking linux-libc-dev (6.17.12-1) over (6.12.57-1) ... Selecting previously unselected package gcc-15-base:amd64. Preparing to unpack .../gcc-15-base_15.2.0-11_amd64.deb ... 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(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 ... 19949 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.4-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.4-1) over (3.5.4-1~deb13u1) ... Setting up libssl3t64:amd64 (3.5.4-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19949 files and directories currently installed.) Preparing to unpack .../libudev1_259-1_amd64.deb ... Unpacking libudev1:amd64 (259-1) over (257.9-1~deb13u1) ... Setting up libudev1:amd64 (259-1) ... (Reading database ... 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Setting up x11-common (1:7.7+26) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up linux-libc-dev (6.17.12-1) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libcom-err2:amd64 (1.47.2-3+b6) ... Setting up libgomp1:amd64 (15.2.0-11) ... Setting up libsemanage-common (3.9-1) ... Setting up libkrb5support0:amd64 (1.22.1-2) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025c-3) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 26 15:49:50 UTC 2025. Universal Time is now: Fri Dec 26 15:49:50 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libblas3:amd64 (3.12.1-7) ... Setting up libfribidi0:amd64 (1.0.16-5) ... Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... Setting up libpng16-16t64:amd64 (1.6.53-1) ... Setting up libatomic1:amd64 (15.2.0-11) ... Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... Setting up libsepol2:amd64 (3.9-2) ... Setting up libncursesw6:amd64 (6.5+20251123-1) ... Setting up libk5crypto3:amd64 (1.22.1-2) ... Setting up libltdl7:amd64 (2.5.4-9) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up libgfortran5:amd64 (15.2.0-11) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libffi8:amd64 (3.5.2-3) ... Setting up mount (2.41.2-4) ... Setting up sensible-utils (0.0.26) ... Setting up libcrypt-dev:amd64 (1:4.5.1-1) ... Setting up libtiff6:amd64 (4.7.1-1) ... Setting up libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libsemanage2:amd64 (3.9-1+b1) ... Setting up mawk (1.3.4.20250131-2) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libpaper2:amd64 (2.2.5-0.3+b3) ... Setting up libc-dev-bin (2.42-6) ... Setting up openssl (3.5.4-1) ... Setting up readline-common (8.3-3) ... Setting up login (1:4.16.0-2+really2.41.2-4) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up liblapack3:amd64 (3.12.1-7) ... Setting up libamd3:amd64 (1:7.12.1+dfsg-1) ... Setting up libcolamd3:amd64 (1:7.12.1+dfsg-1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up libpaper-utils (2.2.5-0.3+b3) ... Setting up libglib2.0-0t64:amd64 (2.86.3-1) ... No schema files found: doing nothing. Setting up libglpk40:amd64 (5.0-2) ... Setting up libp11-kit0:amd64 (0.25.10-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.16.0-1) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up passwd (1:4.18.0-2) ... Setting up libc6-dev:amd64 (2.42-6) ... Setting up libharfbuzz0b:amd64 (12.2.0-1) ... Setting up libgnutls30t64:amd64 (3.8.11-3) ... Setting up libpango-1.0-0:amd64 (1.56.3-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.56.3-2) ... Setting up libpangocairo-1.0-0:amd64 (1.56.3-2) ... Setting up libcurl4t64:amd64 (8.18.0~rc2-1) ... Setting up r-base-core (4.5.2-1) ... Installing new version of config file /etc/R/Makeconf ... Setting up r-cran-scales (1.4.0-1) ... Setting up r-cran-matrix (1.7-4-1) ... Setting up r-cran-mgcv (1.9-4-1) ... Setting up r-cran-littler (0.3.21-2) ... Setting up r-cran-rcpp (1.1.0-1) ... Setting up r-cran-curl (7.0.0+dfsg-1) ... Setting up littler (0.3.21-2) ... Setting up r-cran-digest (0.6.39-1) ... Setting up r-cran-igraph (2.1.4-1+b1) ... Setting up r-cran-rcpparmadillo (15.2.3-1-1) ... Processing triggers for libc-bin (2.42-6) ... Processing triggers for debianutils (5.23.2) ... 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m45.7s DUMP: 99a20c7ef6d1dddda5203f0c2847c637 - 0m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m45.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m45.9s DUMP: Package: r-bioc-phyloseq Status: install ok installed Priority: optional Section: gnu-r Installed-Size: 3134 Maintainer: Debian R Packages Maintainers Architecture: all Version: 1.50.0+dfsg-2 Depends: r-api-4.0, r-api-bioc-3.20, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5) Suggests: r-bioc-biocstyle (>= 2.4), r-bioc-deseq2 (>= 1.16.1), r-bioc-genefilter (>= 1.58), r-cran-knitr (>= 1.16), r-cran-magrittr (>= 1.5), r-bioc-metagenomeseq (>= 1.14), r-cran-rmarkdown (>= 1.6), r-cran-testthat (>= 1.0.2) Description: GNU R handling and analysis of high-throughput microbiome census data The Bioconductor module phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Description-md5: Homepage: https://bioconductor.org/packages/phyloseq/ 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m45.9s INFO: apt-cache does not know about any of the requested packages 0m45.9s INFO: Running scripts post_distupgrade 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_exceptions'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_exceptions'] 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_zz_backports'] 0m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/post_distupgrade_zz_backports'] 0m45.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m46.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m46.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpztnuszbj to sid 0m46.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m46.8s INFO: Running scripts pre_distupgrade 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_exceptions'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m49.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [187 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7452 kB] Fetched 17.9 MB in 2s (9819 kB/s) Reading package lists... 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', 'update'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m53.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libxml2 r-cran-colorspace r-cran-munsell Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: r-cran-s7 The following packages have been kept back: r-bioc-phyloseq The following packages will be upgraded: bsdutils dpkg gcc-15-base libatomic1 libblkid1 libfreetype6 libgcc-s1 libgfortran5 libgomp1 liblastlog2-2 libmount1 libsmartcols1 libstdc++6 libuuid1 libxdmcp6 libxml2 linux-libc-dev login mount r-cran-ade4 r-cran-cli r-cran-colorspace r-cran-data.table r-cran-fansi r-cran-ggplot2 r-cran-igraph r-cran-isoband r-cran-jsonlite r-cran-permute r-cran-rlang util-linux 31 upgraded, 1 newly installed, 0 to remove and 1 not upgraded. Need to get 35.4 MB of archives. After this operation, 2840 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.23.3 [1518 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.3-2 [38.8 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.3-2 [174 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.3-2 [211 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.3-2 [145 kB] Get:6 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.3-2 [1166 kB] Get:7 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.3-2 [164 kB] Get:8 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.3-2 [106 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 15.2.0-12 [9524 B] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-15-base amd64 15.2.0-12 [54.1 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 15.2.0-12 [737 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 15.2.0-12 [140 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 15.2.0-12 [862 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 15.2.0-12 [71.5 kB] Get:15 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.3-2 [94.0 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.14.1+dfsg-1 [493 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.3-2 [29.6 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.3 [710 kB] Get:20 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.17.13-1 [2574 kB] Get:21 http://deb.debian.org/debian sid/main amd64 r-cran-ade4 amd64 1.7-23-2 [5405 kB] Get:22 http://deb.debian.org/debian sid/main amd64 r-cran-cli amd64 3.6.5-1 [1380 kB] Get:23 http://deb.debian.org/debian sid/main amd64 r-cran-colorspace amd64 2.1-2+dfsg-1 [1730 kB] Get:24 http://deb.debian.org/debian sid/main amd64 r-cran-data.table amd64 1.17.8+dfsg-1 [2108 kB] Get:25 http://deb.debian.org/debian sid/main amd64 r-cran-fansi amd64 1.0.7-1 [798 kB] Get:26 http://deb.debian.org/debian sid/main amd64 r-cran-rlang amd64 1.1.6-1 [1714 kB] Get:27 http://deb.debian.org/debian sid/main amd64 r-cran-isoband amd64 0.3.0-1 [1644 kB] Get:28 http://deb.debian.org/debian sid/main amd64 r-cran-s7 amd64 0.2.1-1 [330 kB] Get:29 http://deb.debian.org/debian sid/main amd64 r-cran-ggplot2 all 4.0.1+dfsg-1 [4917 kB] Get:30 http://deb.debian.org/debian sid/main amd64 r-cran-igraph amd64 2.2.1-1 [5372 kB] Get:31 http://deb.debian.org/debian sid/main amd64 r-cran-jsonlite amd64 2.0.0+dfsg-1 [447 kB] Get:32 http://deb.debian.org/debian sid/main amd64 r-cran-permute all 0.9-8-1 [237 kB] Fetched 35.4 MB in 0s (81.8 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 ... 20616 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.23.3_amd64.deb ... Unpacking dpkg (1.23.3) over (1.22.21) ... Setting up dpkg (1.23.3) ... (Reading database ... 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(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 ... 20620 files and directories currently installed.) Preparing to unpack .../00-bsdutils_1%3a2.41.3-2_amd64.deb ... Unpacking bsdutils (1:2.41.3-2) over (1:2.41.2-4) ... Preparing to unpack .../01-libfreetype6_2.14.1+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.14.1+dfsg-1) over (2.13.3+dfsg-1) ... Preparing to unpack .../02-liblastlog2-2_2.41.3-2_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41.3-2) over (2.41.2-4) ... 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Setting up libxdmcp6:amd64 (1:1.1.5-2) ... Setting up r-cran-rlang (1.1.6-1) ... Setting up bsdutils (1:2.41.3-2) ... Setting up liblastlog2-2:amd64 (2.41.3-2) ... Setting up r-cran-fansi (1.0.7-1) ... Setting up linux-libc-dev (6.17.13-1) ... Setting up libgomp1:amd64 (15.2.0-12) ... Setting up r-cran-data.table (1.17.8+dfsg-1) ... Setting up r-cran-ade4 (1.7-23-2) ... Setting up r-cran-cli (3.6.5-1) ... Setting up r-cran-jsonlite (2.0.0+dfsg-1) ... Setting up r-cran-colorspace (2.1-2+dfsg-1) ... Setting up libfreetype6:amd64 (2.14.1+dfsg-1) ... Setting up r-cran-s7 (0.2.1-1) ... Setting up r-cran-isoband (0.3.0-1) ... Setting up libatomic1:amd64 (15.2.0-12) ... Setting up libgfortran5:amd64 (15.2.0-12) ... Setting up mount (2.41.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.3) ... Setting up login (1:4.16.0-2+really2.41.3-2) ... Setting up r-cran-ggplot2 (4.0.1+dfsg-1) ... Setting up r-cran-igraph (2.2.1-1) ... Processing triggers for libc-bin (2.42-6) ... 0m53.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-yf', 'dist-upgrade'] 0m53.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.1s DUMP: 3702d222d7f791a609d037cddd15ac94 - 0m54.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m54.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m54.4s DUMP: Package: r-bioc-phyloseq Version: 1.54.0+dfsg-1 Installed-Size: 3135 Maintainer: Debian R Packages Maintainers Architecture: all Depends: r-api-4.0, r-api-bioc-3.22, r-cran-ade4 (>= 1.7-4), r-cran-ape (>= 5.0), r-bioc-biobase (>= 2.36.2), r-bioc-biocgenerics (>= 0.22.0), r-bioc-biomformat (>= 1.0.0), r-bioc-biostrings (>= 2.40.0), r-cran-cluster (>= 2.0.4), r-cran-data.table (>= 1.10.4), r-cran-foreach (>= 1.4.3), r-cran-ggplot2 (>= 2.1.0), r-cran-igraph (>= 1.0.1), r-bioc-multtest (>= 2.28.0), r-cran-plyr (>= 1.8.3), r-cran-reshape2 (>= 1.4.1), r-cran-scales (>= 0.4.0), r-cran-vegan (>= 2.5) Suggests: r-cran-magrittr (>= 1.5) Description-en: GNU R handling and analysis of high-throughput microbiome census data The Bioconductor module phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. Description-md5: ce1efdc42d4cdfd64fc0152b75e33d3f Homepage: https://bioconductor.org/packages/phyloseq/ Section: gnu-r Priority: optional Filename: pool/main/r/r-bioc-phyloseq/r-bioc-phyloseq_1.54.0+dfsg-1_all.deb Size: 2256488 MD5sum: 4e7e168735cea23448120d0102d4e17c SHA256: dd238c4a9d0430f90b137959a7e162b5f6f7a09d4614b43100d19c48dab1bfe4 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'show', '--no-all-versions', 'r-bioc-phyloseq'] 0m54.4s INFO: apt-cache knows about the following packages: r-bioc-phyloseq 0m54.4s INFO: Running scripts pre_install 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_database-server'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_database-server'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_exceptions'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_exceptions'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_extras'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_extras'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy'] 0m54.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy', 'r-bioc-phyloseq'] 0m54.6s DUMP: r-bioc-phyloseq: Installed: 1.50.0+dfsg-2 Candidate: 1.54.0+dfsg-1 Version table: 1.54.0+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages *** 1.50.0+dfsg-2 100 100 /var/lib/dpkg/status 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-cache', 'policy', 'r-bioc-phyloseq'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-y', 'install', 'r-bioc-phyloseq'] 0m55.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-phyloseq : Depends: r-api-bioc-3.22 but it is not installable E: Unable to satisfy dependencies. Reached two conflicting decisions: 1. r-bioc-phyloseq:amd64=1.54.0+dfsg-1 is selected as an upgrade 2. r-bioc-phyloseq:amd64=1.54.0+dfsg-1 Depends r-api-bioc-3.22 but none of the choices are installable: [no choices] 0m55.2s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpztnuszbj', 'apt-get', '-y', 'install', 'r-bioc-phyloseq'] Reading package lists... Building dependency tree... Reading state information... Solving dependencies... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-bioc-phyloseq : Depends: r-api-bioc-3.22 but it is not installable E: Unable to satisfy dependencies. Reached two conflicting decisions: 1. r-bioc-phyloseq:amd64=1.54.0+dfsg-1 is selected as an upgrade 2. r-bioc-phyloseq:amd64=1.54.0+dfsg-1 Depends r-api-bioc-3.22 but none of the choices are installable: [no choices] 0m56.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/shm'] 0m56.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/shm'] 0m56.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/console'] 0m56.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/console'] 0m56.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/ptmx'] 0m56.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/ptmx'] 0m56.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts'] 0m56.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/dev/pts'] 0m56.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/proc'] 0m56.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpztnuszbj/proc'] 0m56.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m56.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpztnuszbj'] 0m56.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpztnuszbj 0m56.9s ERROR: piuparts run ends. ret=1 End: 2025-12-26 15:50:05 GMT