0s autopkgtest [13:54:56]: starting date and time: 2024-03-16 13:54:56+0000
  0s autopkgtest [13:54:56]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [13:54:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o1qqgw38/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-rcurl,src:curl,src:libpsl,src:openssl,src:orthanc-python --apt-upgrade r-bioc-rtracklayer --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-cran-rcurl/1.98-1.14+dfsg-1build1 curl/8.5.0-2ubuntu7 libpsl/0.21.2-1.1 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-19.secgroup --name adt-noble-arm64-r-bioc-rtracklayer-20240316-135456-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 73s autopkgtest [13:56:09]: testbed dpkg architecture: arm64
 73s autopkgtest [13:56:09]: testbed apt version: 2.7.12
 73s autopkgtest [13:56:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 73s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 74s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
 74s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB]
 74s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3690 kB]
 74s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB]
 74s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB]
 74s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
 74s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB]
 74s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
 74s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4006 kB]
 74s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
 74s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.8 kB]
 74s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
 76s Fetched 9092 kB in 2s (4439 kB/s)
 77s Reading package lists...
 79s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 80s Calculating upgrade...
 81s The following packages will be REMOVED:
 81s   libssl3
 81s The following NEW packages will be installed:
 81s   libssl3t64
 81s The following packages have been kept back:
 81s   curl
 81s The following packages will be upgraded:
 81s   openssl ubuntu-minimal ubuntu-standard
 81s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded.
 81s Need to get 2775 kB of archives.
 81s After this operation, 72.7 kB of additional disk space will be used.
 81s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB]
 81s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB]
 81s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB]
 81s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB]
 82s Fetched 2775 kB in 1s (3973 kB/s)
 83s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
 83s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ...
 83s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ...
 83s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested:
 83s  wget depends on libssl3 (>= 3.0.0).
 83s  u-boot-tools depends on libssl3 (>= 3.0.0).
 83s  tnftp depends on libssl3 (>= 3.0.0).
 83s  tcpdump depends on libssl3 (>= 3.0.0).
 83s  systemd-resolved depends on libssl3 (>= 3.0.0).
 83s  systemd depends on libssl3 (>= 3.0.0).
 83s  sudo depends on libssl3 (>= 3.0.0).
 83s  sbsigntool depends on libssl3 (>= 3.0.0).
 83s  rsync depends on libssl3 (>= 3.0.0).
 83s  python3-cryptography depends on libssl3 (>= 3.0.0).
 83s  openssh-server depends on libssl3 (>= 3.0.10).
 83s  openssh-client depends on libssl3 (>= 3.0.10).
 83s  mtd-utils depends on libssl3 (>= 3.0.0).
 83s  mokutil depends on libssl3 (>= 3.0.0).
 83s  linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0).
 83s  libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0).
 83s  libssh-4:arm64 depends on libssl3 (>= 3.0.0).
 83s  libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0).
 83s  libsasl2-2:arm64 depends on libssl3 (>= 3.0.0).
 83s  libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0).
 83s  libnvme1 depends on libssl3 (>= 3.0.0).
 83s  libkrb5-3:arm64 depends on libssl3 (>= 3.0.0).
 83s  libkmod2:arm64 depends on libssl3 (>= 3.0.0).
 83s  libfido2-1:arm64 depends on libssl3 (>= 3.0.0).
 83s  libcurl4:arm64 depends on libssl3 (>= 3.0.0).
 83s  libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0).
 83s  kmod depends on libssl3 (>= 3.0.0).
 83s  dhcpcd-base depends on libssl3 (>= 3.0.0).
 83s  bind9-libs:arm64 depends on libssl3 (>= 3.0.0).
 83s 
 83s (Reading database ... 
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(Reading database ... 74758 files and directories currently installed.)
 83s Removing libssl3:arm64 (3.0.10-1ubuntu4) ...
 83s Selecting previously unselected package libssl3t64:arm64.
 83s (Reading database ... 
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(Reading database ... 74747 files and directories currently installed.)
 83s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ...
 83s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ...
 83s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ...
 83s Unpacking ubuntu-minimal (1.536) over (1.535) ...
 83s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ...
 83s Unpacking ubuntu-standard (1.536) over (1.535) ...
 83s Setting up ubuntu-minimal (1.536) ...
 83s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ...
 83s Setting up ubuntu-standard (1.536) ...
 83s Setting up openssl (3.0.13-0ubuntu1) ...
 83s Processing triggers for man-db (2.12.0-3) ...
 84s Processing triggers for libc-bin (2.39-0ubuntu2) ...
 84s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 85s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 86s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 86s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 86s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 86s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 88s Reading package lists...
 88s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 89s Calculating upgrade...
 89s The following packages have been kept back:
 89s   curl
 89s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 89s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 90s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.
 94s autopkgtest [13:56:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
 94s autopkgtest [13:56:30]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-rtracklayer
 96s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-rtracklayer 1.62.0-1 (dsc) [2398 B]
 96s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-rtracklayer 1.62.0-1 (tar) [4019 kB]
 96s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-rtracklayer 1.62.0-1 (diff) [27.2 kB]
 96s gpgv: Signature made Thu Nov 30 17:25:54 2023 UTC
 96s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 96s gpgv:                issuer "tillea@rki.de"
 96s gpgv: Can't check signature: No public key
 96s dpkg-source: warning: cannot verify inline signature for ./r-bioc-rtracklayer_1.62.0-1.dsc: no acceptable signature found
 97s autopkgtest [13:56:33]: testing package r-bioc-rtracklayer version 1.62.0-1
 97s autopkgtest [13:56:33]: build not needed
 98s autopkgtest [13:56:34]: test pkg-r-autopkgtest: preparing testbed
100s Reading package lists...
100s Building dependency tree...
100s Reading state information...
100s Starting pkgProblemResolver with broken count: 0
100s Starting 2 pkgProblemResolver with broken count: 0
100s Done
101s The following additional packages will be installed:
101s   build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu
101s   curl dctrl-tools fontconfig fontconfig-config fonts-dejavu-core
101s   fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu
101s   gcc gcc-13 gcc-13-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran
101s   gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu
101s   icu-devtools libasan8 libatomic1 libblas-dev libblas3 libboost-dev
101s   libboost1.83-dev libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0
101s   libcrypt-dev libcurl4t64 libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev
101s   libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
101s   libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev
101s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-jquery
101s   liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
101s   libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0
101s   libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0
101s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libpsl5t64
101s   libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data
101s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
101s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev
101s   node-html5shiv pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core
101s   r-base-dev r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase
101s   r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
101s   r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
101s   r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata
101s   r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
101s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
101s   r-bioc-org.hs.eg.db r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
101s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
101s   r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-abind
101s   r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
101s   r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon
101s   r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-fansi
101s   r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger
101s   r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr
101s   r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
101s   r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats
101s   r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig
101s   r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr
101s   r-cran-r6 r-cran-rappdirs r-cran-rcurl r-cran-restfulr r-cran-rjson
101s   r-cran-rlang r-cran-rsqlite r-cran-runit r-cran-snow r-cran-statmod
101s   r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble
101s   r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr
101s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rpcsvc-proto unzip
101s   x11-common xdg-utils zip zlib1g-dev
101s Suggested packages:
101s   cpp-doc gcc-13-locales cpp-13-doc debtags gcc-13-doc gcc-multilib
101s   manpages-dev autoconf automake libtool flex bison gdb gcc-doc
101s   gdb-aarch64-linux-gnu gfortran-doc gfortran-13-doc libcoarrays-dev
101s   liblapack-doc libboost-doc libboost1.83-doc libboost-atomic1.83-dev
101s   libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev
101s   libboost-contract1.83-dev libboost-coroutine1.83-dev
101s   libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev
101s   libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
101s   libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
101s   libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
101s   libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
101s   libboost-numpy1.83-dev libboost-program-options1.83-dev
101s   libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev
101s   libboost-serialization1.83-dev libboost-stacktrace1.83-dev
101s   libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
101s   libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
101s   libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
101s   glibc-doc icu-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc
101s   tcl8.6 tk8.6 nodejs elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
101s   texlive-base texlive-latex-base texlive-plain-generic
101s   texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
101s   texlive-latex-recommended texlive-latex-extra texinfo r-bioc-go.db
101s   r-bioc-graph r-bioc-biocstyle r-cran-knitr r-bioc-all r-cran-testthat
101s   r-cran-rmarkdown r-bioc-affy r-bioc-deseq2 r-cran-foreach r-cran-bbmisc
101s   r-cran-doparallel r-bioc-variantannotation r-bioc-shortread
101s   r-cran-batchtools r-cran-data.table r-cran-mockery r-cran-webmockr
101s   r-cran-biocmanager r-bioc-hdf5array r-cran-lobstr r-bioc-delayedmatrixstats
101s   r-cran-class r-cran-rcolorbrewer r-cran-r.utils r-bioc-edger
101s   r-bioc-ensembldb r-bioc-annotationfilter r-cran-markdown r-bioc-gviz
101s   r-bioc-annotationhub r-bioc-dexseq r-cran-biasedurn r-cran-ellipse
101s   r-cran-gplots r-cran-locfit r-cran-mass r-bioc-sparsematrixstats
101s   r-bioc-rhdf5 r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-rstudioapi
101s   r-cran-rmysql r-cran-shiny r-cran-lubridate r-cran-getopt r-cran-formattable
101s   r-cran-ggplot2 r-cran-nanotime r-cran-palmerpenguins r-cran-scales
101s   r-cran-units r-cran-vdiffr r-cran-rcpp r-cran-rmpi r-cran-rlecuyer
101s   r-cran-spelling r-cran-bench r-cran-brio r-cran-callr r-cran-evaluate
101s   r-cran-here r-cran-htmltools r-cran-pkgbuild r-cran-pkgload r-cran-plm
101s   r-cran-zoo
101s Recommended packages:
101s   bzip2-doc manpages manpages-dev libc-devtools javascript-common libpng-tools
101s   r-recommended r-doc-html r-cran-testthat r-cran-callr r-cran-covr
101s   r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-mockery
101s   r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
101s   r-cran-rstudioapi r-cran-whoami r-cran-bench r-cran-brio r-cran-decor
101s   r-cran-desc r-cran-ggplot2 r-cran-lobstr r-cran-scales r-cran-rcpp
101s   r-cran-spelling r-cran-later r-cran-httpuv r-cran-webutils
101s   r-cran-rpostgresql r-cran-broom r-cran-rmysql r-cran-unitizer r-cran-testit
101s   r-cran-pkgload r-cran-waldo r-cran-jpeg r-cran-readr r-cran-r.rsp r-cran-sf
101s   r-cran-lintr r-cran-tidyverse r-cran-base64enc r-cran-markdown
101s   r-cran-r.devices r-cran-sodium r-cran-lubridate r-cran-fs r-cran-usethis
101s   r-cran-dbitest r-cran-gert r-cran-gh r-cran-rvest r-cran-data.table
101s   r-cran-mockr r-cran-formattable r-cran-pkgdown r-cran-zeallot
101s   libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
101s   x11-xserver-utils
101s The following packages will be REMOVED:
101s   libcurl4 libpsl5
101s The following NEW packages will be installed:
101s   autopkgtest-satdep build-essential cpp cpp-13 cpp-13-aarch64-linux-gnu
101s   cpp-aarch64-linux-gnu dctrl-tools fontconfig fontconfig-config
101s   fonts-dejavu-core fonts-dejavu-mono g++ g++-13 g++-13-aarch64-linux-gnu
101s   g++-aarch64-linux-gnu gcc gcc-13 gcc-13-aarch64-linux-gnu
101s   gcc-aarch64-linux-gnu gfortran gfortran-13 gfortran-13-aarch64-linux-gnu
101s   gfortran-aarch64-linux-gnu icu-devtools libasan8 libatomic1 libblas-dev
101s   libblas3 libboost-dev libboost1.83-dev libbz2-dev libc-dev-bin libc6-dev
101s   libcairo2 libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdeflate0
101s   libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1
101s   libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23 libitm1
101s   libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev
101s   libjs-jquery liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
101s   libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0
101s   libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0
101s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libpsl5t64
101s   libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data
101s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
101s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev
101s   node-html5shiv pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core
101s   r-base-dev r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase
101s   r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
101s   r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
101s   r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata
101s   r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
101s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
101s   r-bioc-org.hs.eg.db r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
101s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
101s   r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-abind
101s   r-cran-askpass r-cran-bh r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
101s   r-cran-cachem r-cran-cli r-cran-codetools r-cran-cpp11 r-cran-crayon
101s   r-cran-curl r-cran-dbi r-cran-dbplyr r-cran-digest r-cran-dplyr r-cran-fansi
101s   r-cran-fastmap r-cran-filelock r-cran-formatr r-cran-futile.logger
101s   r-cran-futile.options r-cran-generics r-cran-glue r-cran-hms r-cran-httr
101s   r-cran-jsonlite r-cran-lambda.r r-cran-lattice r-cran-lifecycle
101s   r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats
101s   r-cran-memoise r-cran-mime r-cran-openssl r-cran-pillar r-cran-pkgconfig
101s   r-cran-plogr r-cran-png r-cran-prettyunits r-cran-progress r-cran-purrr
101s   r-cran-r6 r-cran-rappdirs r-cran-rcurl r-cran-restfulr r-cran-rjson
101s   r-cran-rlang r-cran-rsqlite r-cran-runit r-cran-snow r-cran-statmod
101s   r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys r-cran-tibble
101s   r-cran-tidyr r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr
101s   r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml rpcsvc-proto unzip
101s   x11-common xdg-utils zip zlib1g-dev
101s The following packages will be upgraded:
101s   curl
101s 1 upgraded, 212 newly installed, 2 to remove and 0 not upgraded.
101s Need to get 324 MB/324 MB of archives.
101s After this operation, 1142 MB of additional disk space will be used.
101s Get:1 /tmp/autopkgtest.owtjzr/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [796 B]
101s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB]
101s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB]
101s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB]
102s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.39-0ubuntu2 [19.7 kB]
102s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-11.11 [1569 kB]
102s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB]
102s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB]
102s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB]
102s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu6 [65.4 kB]
102s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.39-0ubuntu2 [1596 kB]
102s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libisl23 arm64 0.26-3 [713 kB]
102s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libmpc3 arm64 1.3.1-1 [55.3 kB]
102s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.3 MB]
102s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-17ubuntu2 [1028 B]
102s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B]
102s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB]
102s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcc1-0 arm64 14-20240303-1ubuntu1 [44.7 kB]
102s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
102s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libitm1 arm64 14-20240303-1ubuntu1 [27.7 kB]
102s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libatomic1 arm64 14-20240303-1ubuntu1 [11.4 kB]
102s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libasan8 arm64 14-20240303-1ubuntu1 [2919 kB]
102s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 liblsan0 arm64 14-20240303-1ubuntu1 [1282 kB]
102s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libtsan2 arm64 14-20240303-1ubuntu1 [2687 kB]
102s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libubsan1 arm64 14-20240303-1ubuntu1 [1151 kB]
102s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libhwasan0 arm64 14-20240303-1ubuntu1 [1597 kB]
102s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-17ubuntu2 [2464 kB]
102s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [20.1 MB]
103s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-17ubuntu2 [467 kB]
103s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B]
103s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B]
103s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-17ubuntu2 [2322 kB]
103s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [11.7 MB]
103s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-17ubuntu2 [14.4 kB]
103s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B]
103s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B]
103s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
103s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 dctrl-tools arm64 2.24-3build2 [65.2 kB]
103s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
103s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
103s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB]
103s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB]
103s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig arm64 2.15.0-1ubuntu1 [190 kB]
103s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
103s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran-13-dev arm64 13.2.0-17ubuntu2 [478 kB]
103s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13-aarch64-linux-gnu arm64 13.2.0-17ubuntu2 [10.8 MB]
104s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-13 arm64 13.2.0-17ubuntu2 [10.3 kB]
104s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1022 B]
104s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B]
104s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB]
104s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
104s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB]
104s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libboost1.83-dev arm64 1.83.0-2ubuntu1 [15.3 MB]
104s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libboost-dev arm64 1.83.0.1ubuntu2 [4308 B]
104s Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libbz2-dev arm64 1.0.8-5ubuntu1 [35.8 kB]
104s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB]
104s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB]
104s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B]
104s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB]
104s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB]
104s Get:61 http://ftpmaster.internal/ubuntu noble/main arm64 libdatrie1 arm64 0.2.13-3 [21.7 kB]
104s Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB]
104s Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB]
104s Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB]
104s Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
104s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB]
104s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB]
104s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB]
104s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8-dev arm64 2.1.5-2ubuntu1 [304 kB]
104s Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
104s Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
104s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
104s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
104s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
105s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB]
105s Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB]
105s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB]
105s Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libthai-data all 0.1.29-2 [158 kB]
105s Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 libthai0 arm64 0.1.29-2 [18.1 kB]
105s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 libpango-1.0-0 arm64 1.51.0+ds-4 [226 kB]
105s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-4 [41.2 kB]
105s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-4 [27.6 kB]
105s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper1 arm64 1.1.29 [13.1 kB]
105s Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libpaper-utils arm64 1.1.29 [8480 B]
105s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu1 [195 kB]
105s Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu1 [183 kB]
105s Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu1 [6654 B]
105s Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-dev arm64 10.42-4ubuntu1 [679 kB]
105s Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB]
105s Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3ubuntu1 [895 kB]
105s Get:91 http://ftpmaster.internal/ubuntu noble/main arm64 libpng-dev arm64 1.6.43-1 [266 kB]
105s Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline-dev arm64 8.2-3 [177 kB]
105s Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB]
105s Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB]
105s Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB]
105s Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB]
105s Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB]
105s Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB]
105s Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB]
105s Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B]
105s Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.13-2 [760 kB]
105s Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libxt6 arm64 1:1.2.1-1.1 [167 kB]
105s Get:103 http://ftpmaster.internal/ubuntu noble/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
105s Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf-bin arm64 1.8.1-2 [20.4 kB]
105s Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB]
105s Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 pkg-config arm64 1.8.1-2 [7170 B]
105s Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 zip arm64 3.0-13 [172 kB]
105s Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 unzip arm64 6.0-28ubuntu3 [171 kB]
105s Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
105s Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-core arm64 4.3.2-1build1 [26.8 MB]
106s Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma-dev arm64 5.4.5-0.3 [209 kB]
106s Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 r-base-dev all 4.3.2-1build1 [4336 B]
106s Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
106s Get:114 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
106s Get:115 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biobase arm64 2.62.0-1 [2136 kB]
107s Get:116 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-s4vectors arm64 0.40.2+dfsg-1 [2055 kB]
107s Get:117 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-iranges arm64 2.36.0-1 [2250 kB]
107s Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbi all 1.2.2-1 [823 kB]
107s Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bit arm64 4.0.5-1 [1057 kB]
107s Get:120 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bit64 arm64 4.0.5-1 [467 kB]
107s Get:121 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rlang arm64 1.1.3-1 [1663 kB]
107s Get:122 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cli arm64 3.6.2-1 [1377 kB]
107s Get:123 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-glue arm64 1.7.0-1 [154 kB]
107s Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
107s Get:125 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
107s Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-blob all 1.2.4-1 [49.8 kB]
107s Get:127 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fastmap arm64 1.1.1-1 [69.6 kB]
107s Get:128 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cachem arm64 1.0.8-1 [72.3 kB]
107s Get:129 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB]
107s Get:130 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
107s Get:131 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
107s Get:132 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-cpp11 all 0.4.7-1 [266 kB]
107s Get:133 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rsqlite arm64 2.3.4-1 [1371 kB]
107s Get:134 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-curl arm64 5.2.0+dfsg-1 [189 kB]
107s Get:135 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-jsonlite arm64 1.8.8+dfsg-1 [441 kB]
107s Get:136 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-mime arm64 0.12-1 [35.8 kB]
107s Get:137 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-sys arm64 3.4.2-1 [44.3 kB]
107s Get:138 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-askpass arm64 1.2.0-1 [24.4 kB]
107s Get:139 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-openssl arm64 2.1.1+dfsg-2 [402 kB]
107s Get:140 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-r6 all 2.5.1-1 [99.0 kB]
107s Get:141 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
107s Get:142 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-png arm64 0.1-8-1 [39.9 kB]
107s Get:143 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9596 B]
107s Get:144 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-xvector arm64 0.42.0-1 [620 kB]
107s Get:145 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bitops arm64 1.0-7-1 [29.5 kB]
107s Get:146 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 r-cran-rcurl arm64 1.98-1.14+dfsg-1build1 [793 kB]
107s Get:147 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB]
108s Get:148 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3886 kB]
108s Get:149 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-crayon all 1.5.2-1 [164 kB]
108s Get:150 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biostrings arm64 2.70.2+dfsg-1 [13.6 MB]
108s Get:151 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB]
108s Get:152 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-annotationdbi all 1.64.1-1 [4897 kB]
108s Get:153 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xml arm64 3.99-0.16.1-1 [1734 kB]
109s Get:154 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB]
109s Get:155 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-annotate all 1.80.0+dfsg-1 [1730 kB]
109s Get:156 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB]
109s Get:157 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
109s Get:158 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB]
109s Get:159 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB]
109s Get:160 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB]
109s Get:161 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-2 [415 kB]
109s Get:162 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-withr all 2.5.0-1 [225 kB]
109s Get:163 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyselect arm64 1.2.0+dfsg-1 [218 kB]
109s Get:164 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dplyr arm64 1.1.4-1 [1513 kB]
109s Get:165 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-purrr arm64 1.0.2-1 [501 kB]
109s Get:166 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringi arm64 1.8.3-1 [869 kB]
109s Get:167 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-stringr all 1.5.1-1 [290 kB]
109s Get:168 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-tidyr arm64 1.3.1-1 [1154 kB]
109s Get:169 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-dbplyr all 2.4.0+dfsg-1 [1172 kB]
109s Get:170 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-filelock arm64 1.0.3-1 [29.7 kB]
109s Get:171 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [300 kB]
109s Get:172 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocio all 1.12.0+dfsg-1 [213 kB]
109s Get:173 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-formatr all 1.14-1 [152 kB]
109s Get:174 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
109s Get:175 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
109s Get:176 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
109s Get:177 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
109s Get:178 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-codetools all 0.2-19-1 [90.5 kB]
109s Get:179 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-bh all 1.84.0-1 [5962 B]
109s Get:180 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biocparallel arm64 1.36.0-1 [1345 kB]
109s Get:181 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-hms all 1.1.3-1 [96.5 kB]
109s Get:182 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-prettyunits all 1.2.0-1 [162 kB]
109s Get:183 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-progress all 1.2.3-1 [91.9 kB]
109s Get:184 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-digest arm64 0.6.34-1 [182 kB]
109s Get:185 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB]
109s Get:186 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-xml2 arm64 1.3.6-1 [321 kB]
109s Get:187 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-biomart all 2.58.2+dfsg-1 [433 kB]
109s Get:188 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genomicranges arm64 1.54.1+dfsg-1 [1822 kB]
109s Get:189 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-rhtslib arm64 2.4.1+dfsg-1 [1357 kB]
109s Get:190 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-rsamtools arm64 2.18.0+dfsg-1 [3629 kB]
109s Get:191 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrixstats arm64 1.2.0-1 [475 kB]
109s Get:192 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB]
109s Get:193 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-lattice arm64 0.22-5-1 [1342 kB]
110s Get:194 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-matrix arm64 1.6-5-1 [3776 kB]
110s Get:195 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-abind all 1.4-5-2 [63.6 kB]
110s Get:196 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-s4arrays arm64 1.2.0+dfsg-1 [501 kB]
110s Get:197 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-sparsearray arm64 1.2.4+dfsg-1 [1195 kB]
110s Get:198 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-delayedarray arm64 0.28.0+dfsg-1 [1786 kB]
110s Get:199 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1134 kB]
110s Get:200 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genomicalignments arm64 1.38.2-1 [2133 kB]
110s Get:201 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-littler arm64 0.3.19-1 [93.4 kB]
110s Get:202 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-rjson arm64 0.2.21-1 [142 kB]
110s Get:203 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-yaml arm64 2.3.8-1 [107 kB]
110s Get:204 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-restfulr arm64 0.0.15-1 [380 kB]
110s Get:205 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-rtracklayer arm64 1.62.0-1 [5104 kB]
111s Get:206 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-bsgenome all 1.70.2-1 [6975 kB]
111s Get:207 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-survival arm64 3.5-8-1 [6116 kB]
111s Get:208 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genefilter arm64 1.84.0-1 [1122 kB]
111s Get:209 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-genomicfeatures all 1.54.1+dfsg-1 [1817 kB]
111s Get:210 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-statmod arm64 1.5.0-1 [294 kB]
111s Get:211 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-limma arm64 3.58.1+dfsg-1 [1897 kB]
111s Get:212 http://ftpmaster.internal/ubuntu noble/universe arm64 r-bioc-org.hs.eg.db all 3.18.0-1 [64.1 MB]
114s Get:213 http://ftpmaster.internal/ubuntu noble/universe arm64 r-cran-runit all 0.4.32-3 [283 kB]
115s Preconfiguring packages ...
115s Fetched 324 MB in 13s (25.8 MB/s)
115s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested:
115s  wget depends on libpsl5 (>= 0.16.0).
115s  libcurl4:arm64 depends on libpsl5 (>= 0.16.0).
115s  libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0).
115s 
115s (Reading database ... 
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115s Removing libpsl5:arm64 (0.21.2-1build1) ...
115s Selecting previously unselected package libpsl5t64:arm64.
115s (Reading database ... 
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115s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ...
115s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ...
115s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ...
115s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ...
115s (Reading database ... 
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115s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ...
115s Selecting previously unselected package libcurl4t64:arm64.
115s (Reading database ... 
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115s Preparing to unpack .../000-libcurl4t64_8.5.0-2ubuntu7_arm64.deb ...
115s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ...
115s Selecting previously unselected package libc-dev-bin.
115s Preparing to unpack .../001-libc-dev-bin_2.39-0ubuntu2_arm64.deb ...
115s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
115s Selecting previously unselected package linux-libc-dev:arm64.
115s Preparing to unpack .../002-linux-libc-dev_6.8.0-11.11_arm64.deb ...
115s Unpacking linux-libc-dev:arm64 (6.8.0-11.11) ...
115s Selecting previously unselected package libcrypt-dev:arm64.
115s Preparing to unpack .../003-libcrypt-dev_1%3a4.4.36-4_arm64.deb ...
115s Unpacking libcrypt-dev:arm64 (1:4.4.36-4) ...
115s Selecting previously unselected package libtirpc-dev:arm64.
115s Preparing to unpack .../004-libtirpc-dev_1.3.4+ds-1build1_arm64.deb ...
115s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1build1) ...
116s Selecting previously unselected package libnsl-dev:arm64.
116s Preparing to unpack .../005-libnsl-dev_1.3.0-3_arm64.deb ...
116s Unpacking libnsl-dev:arm64 (1.3.0-3) ...
116s Selecting previously unselected package rpcsvc-proto.
116s Preparing to unpack .../006-rpcsvc-proto_1.4.2-0ubuntu6_arm64.deb ...
116s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
116s Selecting previously unselected package libc6-dev:arm64.
116s Preparing to unpack .../007-libc6-dev_2.39-0ubuntu2_arm64.deb ...
116s Unpacking libc6-dev:arm64 (2.39-0ubuntu2) ...
116s Selecting previously unselected package libisl23:arm64.
116s Preparing to unpack .../008-libisl23_0.26-3_arm64.deb ...
116s Unpacking libisl23:arm64 (0.26-3) ...
116s Selecting previously unselected package libmpc3:arm64.
116s Preparing to unpack .../009-libmpc3_1.3.1-1_arm64.deb ...
116s Unpacking libmpc3:arm64 (1.3.1-1) ...
116s Selecting previously unselected package cpp-13-aarch64-linux-gnu.
116s Preparing to unpack .../010-cpp-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
116s Unpacking cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
116s Selecting previously unselected package cpp-13.
116s Preparing to unpack .../011-cpp-13_13.2.0-17ubuntu2_arm64.deb ...
116s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
116s Selecting previously unselected package cpp-aarch64-linux-gnu.
116s Preparing to unpack .../012-cpp-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
116s Unpacking cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
116s Selecting previously unselected package cpp.
116s Preparing to unpack .../013-cpp_4%3a13.2.0-7ubuntu1_arm64.deb ...
116s Unpacking cpp (4:13.2.0-7ubuntu1) ...
116s Selecting previously unselected package libcc1-0:arm64.
116s Preparing to unpack .../014-libcc1-0_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libcc1-0:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libgomp1:arm64.
116s Preparing to unpack .../015-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libitm1:arm64.
116s Preparing to unpack .../016-libitm1_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libitm1:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libatomic1:arm64.
116s Preparing to unpack .../017-libatomic1_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libatomic1:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libasan8:arm64.
116s Preparing to unpack .../018-libasan8_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libasan8:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package liblsan0:arm64.
116s Preparing to unpack .../019-liblsan0_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking liblsan0:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libtsan2:arm64.
116s Preparing to unpack .../020-libtsan2_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libtsan2:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libubsan1:arm64.
116s Preparing to unpack .../021-libubsan1_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libubsan1:arm64 (14-20240303-1ubuntu1) ...
116s Selecting previously unselected package libhwasan0:arm64.
116s Preparing to unpack .../022-libhwasan0_14-20240303-1ubuntu1_arm64.deb ...
116s Unpacking libhwasan0:arm64 (14-20240303-1ubuntu1) ...
117s Selecting previously unselected package libgcc-13-dev:arm64.
117s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_arm64.deb ...
117s Unpacking libgcc-13-dev:arm64 (13.2.0-17ubuntu2) ...
117s Selecting previously unselected package gcc-13-aarch64-linux-gnu.
117s Preparing to unpack .../024-gcc-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
117s Unpacking gcc-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
117s Selecting previously unselected package gcc-13.
117s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_arm64.deb ...
117s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
117s Selecting previously unselected package gcc-aarch64-linux-gnu.
117s Preparing to unpack .../026-gcc-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
117s Unpacking gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
117s Selecting previously unselected package gcc.
117s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_arm64.deb ...
117s Unpacking gcc (4:13.2.0-7ubuntu1) ...
117s Selecting previously unselected package libstdc++-13-dev:arm64.
117s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_arm64.deb ...
117s Unpacking libstdc++-13-dev:arm64 (13.2.0-17ubuntu2) ...
117s Selecting previously unselected package g++-13-aarch64-linux-gnu.
117s Preparing to unpack .../029-g++-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
117s Unpacking g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
118s Selecting previously unselected package g++-13.
118s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_arm64.deb ...
118s Unpacking g++-13 (13.2.0-17ubuntu2) ...
118s Selecting previously unselected package g++-aarch64-linux-gnu.
118s Preparing to unpack .../031-g++-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
118s Unpacking g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
118s Selecting previously unselected package g++.
118s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_arm64.deb ...
118s Unpacking g++ (4:13.2.0-7ubuntu1) ...
118s Selecting previously unselected package build-essential.
118s Preparing to unpack .../033-build-essential_12.10ubuntu1_arm64.deb ...
118s Unpacking build-essential (12.10ubuntu1) ...
118s Selecting previously unselected package dctrl-tools.
118s Preparing to unpack .../034-dctrl-tools_2.24-3build2_arm64.deb ...
118s Unpacking dctrl-tools (2.24-3build2) ...
118s Selecting previously unselected package fonts-dejavu-mono.
118s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
118s Unpacking fonts-dejavu-mono (2.37-8) ...
118s Selecting previously unselected package fonts-dejavu-core.
118s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
118s Unpacking fonts-dejavu-core (2.37-8) ...
118s Selecting previously unselected package fontconfig-config.
118s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ...
118s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
118s Selecting previously unselected package libfontconfig1:arm64.
118s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ...
118s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ...
118s Selecting previously unselected package fontconfig.
118s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_arm64.deb ...
118s Unpacking fontconfig (2.15.0-1ubuntu1) ...
118s Selecting previously unselected package libgfortran5:arm64.
118s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
118s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
118s Selecting previously unselected package libgfortran-13-dev:arm64.
118s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_arm64.deb ...
118s Unpacking libgfortran-13-dev:arm64 (13.2.0-17ubuntu2) ...
118s Selecting previously unselected package gfortran-13-aarch64-linux-gnu.
118s Preparing to unpack .../042-gfortran-13-aarch64-linux-gnu_13.2.0-17ubuntu2_arm64.deb ...
118s Unpacking gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
119s Selecting previously unselected package gfortran-13.
119s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_arm64.deb ...
119s Unpacking gfortran-13 (13.2.0-17ubuntu2) ...
119s Selecting previously unselected package gfortran-aarch64-linux-gnu.
119s Preparing to unpack .../044-gfortran-aarch64-linux-gnu_4%3a13.2.0-7ubuntu1_arm64.deb ...
119s Unpacking gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
119s Selecting previously unselected package gfortran.
119s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_arm64.deb ...
119s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
119s Selecting previously unselected package icu-devtools.
119s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_arm64.deb ...
119s Unpacking icu-devtools (74.2-1ubuntu1) ...
119s Selecting previously unselected package libblas3:arm64.
119s Preparing to unpack .../047-libblas3_3.12.0-3_arm64.deb ...
119s Unpacking libblas3:arm64 (3.12.0-3) ...
119s Selecting previously unselected package libblas-dev:arm64.
119s Preparing to unpack .../048-libblas-dev_3.12.0-3_arm64.deb ...
119s Unpacking libblas-dev:arm64 (3.12.0-3) ...
119s Selecting previously unselected package libboost1.83-dev:arm64.
119s Preparing to unpack .../049-libboost1.83-dev_1.83.0-2ubuntu1_arm64.deb ...
119s Unpacking libboost1.83-dev:arm64 (1.83.0-2ubuntu1) ...
121s Selecting previously unselected package libboost-dev:arm64.
121s Preparing to unpack .../050-libboost-dev_1.83.0.1ubuntu2_arm64.deb ...
121s Unpacking libboost-dev:arm64 (1.83.0.1ubuntu2) ...
121s Selecting previously unselected package libbz2-dev:arm64.
121s Preparing to unpack .../051-libbz2-dev_1.0.8-5ubuntu1_arm64.deb ...
121s Unpacking libbz2-dev:arm64 (1.0.8-5ubuntu1) ...
121s Selecting previously unselected package libpixman-1-0:arm64.
121s Preparing to unpack .../052-libpixman-1-0_0.42.2-1_arm64.deb ...
121s Unpacking libpixman-1-0:arm64 (0.42.2-1) ...
121s Selecting previously unselected package libxcb-render0:arm64.
121s Preparing to unpack .../053-libxcb-render0_1.15-1_arm64.deb ...
121s Unpacking libxcb-render0:arm64 (1.15-1) ...
121s Selecting previously unselected package libxcb-shm0:arm64.
121s Preparing to unpack .../054-libxcb-shm0_1.15-1_arm64.deb ...
121s Unpacking libxcb-shm0:arm64 (1.15-1) ...
121s Selecting previously unselected package libxrender1:arm64.
121s Preparing to unpack .../055-libxrender1_1%3a0.9.10-1.1_arm64.deb ...
121s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ...
121s Selecting previously unselected package libcairo2:arm64.
121s Preparing to unpack .../056-libcairo2_1.18.0-1_arm64.deb ...
121s Unpacking libcairo2:arm64 (1.18.0-1) ...
121s Selecting previously unselected package libdatrie1:arm64.
121s Preparing to unpack .../057-libdatrie1_0.2.13-3_arm64.deb ...
121s Unpacking libdatrie1:arm64 (0.2.13-3) ...
121s Selecting previously unselected package libdeflate0:arm64.
121s Preparing to unpack .../058-libdeflate0_1.19-1_arm64.deb ...
121s Unpacking libdeflate0:arm64 (1.19-1) ...
121s Selecting previously unselected package libgraphite2-3:arm64.
121s Preparing to unpack .../059-libgraphite2-3_1.3.14-2_arm64.deb ...
121s Unpacking libgraphite2-3:arm64 (1.3.14-2) ...
121s Selecting previously unselected package libharfbuzz0b:arm64.
121s Preparing to unpack .../060-libharfbuzz0b_8.3.0-2_arm64.deb ...
121s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ...
121s Selecting previously unselected package x11-common.
121s Preparing to unpack .../061-x11-common_1%3a7.7+23ubuntu2_all.deb ...
121s Unpacking x11-common (1:7.7+23ubuntu2) ...
121s Selecting previously unselected package libice6:arm64.
121s Preparing to unpack .../062-libice6_2%3a1.0.10-1build2_arm64.deb ...
121s Unpacking libice6:arm64 (2:1.0.10-1build2) ...
121s Selecting previously unselected package libicu-dev:arm64.
121s Preparing to unpack .../063-libicu-dev_74.2-1ubuntu1_arm64.deb ...
121s Unpacking libicu-dev:arm64 (74.2-1ubuntu1) ...
122s Selecting previously unselected package libjpeg-turbo8:arm64.
122s Preparing to unpack .../064-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ...
122s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ...
122s Selecting previously unselected package libjpeg-turbo8-dev:arm64.
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125s Selecting previously unselected package r-base-core.
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125s Selecting previously unselected package liblzma-dev:arm64.
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125s Selecting previously unselected package r-bioc-biocgenerics.
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125s Selecting previously unselected package r-bioc-s4vectors.
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125s Selecting previously unselected package r-bioc-iranges.
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125s Selecting previously unselected package r-cran-dbi.
126s Preparing to unpack .../114-r-cran-dbi_1.2.2-1_all.deb ...
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126s Selecting previously unselected package r-cran-rlang.
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126s Selecting previously unselected package r-cran-cli.
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126s Selecting previously unselected package r-cran-glue.
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126s Selecting previously unselected package r-cran-cpp11.
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127s Selecting previously unselected package r-cran-rsqlite.
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127s Selecting previously unselected package r-cran-curl.
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127s Selecting previously unselected package r-cran-jsonlite.
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127s Selecting previously unselected package r-cran-mime.
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127s Selecting previously unselected package r-cran-sys.
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127s Selecting previously unselected package r-cran-askpass.
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127s Selecting previously unselected package r-cran-openssl.
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127s Selecting previously unselected package r-cran-r6.
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127s Selecting previously unselected package r-cran-png.
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127s Selecting previously unselected package r-bioc-zlibbioc.
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127s Selecting previously unselected package r-bioc-xvector.
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127s Selecting previously unselected package r-cran-bitops.
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127s Selecting previously unselected package r-cran-rcurl.
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127s Selecting previously unselected package r-bioc-genomeinfodbdata.
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127s Selecting previously unselected package r-cran-crayon.
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127s Selecting previously unselected package r-bioc-biostrings.
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128s Selecting previously unselected package r-bioc-keggrest.
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128s Selecting previously unselected package r-bioc-annotationdbi.
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128s Selecting previously unselected package r-cran-xml.
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128s Selecting previously unselected package r-cran-xtable.
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128s Selecting previously unselected package r-bioc-annotate.
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128s Selecting previously unselected package r-cran-generics.
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128s Selecting previously unselected package r-cran-magrittr.
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128s Selecting previously unselected package r-cran-fansi.
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128s Selecting previously unselected package r-cran-utf8.
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128s Selecting previously unselected package r-cran-pillar.
128s Preparing to unpack .../156-r-cran-pillar_1.9.0+dfsg-1_all.deb ...
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128s Selecting previously unselected package r-cran-tibble.
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128s Selecting previously unselected package r-cran-withr.
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128s Selecting previously unselected package r-cran-tidyselect.
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128s Selecting previously unselected package r-cran-dplyr.
128s Preparing to unpack .../160-r-cran-dplyr_1.1.4-1_arm64.deb ...
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128s Selecting previously unselected package r-cran-purrr.
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128s Unpacking r-cran-purrr (1.0.2-1) ...
128s Selecting previously unselected package r-cran-stringi.
128s Preparing to unpack .../162-r-cran-stringi_1.8.3-1_arm64.deb ...
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128s Selecting previously unselected package r-cran-stringr.
128s Preparing to unpack .../163-r-cran-stringr_1.5.1-1_all.deb ...
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129s Selecting previously unselected package r-cran-tidyr.
129s Preparing to unpack .../164-r-cran-tidyr_1.3.1-1_arm64.deb ...
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129s Selecting previously unselected package r-cran-dbplyr.
129s Preparing to unpack .../165-r-cran-dbplyr_2.4.0+dfsg-1_all.deb ...
129s Unpacking r-cran-dbplyr (2.4.0+dfsg-1) ...
129s Selecting previously unselected package r-cran-filelock.
129s Preparing to unpack .../166-r-cran-filelock_1.0.3-1_arm64.deb ...
129s Unpacking r-cran-filelock (1.0.3-1) ...
129s Selecting previously unselected package r-bioc-biocfilecache.
129s Preparing to unpack .../167-r-bioc-biocfilecache_2.10.1+dfsg-1_all.deb ...
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129s Selecting previously unselected package r-bioc-biocio.
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129s Selecting previously unselected package r-cran-formatr.
129s Preparing to unpack .../169-r-cran-formatr_1.14-1_all.deb ...
129s Unpacking r-cran-formatr (1.14-1) ...
129s Selecting previously unselected package r-cran-lambda.r.
129s Preparing to unpack .../170-r-cran-lambda.r_1.2.4-2build1_all.deb ...
129s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
129s Selecting previously unselected package r-cran-futile.options.
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129s Selecting previously unselected package r-cran-futile.logger.
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129s Selecting previously unselected package r-cran-snow.
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129s Unpacking r-cran-snow (1:0.4.4-2) ...
129s Selecting previously unselected package r-cran-codetools.
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129s Selecting previously unselected package r-cran-bh.
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129s Unpacking r-cran-bh (1.84.0-1) ...
129s Selecting previously unselected package r-bioc-biocparallel.
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129s Selecting previously unselected package r-cran-hms.
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129s Unpacking r-cran-hms (1.1.3-1) ...
129s Selecting previously unselected package r-cran-prettyunits.
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129s Selecting previously unselected package r-cran-digest.
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129s Selecting previously unselected package r-cran-rappdirs.
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129s Unpacking r-cran-rappdirs (0.3.3-1) ...
129s Selecting previously unselected package r-cran-xml2.
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129s Selecting previously unselected package r-bioc-biomart.
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129s Selecting previously unselected package r-bioc-genomicranges.
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130s Selecting previously unselected package r-bioc-rsamtools.
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130s Unpacking r-bioc-rsamtools (2.18.0+dfsg-1) ...
130s Selecting previously unselected package r-cran-matrixstats.
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130s Unpacking r-cran-matrixstats (1.2.0-1) ...
130s Selecting previously unselected package r-bioc-matrixgenerics.
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130s Unpacking r-bioc-matrixgenerics (1.14.0-1) ...
130s Selecting previously unselected package r-cran-lattice.
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130s Unpacking r-cran-lattice (0.22-5-1) ...
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130s Selecting previously unselected package r-cran-abind.
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130s Unpacking r-cran-abind (1.4-5-2) ...
130s Selecting previously unselected package r-bioc-s4arrays.
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130s Selecting previously unselected package r-cran-littler.
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131s Unpacking r-cran-restfulr (0.0.15-1) ...
131s Selecting previously unselected package r-bioc-rtracklayer.
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131s Selecting previously unselected package r-bioc-bsgenome.
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131s Selecting previously unselected package r-cran-survival.
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131s Selecting previously unselected package r-bioc-genefilter.
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131s Selecting previously unselected package r-bioc-genomicfeatures.
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131s Unpacking r-bioc-genomicfeatures (1.54.1+dfsg-1) ...
131s Selecting previously unselected package r-cran-statmod.
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133s Setting up libgraphite2-3:arm64 (1.3.14-2) ...
133s Setting up libpixman-1-0:arm64 (0.42.2-1) ...
133s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ...
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133s 
133s Creating config file /etc/papersize with new version
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133s Setting up libdatrie1:arm64 (0.2.13-3) ...
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133s Setting up unzip (6.0-28ubuntu3) ...
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134s Setting up cpp-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
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136s Setting up g++-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
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136s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
136s Setting up gfortran-13-aarch64-linux-gnu (13.2.0-17ubuntu2) ...
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136s Setting up r-base-core (4.3.2-1build1) ...
136s 
136s Creating config file /etc/R/Renviron with new version
136s Setting up r-cran-crayon (1.5.2-1) ...
136s Setting up r-cran-futile.options (1.0.1-3build1) ...
136s Setting up r-cran-lattice (0.22-5-1) ...
136s Setting up r-cran-formatr (1.14-1) ...
136s Setting up r-cran-xml (3.99-0.16.1-1) ...
136s Setting up r-cran-statmod (1.5.0-1) ...
136s Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
136s Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ...
136s Setting up r-cran-r6 (2.5.1-1) ...
136s Setting up r-cran-magrittr (2.0.3-1) ...
136s Setting up r-cran-rappdirs (0.3.3-1) ...
136s Setting up r-cran-filelock (1.0.3-1) ...
136s Setting up r-bioc-genomeinfodbdata (1.2.11-2) ...
136s Setting up r-cran-littler (0.3.19-1) ...
136s Setting up r-cran-bh (1.84.0-1) ...
136s Setting up r-cran-curl (5.2.0+dfsg-1) ...
136s Setting up r-cran-codetools (0.2-19-1) ...
136s Setting up r-bioc-biocgenerics (0.48.1-2) ...
136s Setting up r-cran-rlang (1.1.3-1) ...
136s Setting up r-cran-matrixstats (1.2.0-1) ...
136s Setting up r-bioc-matrixgenerics (1.14.0-1) ...
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136s Setting up r-cran-plogr (0.2.0-3build1) ...
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136s Setting up r-cran-mime (0.12-1) ...
136s Setting up r-cran-generics (0.1.3-1) ...
136s Setting up r-cran-abind (1.4-5-2) ...
136s Setting up r-cran-digest (0.6.34-1) ...
136s Setting up r-cran-yaml (2.3.8-1) ...
136s Setting up r-cran-lambda.r (1.2.4-2build1) ...
136s Setting up r-cran-dbi (1.2.2-1) ...
136s Setting up r-cran-prettyunits (1.2.0-1) ...
136s Setting up r-cran-fansi (1.0.5-1) ...
136s Setting up r-cran-snow (1:0.4.4-2) ...
136s Setting up r-cran-glue (1.7.0-1) ...
136s Setting up r-cran-bit (4.0.5-1) ...
136s Setting up r-cran-xtable (1:1.8-4-2) ...
136s Setting up r-cran-cli (3.6.2-1) ...
136s Setting up gfortran (4:13.2.0-7ubuntu1) ...
136s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
136s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
136s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
136s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
136s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
136s Setting up r-cran-bitops (1.0-7-1) ...
136s Setting up r-cran-bit64 (4.0.5-1) ...
136s Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ...
136s Setting up r-cran-askpass (1.2.0-1) ...
136s Setting up r-cran-fastmap (1.1.1-1) ...
136s Setting up r-cran-png (0.1-8-1) ...
136s Setting up r-bioc-biobase (2.62.0-1) ...
136s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
136s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
136s Setting up r-cran-utf8 (1.2.4-1) ...
136s Setting up r-cran-stringi (1.8.3-1) ...
136s Setting up r-cran-cpp11 (0.4.7-1) ...
136s Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ...
136s Setting up r-cran-runit (0.4.32-3) ...
136s Setting up r-cran-futile.logger (1.4.3-4build1) ...
136s Setting up r-bioc-limma (3.58.1+dfsg-1) ...
136s Setting up r-cran-matrix (1.6-5-1) ...
136s Setting up g++ (4:13.2.0-7ubuntu1) ...
136s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
136s Setting up r-cran-cachem (1.0.8-1) ...
136s Setting up build-essential (12.10ubuntu1) ...
136s Setting up r-bioc-iranges (2.36.0-1) ...
136s Setting up r-cran-rjson (0.2.21-1) ...
136s Setting up r-cran-rcurl (1.98-1.14+dfsg-1build1) ...
136s Setting up r-cran-restfulr (0.0.15-1) ...
136s Setting up r-cran-vctrs (0.6.5-1) ...
136s Setting up r-cran-pillar (1.9.0+dfsg-1) ...
136s Setting up r-cran-openssl (2.1.1+dfsg-2) ...
136s Setting up r-base-dev (4.3.2-1build1) ...
136s Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ...
136s Setting up r-cran-stringr (1.5.1-1) ...
136s Setting up r-bioc-biocparallel (1.36.0-1) ...
136s Setting up r-bioc-rhtslib (2.4.1+dfsg-1) ...
136s Setting up r-cran-xml2 (1.3.6-1) ...
136s Setting up r-cran-tibble (3.2.1+dfsg-2) ...
136s Setting up r-cran-survival (3.5-8-1) ...
136s Setting up r-bioc-biocio (1.12.0+dfsg-1) ...
136s Setting up r-cran-tidyselect (1.2.0+dfsg-1) ...
136s Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ...
136s Setting up r-cran-httr (1.4.7+dfsg-1) ...
136s Setting up r-cran-hms (1.1.3-1) ...
136s Setting up r-cran-memoise (2.0.1-1) ...
136s Setting up r-cran-purrr (1.0.2-1) ...
136s Setting up r-cran-blob (1.2.4-1) ...
136s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
136s Setting up r-bioc-xvector (0.42.0-1) ...
136s Setting up r-cran-dplyr (1.1.4-1) ...
136s Setting up r-cran-rsqlite (2.3.4-1) ...
136s Setting up r-cran-progress (1.2.3-1) ...
136s Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ...
136s Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ...
136s Setting up r-bioc-biostrings (2.70.2+dfsg-1) ...
136s Setting up r-cran-tidyr (1.3.1-1) ...
136s Setting up r-bioc-rsamtools (2.18.0+dfsg-1) ...
136s Setting up r-cran-dbplyr (2.4.0+dfsg-1) ...
136s Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ...
136s Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ...
136s Setting up r-bioc-biocfilecache (2.10.1+dfsg-1) ...
136s Setting up r-bioc-keggrest (1.42.0+dfsg-1) ...
136s Setting up r-bioc-annotationdbi (1.64.1-1) ...
136s Setting up r-bioc-annotate (1.80.0+dfsg-1) ...
136s Setting up r-bioc-biomart (2.58.2+dfsg-1) ...
136s Setting up r-bioc-genefilter (1.84.0-1) ...
136s Setting up r-bioc-genomicalignments (1.38.2-1) ...
136s Setting up r-bioc-org.hs.eg.db (3.18.0-1) ...
136s Setting up r-bioc-rtracklayer (1.62.0-1) ...
136s Setting up r-bioc-genomicfeatures (1.54.1+dfsg-1) ...
136s Setting up r-bioc-bsgenome (1.70.2-1) ...
136s Setting up autopkgtest-satdep (0) ...
136s Processing triggers for man-db (2.12.0-3) ...
137s Processing triggers for install-info (7.1-3) ...
137s Processing triggers for libc-bin (2.39-0ubuntu2) ...
148s (Reading database ... 105237 files and directories currently installed.)
148s Removing autopkgtest-satdep (0) ...
149s autopkgtest [13:57:25]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
149s autopkgtest [13:57:25]: test pkg-r-autopkgtest: [-----------------------
149s Test: Try to load the R library rtracklayer
149s 
149s R version 4.3.2 (2023-10-31) -- "Eye Holes"
149s Copyright (C) 2023 The R Foundation for Statistical Computing
149s Platform: aarch64-unknown-linux-gnu (64-bit)
149s 
149s R is free software and comes with ABSOLUTELY NO WARRANTY.
149s You are welcome to redistribute it under certain conditions.
149s Type 'license()' or 'licence()' for distribution details.
149s 
149s R is a collaborative project with many contributors.
149s Type 'contributors()' for more information and
149s 'citation()' on how to cite R or R packages in publications.
149s 
149s Type 'demo()' for some demos, 'help()' for on-line help, or
149s 'help.start()' for an HTML browser interface to help.
149s Type 'q()' to quit R.
149s 
150s > library('rtracklayer')
150s Loading required package: GenomicRanges
150s Loading required package: stats4
150s Loading required package: BiocGenerics
150s 
150s Attaching package: ‘BiocGenerics’
150s 
150s The following objects are masked from ‘package:stats’:
150s 
150s     IQR, mad, sd, var, xtabs
150s 
150s The following objects are masked from ‘package:base’:
150s 
150s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
150s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
150s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
150s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
150s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
150s     table, tapply, union, unique, unsplit, which.max, which.min
150s 
150s Loading required package: S4Vectors
150s 
150s Attaching package: ‘S4Vectors’
150s 
150s The following object is masked from ‘package:utils’:
150s 
150s     findMatches
150s 
150s The following objects are masked from ‘package:base’:
150s 
150s     expand.grid, I, unname
150s 
150s Loading required package: IRanges
151s Loading required package: GenomeInfoDb
159s > 
159s > 
159s Other tests are currently unsupported!
159s They will be progressively added.
160s autopkgtest [13:57:36]: test pkg-r-autopkgtest: -----------------------]
160s autopkgtest [13:57:36]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
160s pkg-r-autopkgtest    PASS
160s autopkgtest [13:57:36]: @@@@@@@@@@@@@@@@@@@@ summary
160s pkg-r-autopkgtest    PASS
165s Creating nova instance adt-noble-arm64-r-bioc-rtracklayer-20240316-135456-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...