0s autopkgtest [17:04:41]: starting date and time: 2024-04-09 17:04:41+0000 0s autopkgtest [17:04:41]: git checkout: 43bc6cdf gitlab-ci: do not include the salsa pipeline 0s autopkgtest [17:04:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._gxeriu6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:curl --apt-upgrade r-bioc-variantannotation --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=curl/8.5.0-2ubuntu10 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-24.secgroup --name adt-noble-amd64-r-bioc-variantannotation-20240409-170428-juju-7f2275-prod-proposed-migration-environment-2-84dc7795-9d5d-42a8-882a-82bb09dece97 --image adt/ubuntu-noble-amd64-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/ 276s autopkgtest [17:09:17]: testbed dpkg architecture: amd64 276s autopkgtest [17:09:17]: testbed apt version: 2.7.14build2 276s autopkgtest [17:09:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 277s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 277s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4796 B] 277s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [7716 B] 277s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [338 kB] 277s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [747 kB] 277s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [266 kB] 277s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [353 kB] 277s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 277s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [3680 B] 277s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [20.0 kB] 277s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 277s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [410 kB] 277s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [896 kB] 277s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 277s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [1076 B] 277s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [4760 B] 277s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 279s Fetched 3183 kB in 0s (7334 kB/s) 279s Reading package lists... 305s Reading package lists...Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 305s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 305s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 305s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 305s 305s Building dependency tree... 305s Reading state information... 305s Calculating upgrade... 305s The following packages will be upgraded: 305s curl libcurl3t64-gnutls libcurl4t64 305s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Need to get 900 kB of archives. 305s After this operation, 0 B of additional disk space will be used. 305s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 curl amd64 8.5.0-2ubuntu10 [227 kB] 305s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcurl4t64 amd64 8.5.0-2ubuntu10 [340 kB] 305s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcurl3t64-gnutls amd64 8.5.0-2ubuntu10 [333 kB] 305s Fetched 900 kB in 0s (27.8 MB/s) 305s (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 ... 73681 files and directories currently installed.) 305s Preparing to unpack .../curl_8.5.0-2ubuntu10_amd64.deb ... 305s Unpacking curl (8.5.0-2ubuntu10) over (8.5.0-2ubuntu9) ... 305s Preparing to unpack .../libcurl4t64_8.5.0-2ubuntu10_amd64.deb ... 305s Unpacking libcurl4t64:amd64 (8.5.0-2ubuntu10) over (8.5.0-2ubuntu9) ... 305s Preparing to unpack .../libcurl3t64-gnutls_8.5.0-2ubuntu10_amd64.deb ... 305s Unpacking libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10) over (8.5.0-2ubuntu9) ... 305s Setting up libcurl4t64:amd64 (8.5.0-2ubuntu10) ... 305s Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10) ... 305s Setting up curl (8.5.0-2ubuntu10) ... 305s Processing triggers for man-db (2.12.0-4build1) ... 305s Processing triggers for libc-bin (2.39-0ubuntu8) ... 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s Calculating upgrade... 305s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Reading package lists... 305s Building dependency tree... 305s Reading state information... 305s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 305s Reading package lists... 306s autopkgtest [17:09:47]: testbed running kernel: Linux 6.8.0-22-generic #22-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 4 22:30:32 UTC 2024 306s autopkgtest [17:09:47]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-variantannotation 315s Get:1 http://ftpmaster.internal/ubuntu noble-updates/universe r-bioc-variantannotation 1.48.1-1 (dsc) [2587 B] 315s Get:2 http://ftpmaster.internal/ubuntu noble-updates/universe r-bioc-variantannotation 1.48.1-1 (tar) [1887 kB] 315s Get:3 http://ftpmaster.internal/ubuntu noble-updates/universe r-bioc-variantannotation 1.48.1-1 (diff) [7900 B] 315s gpgv: Signature made Fri Dec 1 09:59:29 2023 UTC 315s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 315s gpgv: issuer "tillea@rki.de" 315s gpgv: Can't check signature: No public key 315s dpkg-source: warning: cannot verify inline signature for ./r-bioc-variantannotation_1.48.1-1.dsc: no acceptable signature found 315s autopkgtest [17:09:50]: testing package r-bioc-variantannotation version 1.48.1-1 316s autopkgtest [17:09:57]: build not needed 372s autopkgtest [17:10:53]: test pkg-r-autopkgtest: preparing testbed 391s Reading package lists... 391s Building dependency tree... 391s Reading state information... 392s Starting pkgProblemResolver with broken count: 0 392s Starting 2 pkgProblemResolver with broken count: 0 392s Done 392s The following additional packages will be installed: 392s build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu 392s dctrl-tools fontconfig fonts-font-awesome fonts-glyphicons-halflings 392s fonts-lmodern fonts-mathjax g++ g++-13 g++-13-x86-64-linux-gnu 392s g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu 392s gcc-x86-64-linux-gnu gfortran gfortran-13 gfortran-13-x86-64-linux-gnu 392s gfortran-x86-64-linux-gnu icu-devtools javascript-common libasan8 libatomic1 392s libbibtex-parser-perl libblas-dev libblas3 libboost-dev libboost1.83-dev 392s libbz2-dev libcairo2 libcc1-0 libdatrie1 libgcc-13-dev libgfortran-13-dev 392s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 392s libicu-dev libio-string-perl libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev 392s libjpeg8-dev libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim 392s libjs-highlight.js libjs-jquery libjs-jquery-datatables 392s libjs-jquery-datatables-extensions libjs-jquery-selectize.js libjs-jquery-ui 392s libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr 392s libjs-popper.js libjs-prettify libjs-sifter.js 392s libjs-twitter-bootstrap-datepicker libkpathsea6 liblapack-dev liblapack3 392s liblatex-tounicode-perl liblsan0 liblua5.4-0 liblzma-dev libmpc3 392s libncurses-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 392s libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev 392s libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libptexenc1 392s libquadmath0 libreadline-dev libsm6 libstdc++-13-dev libsynctex2 libtcl8.6 392s libteckit0 libtexlua53-5 libthai-data libthai0 libtk8.6 libtsan2 libubsan1 392s libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxrender1 392s libxss1 libxt6t64 libzzip-0-13t64 node-bootstrap-sass node-html5shiv 392s node-normalize.css pandoc pandoc-data pkg-config pkg-r-autopkgtest pkgconf 392s pkgconf-bin r-base-core r-base-dev r-bioc-annotationdbi r-bioc-annotationhub 392s r-bioc-biobase r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio 392s r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart 392s r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb 392s r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures 392s r-bioc-genomicranges r-bioc-interactivedisplaybase r-bioc-iranges 392s r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools 392s r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-snpstats 392s r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-variantannotation 392s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc 392s r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops 392s r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli 392s r-cran-codetools r-cran-colorspace r-cran-commonmark r-cran-cpp11 392s r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr 392s r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate 392s r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-fontawesome 392s r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options 392s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr 392s r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr 392s r-cran-isoband r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling 392s r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle 392s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 392s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 392s r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 392s r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr 392s r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl 392s r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite 392s r-cran-runit r-cran-sass r-cran-scales r-cran-shiny r-cran-snow 392s r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys 392s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 392s r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xml 392s r-cran-xml2 r-cran-xtable r-cran-yaml t1utils tex-common texlive-base 392s texlive-bibtex-extra texlive-binaries texlive-latex-base unzip x11-common 392s xdg-utils zip zlib1g-dev 392s Suggested packages: 392s cpp-doc gcc-13-locales cpp-13-doc debtags g++-multilib g++-13-multilib 392s gcc-13-doc gcc-multilib manpages-dev autoconf automake libtool flex bison 392s gdb gcc-doc gcc-13-multilib gdb-x86-64-linux-gnu gfortran-multilib 392s gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev apache2 392s | lighttpd | httpd liblapack-doc libboost-doc libboost1.83-doc 392s libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev 392s libboost-context1.83-dev libboost-contract1.83-dev 392s libboost-coroutine1.83-dev libboost-date-time1.83-dev 392s libboost-exception1.83-dev libboost-fiber1.83-dev 392s libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev 392s libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev 392s libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev 392s libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev 392s libboost-numpy1.83-dev libboost-program-options1.83-dev 392s libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev 392s libboost-serialization1.83-dev libboost-stacktrace1.83-dev 392s libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev 392s libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev 392s libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev 392s icu-doc libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix 392s libjs-mathjax-doc liblzma-doc ncurses-doc readline-doc libstdc++-13-doc 392s tcl8.6 tk8.6 nodejs texlive-latex-recommended texlive-xetex texlive-luatex 392s pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin groff 392s ghc php python ruby libjs-katex citation-style-language-styles elpa-ess 392s r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-plain-generic 392s texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texinfo 392s r-bioc-go.db r-bioc-org.hs.eg.db r-bioc-graph r-bioc-ensembldb 392s r-bioc-experimenthub r-bioc-all r-cran-testthat r-bioc-affy r-bioc-deseq2 392s r-bioc-annotate r-cran-foreach r-cran-bbmisc r-cran-doparallel 392s r-bioc-shortread r-cran-batchtools r-cran-data.table r-cran-mockery 392s r-cran-webmockr r-bioc-hdf5array r-bioc-genefilter r-cran-lobstr 392s r-bioc-delayedmatrixstats r-cran-r.utils r-bioc-edger 392s r-bioc-annotationfilter r-cran-markdown r-bioc-gviz r-bioc-dexseq 392s r-bioc-sparsematrixstats r-bioc-limma r-cran-hexbin r-bioc-rhdf5 392s r-cran-roxygen2 r-cran-ff r-cran-covr r-cran-kernsmooth r-cran-kernlab 392s r-cran-mvtnorm r-cran-vcd r-cran-shinyjs r-cran-jpeg r-cran-viridis 392s r-cran-rstudioapi r-cran-rmysql r-cran-lubridate r-cran-magick r-cran-sf 392s r-cran-getopt r-cran-formattable r-cran-nanotime r-cran-palmerpenguins 392s r-cran-units r-cran-vdiffr r-cran-inline r-cran-rmpi r-cran-rlecuyer 392s r-cran-spelling r-cran-bench r-cran-brio r-cran-callr r-cran-here 392s r-cran-pkgbuild r-cran-pkgload r-cran-plm r-cran-zoo debhelper ghostscript 392s gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 392s hintview texlive-latex-base-doc wp2latex 392s Recommended packages: 392s bzip2-doc node-jquery libpng-tools r-recommended r-doc-html r-cran-testthat 392s r-cran-remotes r-cran-downlit r-cran-rstudioapi r-cran-miniui 392s r-cran-rsconnect r-cran-testit r-cran-tufte r-cran-webshot r-cran-thematic 392s r-cran-callr r-cran-covr r-cran-mockery r-cran-processx r-cran-ps 392s r-cran-rprojroot r-cran-whoami r-cran-bench r-cran-brio r-cran-decor 392s r-cran-desc r-cran-lobstr r-cran-spelling r-cran-webutils r-cran-rpostgresql 392s r-cran-broom r-cran-rmysql r-cran-future w3m | www-browser r-cran-unitizer 392s r-cran-rsvg r-cran-pkgload r-cran-hexbin r-cran-hmisc r-cran-mapproj 392s r-cran-maps r-cran-multcomp r-cran-profvis r-cran-quantreg r-cran-ragg 392s r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-waldo 392s r-cran-cairo r-cran-markdown r-cran-jpeg r-cran-readr r-cran-r.rsp 392s r-cran-gridsvg r-cran-magick r-cran-reticulate r-cran-rgl r-cran-tikzdevice 392s node-highlight.js r-cran-lintr r-cran-tidyverse r-cran-r.devices 392s r-cran-sodium r-cran-lubridate r-cran-usethis r-cran-dygraphs r-cran-dbitest 392s r-cran-gert r-cran-gh r-cran-rvest r-cran-dichromat r-cran-data.table 392s r-cran-mockr r-cran-formattable r-cran-pkgdown r-cran-zeallot r-cran-renv 392s lmodern dvisvgm libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl 392s x11-utils x11-xserver-utils 392s The following NEW packages will be installed: 392s autopkgtest-satdep build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu 392s cpp-x86-64-linux-gnu dctrl-tools fontconfig fonts-font-awesome 392s fonts-glyphicons-halflings fonts-lmodern fonts-mathjax g++ g++-13 392s g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13 gcc-13-base 392s gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13 392s gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools 392s javascript-common libasan8 libatomic1 libbibtex-parser-perl libblas-dev 392s libblas3 libboost-dev libboost1.83-dev libbz2-dev libcairo2 libcc1-0 392s libdatrie1 libgcc-13-dev libgfortran-13-dev libgfortran5 libgomp1 392s libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libio-string-perl 392s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-bootstrap 392s libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery 392s libjs-jquery-datatables libjs-jquery-datatables-extensions 392s libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr 392s libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js 392s libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker 392s libkpathsea6 liblapack-dev liblapack3 liblatex-tounicode-perl liblsan0 392s liblua5.4-0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0 392s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 392s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 392s libpng-dev libpotrace0 libptexenc1 libquadmath0 libreadline-dev libsm6 392s libstdc++-13-dev libsynctex2 libtcl8.6 libteckit0 libtexlua53-5 libthai-data 392s libthai0 libtk8.6 libtsan2 libubsan1 libxaw7 libxcb-render0 libxcb-shm0 392s libxft2 libxi6 libxmu6 libxrender1 libxss1 libxt6t64 libzzip-0-13t64 392s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 392s pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 392s r-bioc-annotationdbi r-bioc-annotationhub r-bioc-biobase 392s r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel 392s r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart r-bioc-biostrings 392s r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb 392s r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures 392s r-bioc-genomicranges r-bioc-interactivedisplaybase r-bioc-iranges 392s r-bioc-keggrest r-bioc-matrixgenerics r-bioc-rhtslib r-bioc-rsamtools 392s r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-snpstats 392s r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-variantannotation 392s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc 392s r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops 392s r-cran-blob r-cran-bookdown r-cran-bslib r-cran-cachem r-cran-cli 392s r-cran-codetools r-cran-colorspace r-cran-commonmark r-cran-cpp11 392s r-cran-crayon r-cran-crosstalk r-cran-curl r-cran-dbi r-cran-dbplyr 392s r-cran-digest r-cran-dplyr r-cran-dt r-cran-ellipsis r-cran-evaluate 392s r-cran-fansi r-cran-farver r-cran-fastmap r-cran-filelock r-cran-fontawesome 392s r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options 392s r-cran-generics r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-highr 392s r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-httpuv r-cran-httr 392s r-cran-isoband r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling 392s r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle 392s r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats 392s r-cran-memoise r-cran-mgcv r-cran-mime r-cran-munsell r-cran-nlme 392s r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr 392s r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr 392s r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl 392s r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rsqlite 392s r-cran-runit r-cran-sass r-cran-scales r-cran-shiny r-cran-snow 392s r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-survival r-cran-sys 392s r-cran-tibble r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 392s r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-xfun r-cran-xml 392s r-cran-xml2 r-cran-xtable r-cran-yaml t1utils tex-common texlive-base 392s texlive-bibtex-extra texlive-binaries texlive-latex-base unzip x11-common 392s xdg-utils zip zlib1g-dev 392s 0 upgraded, 282 newly installed, 0 to remove and 0 not upgraded. 392s Need to get 454 MB/454 MB of archives. 392s After this operation, 1375 MB of additional disk space will be used. 392s Get:1 /tmp/autopkgtest.dfOKim/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [776 B] 392s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-23ubuntu3 [48.6 kB] 392s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 392s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 392s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [11.2 MB] 392s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-23ubuntu3 [1034 B] 392s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 392s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 392s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240330-1ubuntu2 [47.7 kB] 392s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240330-1ubuntu2 [147 kB] 392s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240330-1ubuntu2 [29.1 kB] 392s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240330-1ubuntu2 [10.4 kB] 392s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240330-1ubuntu2 [3020 kB] 392s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240330-1ubuntu2 [1310 kB] 392s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240330-1ubuntu2 [2731 kB] 392s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240330-1ubuntu2 [1172 kB] 392s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240330-1ubuntu2 [1629 kB] 392s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240330-1ubuntu2 [155 kB] 392s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu3 [2687 kB] 392s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [21.9 MB] 393s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-23ubuntu3 [479 kB] 393s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 393s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 393s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu3 [2398 kB] 393s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [12.5 MB] 393s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-23ubuntu3 [14.5 kB] 393s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 393s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 393s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 393s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB] 393s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] 393s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 393s Get:33 http://ftpmaster.internal/ubuntu noble/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 393s Get:34 http://ftpmaster.internal/ubuntu noble/universe amd64 fonts-lmodern all 2.005-1 [4799 kB] 393s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 393s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240330-1ubuntu2 [930 kB] 393s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-23ubuntu3 [942 kB] 393s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [11.6 MB] 393s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-23ubuntu3 [10.9 kB] 393s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B] 393s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B] 393s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] 393s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 javascript-common all 11+nmu1 [5936 B] 393s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 393s Get:45 http://ftpmaster.internal/ubuntu noble/universe amd64 liblatex-tounicode-perl all 0.54-2 [29.0 kB] 393s Get:46 http://ftpmaster.internal/ubuntu noble/universe amd64 libbibtex-parser-perl all 1.04+dfsg-1 [16.7 kB] 393s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 393s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB] 393s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libboost1.83-dev amd64 1.83.0-2.1ubuntu3 [10.7 MB] 393s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libboost-dev amd64 1.83.0.1ubuntu2 [4308 B] 393s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] 393s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 393s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 393s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 393s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 393s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-3 [566 kB] 393s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 393s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 393s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 393s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 393s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 393s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] 393s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] 393s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 393s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 393s Get:66 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 393s Get:67 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB] 393s Get:68 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB] 393s Get:69 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-d3 all 3.5.17-4 [132 kB] 393s Get:70 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 393s Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 393s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 393s Get:73 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 393s Get:74 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-datatables-extensions all 0.0+git20150910.28fd64e+dfsg-5 [648 kB] 393s Get:75 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 393s Get:76 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B] 393s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 393s Get:78 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 393s Get:79 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB] 393s Get:80 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB] 393s Get:81 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB] 393s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libkpathsea6 amd64 2023.20230311.66589-9build3 [63.0 kB] 393s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 393s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB] 393s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 liblua5.4-0 amd64 5.4.6-3build2 [166 kB] 393s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] 393s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 393s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 393s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1build1 [231 kB] 393s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1build1 [42.5 kB] 393s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1build1 [28.8 kB] 393s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 393s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 393s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB] 393s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB] 393s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B] 393s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB] 393s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] 393s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB] 393s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-5build1 [264 kB] 393s Get:101 http://ftpmaster.internal/ubuntu noble/universe amd64 libpotrace0 amd64 1.16-2 [17.2 kB] 393s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libptexenc1 amd64 2023.20230311.66589-9build3 [40.4 kB] 393s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-4build1 [167 kB] 393s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 393s Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libsynctex2 amd64 2023.20230311.66589-9build3 [59.6 kB] 393s Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 393s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB] 393s Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libtexlua53-5 amd64 2023.20230311.66589-9build3 [123 kB] 393s Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 393s Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 393s Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 393s Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 393s Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB] 393s Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libxaw7 amd64 2:1.0.14-1build2 [187 kB] 393s Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libxi6 amd64 2:1.8.1-1 [32.4 kB] 393s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB] 393s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB] 393s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 393s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 393s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 pandoc-data all 3.1.3-1 [92.4 kB] 393s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 pandoc amd64 3.1.3+ds-2 [26.9 MB] 394s Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] 394s Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] 394s Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B] 394s Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 394s Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 394s Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 394s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.3-2build2 [27.1 MB] 394s Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [176 kB] 394s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.3-2build2 [4334 B] 394s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 394s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocgenerics all 0.48.1-2 [595 kB] 394s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biobase amd64 2.62.0-1 [2136 kB] 394s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2056 kB] 394s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-iranges amd64 2.36.0-1 [2252 kB] 394s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB] 394s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit amd64 4.0.5-1 [1063 kB] 394s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit64 amd64 4.0.5-1 [465 kB] 394s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB] 394s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 394s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 394s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 394s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 394s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB] 394s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB] 394s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB] 394s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB] 394s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 394s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB] 394s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB] 394s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rsqlite amd64 2.3.4-1 [1364 kB] 394s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-curl amd64 5.2.0+dfsg-1build2 [177 kB] 394s Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB] 394s Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mime amd64 0.12-1 [35.8 kB] 394s Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sys amd64 3.4.2-1 [44.6 kB] 394s Get:156 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-askpass amd64 1.2.0-1 [24.6 kB] 394s Get:157 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-openssl amd64 2.1.1+dfsg-2build2 [402 kB] 394s Get:158 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 394s Get:159 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] 394s Get:160 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB] 394s Get:161 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9596 B] 394s Get:162 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-xvector amd64 0.42.0-1 [621 kB] 394s Get:163 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB] 394s Get:164 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1build2 [793 kB] 394s Get:165 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB] 394s Get:166 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3886 kB] 394s Get:167 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB] 394s Get:168 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.6 MB] 394s Get:169 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB] 394s Get:170 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-annotationdbi all 1.64.1-1 [4897 kB] 394s Get:171 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 394s Get:172 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 394s Get:173 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 394s Get:174 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 394s Get:175 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 394s Get:176 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 394s Get:177 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB] 394s Get:178 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyselect amd64 1.2.0+dfsg-1 [218 kB] 394s Get:179 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dplyr amd64 1.1.4-1 [1515 kB] 394s Get:180 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-purrr amd64 1.0.2-1 [502 kB] 394s Get:181 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringi amd64 1.8.3-1 [873 kB] 394s Get:182 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB] 394s Get:183 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB] 394s Get:184 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbplyr all 2.4.0+dfsg-1 [1172 kB] 394s Get:185 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB] 395s Get:186 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocfilecache all 2.10.1+dfsg-1 [300 kB] 395s Get:187 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB] 395s Get:188 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocversion all 3.18.1-1 [11.0 kB] 395s Get:189 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB] 395s Get:190 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-yaml amd64 2.3.8-1 [108 kB] 395s Get:191 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB] 395s Get:192 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgkitten all 0.2.3-1 [25.1 kB] 395s Get:193 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcpp amd64 1.0.12-1 [1981 kB] 395s Get:194 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-later amd64 1.3.2+dfsg-1 [123 kB] 395s Get:195 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-promises amd64 1.2.1+dfsg-1 [284 kB] 395s Get:196 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-httpuv amd64 1.6.14+dfsg-1build2 [510 kB] 395s Get:197 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB] 395s Get:198 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB] 395s Get:199 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-digest amd64 0.6.34-1 [186 kB] 395s Get:200 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ellipsis amd64 0.3.2-2 [35.6 kB] 395s Get:201 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-htmltools amd64 0.5.7-1 [369 kB] 395s Get:202 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fontawesome all 0.5.2-1 [1300 kB] 395s Get:203 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB] 395s Get:204 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-commonmark amd64 1.9.1-1 [131 kB] 395s Get:205 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB] 395s Get:206 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fs amd64 1.6.3+dfsg-1build2 [229 kB] 395s Get:207 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sass amd64 0.4.8+dfsg-1 [996 kB] 395s Get:208 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bslib all 0.6.1+dfsg-1 [5138 kB] 395s Get:209 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 395s Get:210 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-shiny all 1.8.0+dfsg-1 [2762 kB] 395s Get:211 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-evaluate all 0.23-1 [90.2 kB] 395s Get:212 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xfun amd64 0.41+dfsg-1 [415 kB] 395s Get:213 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-highr all 0.10+dfsg-1 [38.3 kB] 395s Get:214 http://ftpmaster.internal/ubuntu noble/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 395s Get:215 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-knitr all 1.45+dfsg-1 [917 kB] 395s Get:216 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tinytex all 0.49-1 [141 kB] 395s Get:217 http://ftpmaster.internal/ubuntu noble/universe amd64 libjs-modernizr all 2.6.2+ds1-5 [48.3 kB] 395s Get:218 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rmarkdown all 2.25+dfsg-3 [1481 kB] 395s Get:219 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-htmlwidgets all 1.6.4+dfsg-1 [123 kB] 395s Get:220 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lazyeval amd64 0.2.2-1build1 [144 kB] 395s Get:221 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crosstalk all 1.2.1+dfsg-1 [177 kB] 395s Get:222 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dt all 0.31+dfsg-1 [265 kB] 395s Get:223 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-interactivedisplaybase all 1.40.0+dfsg-1 [30.4 kB] 395s Get:224 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-annotationhub all 3.10.0+dfsg-1 [454 kB] 395s Get:225 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocio all 1.12.0+dfsg-1 [213 kB] 395s Get:226 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-formatr all 1.14-1 [152 kB] 395s Get:227 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB] 395s Get:228 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB] 395s Get:229 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB] 395s Get:230 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB] 395s Get:231 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB] 395s Get:232 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bh all 1.84.0-1 [5962 B] 395s Get:233 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocparallel amd64 1.36.0-1 [1347 kB] 395s Get:234 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bookdown all 0.37+dfsg-1 [1408 kB] 395s Get:235 http://ftpmaster.internal/ubuntu noble/universe amd64 tex-common all 6.18 [32.8 kB] 395s Get:236 http://ftpmaster.internal/ubuntu noble/main amd64 t1utils amd64 1.41-4build2 [61.3 kB] 395s Get:237 http://ftpmaster.internal/ubuntu noble/universe amd64 texlive-binaries amd64 2023.20230311.66589-9build3 [8529 kB] 395s Get:238 http://ftpmaster.internal/ubuntu noble/universe amd64 texlive-base all 2023.20240207-1 [21.7 MB] 395s Get:239 http://ftpmaster.internal/ubuntu noble/universe amd64 texlive-latex-base all 2023.20240207-1 [1238 kB] 395s Get:240 http://ftpmaster.internal/ubuntu noble/universe amd64 texlive-bibtex-extra all 2023.20240207-1 [79.1 MB] 396s Get:241 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocstyle all 2.30.0+dfsg-1 [451 kB] 396s Get:242 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xml amd64 3.99-0.16.1-1 [1733 kB] 396s Get:243 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-hms all 1.1.3-1 [96.5 kB] 396s Get:244 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB] 396s Get:245 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB] 396s Get:246 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xml2 amd64 1.3.6-1 [322 kB] 396s Get:247 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biomart all 2.58.2+dfsg-1 [433 kB] 396s Get:248 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1823 kB] 396s Get:249 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-3build2 [1361 kB] 396s Get:250 http://ftpmaster.internal/ubuntu noble-updates/universe amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1 [3640 kB] 396s Get:251 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixstats amd64 1.2.0-1 [488 kB] 396s Get:252 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB] 396s Get:253 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 396s Get:254 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 396s Get:255 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB] 396s Get:256 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [501 kB] 396s Get:257 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1195 kB] 396s Get:258 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1787 kB] 396s Get:259 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1134 kB] 396s Get:260 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2133 kB] 396s Get:261 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rjson amd64 0.2.21-1 [143 kB] 396s Get:262 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB] 396s Get:263 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5108 kB] 396s Get:264 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-bsgenome all 1.70.2-1 [6975 kB] 396s Get:265 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicfeatures all 1.54.3+dfsg-1 [1823 kB] 396s Get:266 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] 396s Get:267 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-snpstats amd64 1.52.0+dfsg-1 [7242 kB] 396s Get:268 http://ftpmaster.internal/ubuntu noble-updates/universe amd64 r-bioc-variantannotation amd64 1.48.1-1 [3527 kB] 396s Get:269 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 396s Get:270 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB] 396s Get:271 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 396s Get:272 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 396s Get:273 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] 396s Get:274 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] 396s Get:275 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 396s Get:276 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 396s Get:277 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB] 396s Get:278 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 396s Get:279 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 396s Get:280 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 396s Get:281 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 396s Get:282 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-runit all 0.4.33-1 [377 kB] 404s Preconfiguring packages ... 404s Fetched 454 MB in 4s (110 MB/s) 404s Selecting previously unselected package gcc-13-base:amd64. 404s (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 ... 73681 files and directories currently installed.) 404s Preparing to unpack .../000-gcc-13-base_13.2.0-23ubuntu3_amd64.deb ... 404s Unpacking gcc-13-base:amd64 (13.2.0-23ubuntu3) ... 404s Selecting previously unselected package libisl23:amd64. 404s Preparing to unpack .../001-libisl23_0.26-3_amd64.deb ... 404s Unpacking libisl23:amd64 (0.26-3) ... 404s Selecting previously unselected package libmpc3:amd64. 404s Preparing to unpack .../002-libmpc3_1.3.1-1_amd64.deb ... 404s Unpacking libmpc3:amd64 (1.3.1-1) ... 404s Selecting previously unselected package cpp-13-x86-64-linux-gnu. 404s Preparing to unpack .../003-cpp-13-x86-64-linux-gnu_13.2.0-23ubuntu3_amd64.deb ... 404s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu3) ... 404s Selecting previously unselected package cpp-13. 404s Preparing to unpack .../004-cpp-13_13.2.0-23ubuntu3_amd64.deb ... 404s Unpacking cpp-13 (13.2.0-23ubuntu3) ... 404s Selecting previously unselected package cpp-x86-64-linux-gnu. 404s Preparing to unpack .../005-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 404s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 404s Selecting previously unselected package cpp. 404s Preparing to unpack .../006-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ... 404s Unpacking cpp (4:13.2.0-7ubuntu1) ... 404s Selecting previously unselected package libcc1-0:amd64. 404s Preparing to unpack .../007-libcc1-0_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking libcc1-0:amd64 (14-20240330-1ubuntu2) ... 404s Selecting previously unselected package libgomp1:amd64. 404s Preparing to unpack .../008-libgomp1_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking libgomp1:amd64 (14-20240330-1ubuntu2) ... 404s Selecting previously unselected package libitm1:amd64. 404s Preparing to unpack .../009-libitm1_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking libitm1:amd64 (14-20240330-1ubuntu2) ... 404s Selecting previously unselected package libatomic1:amd64. 404s Preparing to unpack .../010-libatomic1_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking libatomic1:amd64 (14-20240330-1ubuntu2) ... 404s Selecting previously unselected package libasan8:amd64. 404s Preparing to unpack .../011-libasan8_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking libasan8:amd64 (14-20240330-1ubuntu2) ... 404s Selecting previously unselected package liblsan0:amd64. 404s Preparing to unpack .../012-liblsan0_14-20240330-1ubuntu2_amd64.deb ... 404s Unpacking 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previously unselected package libjs-microplugin.js. 404s Preparing to unpack .../074-libjs-microplugin.js_0.0.3+dfsg-1.1_all.deb ... 404s Unpacking libjs-microplugin.js (0.0.3+dfsg-1.1) ... 404s Selecting previously unselected package libjs-jquery-selectize.js. 404s Preparing to unpack .../075-libjs-jquery-selectize.js_0.12.6+dfsg-1.1_all.deb ... 404s Unpacking libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ... 404s Selecting previously unselected package libjs-jquery-ui. 404s Preparing to unpack .../076-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 404s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 404s Selecting previously unselected package libjs-json. 404s Preparing to unpack .../077-libjs-json_0~20221030+~1.0.8-1_all.deb ... 404s Unpacking libjs-json (0~20221030+~1.0.8-1) ... 404s Selecting previously unselected package libjs-lunr. 404s Preparing to unpack .../078-libjs-lunr_2.3.9~dfsg-2_all.deb ... 404s Unpacking libjs-lunr (2.3.9~dfsg-2) ... 404s Selecting previously unselected package 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404s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 404s Selecting previously unselected package libxt6t64:amd64. 404s Preparing to unpack .../110-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 404s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 404s Selecting previously unselected package libxmu6:amd64. 404s Preparing to unpack .../111-libxmu6_2%3a1.1.3-3build2_amd64.deb ... 404s Unpacking libxmu6:amd64 (2:1.1.3-3build2) ... 404s Selecting previously unselected package libxaw7:amd64. 404s Preparing to unpack .../112-libxaw7_2%3a1.0.14-1build2_amd64.deb ... 404s Unpacking libxaw7:amd64 (2:1.0.14-1build2) ... 404s Selecting previously unselected package libxi6:amd64. 404s Preparing to unpack .../113-libxi6_2%3a1.8.1-1_amd64.deb ... 404s Unpacking libxi6:amd64 (2:1.8.1-1) ... 405s Selecting previously unselected package libzzip-0-13t64:amd64. 405s Preparing to unpack .../114-libzzip-0-13t64_0.13.72+dfsg.1-1.2build1_amd64.deb ... 405s Unpacking libzzip-0-13t64:amd64 (0.13.72+dfsg.1-1.2build1) ... 405s Selecting previously unselected package node-bootstrap-sass. 405s Preparing to unpack .../115-node-bootstrap-sass_3.4.3-2_all.deb ... 405s Unpacking node-bootstrap-sass (3.4.3-2) ... 405s Selecting previously unselected package node-html5shiv. 405s Preparing to unpack .../116-node-html5shiv_3.7.3+dfsg-5_all.deb ... 405s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 405s Selecting previously unselected package node-normalize.css. 405s Preparing to unpack .../117-node-normalize.css_8.0.1-5_all.deb ... 405s Unpacking node-normalize.css (8.0.1-5) ... 405s Selecting previously unselected package pandoc-data. 405s Preparing to unpack .../118-pandoc-data_3.1.3-1_all.deb ... 405s Unpacking pandoc-data (3.1.3-1) ... 405s Selecting previously unselected package pandoc. 405s Preparing to unpack .../119-pandoc_3.1.3+ds-2_amd64.deb ... 405s Unpacking pandoc (3.1.3+ds-2) ... 405s Selecting previously unselected package pkgconf-bin. 405s Preparing to unpack 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.../126-r-base-core_4.3.3-2build2_amd64.deb ... 406s Unpacking r-base-core (4.3.3-2build2) ... 406s Selecting previously unselected package liblzma-dev:amd64. 406s Preparing to unpack .../127-liblzma-dev_5.6.1+really5.4.5-1_amd64.deb ... 406s Unpacking liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... 406s Selecting previously unselected package r-base-dev. 406s Preparing to unpack .../128-r-base-dev_4.3.3-2build2_all.deb ... 406s Unpacking r-base-dev (4.3.3-2build2) ... 406s Selecting previously unselected package pkg-r-autopkgtest. 406s Preparing to unpack .../129-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 406s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 406s Selecting previously unselected package r-bioc-biocgenerics. 406s Preparing to unpack .../130-r-bioc-biocgenerics_0.48.1-2_all.deb ... 406s Unpacking r-bioc-biocgenerics (0.48.1-2) ... 406s Selecting previously unselected package r-bioc-biobase. 406s Preparing to unpack .../131-r-bioc-biobase_2.62.0-1_amd64.deb ... 406s Unpacking r-bioc-biobase (2.62.0-1) ... 406s Selecting previously unselected package r-bioc-s4vectors. 406s Preparing to unpack .../132-r-bioc-s4vectors_0.40.2+dfsg-1_amd64.deb ... 406s Unpacking r-bioc-s4vectors (0.40.2+dfsg-1) ... 406s Selecting previously unselected package r-bioc-iranges. 406s Preparing to unpack .../133-r-bioc-iranges_2.36.0-1_amd64.deb ... 406s Unpacking r-bioc-iranges (2.36.0-1) ... 406s Selecting previously unselected package r-cran-dbi. 406s Preparing to unpack .../134-r-cran-dbi_1.2.2-1_all.deb ... 406s Unpacking r-cran-dbi (1.2.2-1) ... 406s Selecting previously unselected package r-cran-bit. 406s Preparing to unpack .../135-r-cran-bit_4.0.5-1_amd64.deb ... 406s Unpacking r-cran-bit (4.0.5-1) ... 406s Selecting previously unselected package r-cran-bit64. 406s Preparing to unpack .../136-r-cran-bit64_4.0.5-1_amd64.deb ... 406s Unpacking r-cran-bit64 (4.0.5-1) ... 406s Selecting previously unselected package r-cran-rlang. 406s Preparing to unpack .../137-r-cran-rlang_1.1.3-1_amd64.deb ... 406s Unpacking r-cran-rlang (1.1.3-1) ... 406s Selecting previously unselected package r-cran-cli. 406s Preparing to unpack .../138-r-cran-cli_3.6.2-1_amd64.deb ... 406s Unpacking r-cran-cli (3.6.2-1) ... 406s Selecting previously unselected package r-cran-glue. 406s Preparing to unpack .../139-r-cran-glue_1.7.0-1_amd64.deb ... 406s Unpacking r-cran-glue (1.7.0-1) ... 406s Selecting previously unselected package r-cran-lifecycle. 406s Preparing to unpack .../140-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 406s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 406s Selecting previously unselected package r-cran-vctrs. 406s Preparing to unpack .../141-r-cran-vctrs_0.6.5-1_amd64.deb ... 406s Unpacking r-cran-vctrs (0.6.5-1) ... 406s Selecting previously unselected package r-cran-blob. 406s Preparing to unpack .../142-r-cran-blob_1.2.4-1_all.deb ... 406s Unpacking r-cran-blob (1.2.4-1) ... 407s Selecting previously unselected package r-cran-fastmap. 407s Preparing to unpack .../143-r-cran-fastmap_1.1.1-1_amd64.deb ... 407s Unpacking r-cran-fastmap (1.1.1-1) ... 407s Selecting previously unselected package r-cran-cachem. 407s Preparing to unpack .../144-r-cran-cachem_1.0.8-1_amd64.deb ... 407s Unpacking r-cran-cachem (1.0.8-1) ... 407s Selecting previously unselected package r-cran-memoise. 407s Preparing to unpack .../145-r-cran-memoise_2.0.1-1_all.deb ... 407s Unpacking r-cran-memoise (2.0.1-1) ... 407s Selecting previously unselected package r-cran-pkgconfig. 407s Preparing to unpack .../146-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 407s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 407s Selecting previously unselected package r-cran-plogr. 407s Preparing to unpack .../147-r-cran-plogr_0.2.0-3build1_all.deb ... 407s Unpacking r-cran-plogr (0.2.0-3build1) ... 407s Selecting previously unselected package r-cran-cpp11. 407s Preparing to unpack .../148-r-cran-cpp11_0.4.7-1_all.deb ... 407s Unpacking r-cran-cpp11 (0.4.7-1) ... 407s Selecting previously unselected package r-cran-rsqlite. 407s Preparing to unpack .../149-r-cran-rsqlite_2.3.4-1_amd64.deb ... 407s Unpacking r-cran-rsqlite (2.3.4-1) ... 407s Selecting previously unselected package r-cran-curl. 407s Preparing to unpack .../150-r-cran-curl_5.2.0+dfsg-1build2_amd64.deb ... 407s Unpacking r-cran-curl (5.2.0+dfsg-1build2) ... 407s Selecting previously unselected package r-cran-jsonlite. 407s Preparing to unpack .../151-r-cran-jsonlite_1.8.8+dfsg-1_amd64.deb ... 407s Unpacking r-cran-jsonlite (1.8.8+dfsg-1) ... 407s Selecting previously unselected package r-cran-mime. 407s Preparing to unpack .../152-r-cran-mime_0.12-1_amd64.deb ... 407s Unpacking r-cran-mime (0.12-1) ... 407s Selecting previously unselected package r-cran-sys. 407s Preparing to unpack .../153-r-cran-sys_3.4.2-1_amd64.deb ... 407s Unpacking r-cran-sys (3.4.2-1) ... 407s Selecting previously unselected package r-cran-askpass. 407s Preparing to unpack .../154-r-cran-askpass_1.2.0-1_amd64.deb ... 407s Unpacking r-cran-askpass (1.2.0-1) ... 407s Selecting previously unselected package r-cran-openssl. 407s Preparing to unpack .../155-r-cran-openssl_2.1.1+dfsg-2build2_amd64.deb ... 407s Unpacking r-cran-openssl (2.1.1+dfsg-2build2) ... 407s Selecting previously unselected package r-cran-r6. 407s Preparing to unpack .../156-r-cran-r6_2.5.1-1_all.deb ... 407s Unpacking r-cran-r6 (2.5.1-1) ... 407s Selecting previously unselected package r-cran-httr. 407s Preparing to unpack .../157-r-cran-httr_1.4.7+dfsg-1_all.deb ... 407s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 407s Selecting previously unselected package r-cran-png. 407s Preparing to unpack .../158-r-cran-png_0.1-8-1build2_amd64.deb ... 407s Unpacking r-cran-png (0.1-8-1build2) ... 407s Selecting previously unselected package r-bioc-zlibbioc. 407s Preparing to unpack .../159-r-bioc-zlibbioc_1.48.0+dfsg-1_all.deb ... 407s Unpacking r-bioc-zlibbioc (1.48.0+dfsg-1) ... 407s Selecting previously unselected package r-bioc-xvector. 407s Preparing to unpack .../160-r-bioc-xvector_0.42.0-1_amd64.deb ... 407s Unpacking r-bioc-xvector (0.42.0-1) ... 407s Selecting previously unselected package r-cran-bitops. 407s Preparing to unpack .../161-r-cran-bitops_1.0-7-1_amd64.deb ... 407s Unpacking r-cran-bitops (1.0-7-1) ... 407s Selecting previously unselected package r-cran-rcurl. 407s Preparing to unpack .../162-r-cran-rcurl_1.98-1.14+dfsg-1build2_amd64.deb ... 407s Unpacking r-cran-rcurl (1.98-1.14+dfsg-1build2) ... 407s Selecting previously unselected package r-bioc-genomeinfodbdata. 407s Preparing to unpack .../163-r-bioc-genomeinfodbdata_1.2.11-2_all.deb ... 407s Unpacking r-bioc-genomeinfodbdata (1.2.11-2) ... 407s Selecting previously unselected package r-bioc-genomeinfodb. 407s Preparing to unpack .../164-r-bioc-genomeinfodb_1.38.6+dfsg-1_all.deb ... 407s Unpacking r-bioc-genomeinfodb (1.38.6+dfsg-1) ... 407s Selecting previously unselected package r-cran-crayon. 407s Preparing to unpack .../165-r-cran-crayon_1.5.2-1_all.deb ... 407s Unpacking r-cran-crayon (1.5.2-1) ... 407s Selecting previously unselected package r-bioc-biostrings. 407s Preparing to unpack .../166-r-bioc-biostrings_2.70.2+dfsg-1_amd64.deb ... 407s Unpacking r-bioc-biostrings (2.70.2+dfsg-1) ... 408s Selecting previously unselected package r-bioc-keggrest. 408s Preparing to unpack .../167-r-bioc-keggrest_1.42.0+dfsg-1_all.deb ... 408s Unpacking r-bioc-keggrest (1.42.0+dfsg-1) ... 408s Selecting previously unselected package r-bioc-annotationdbi. 408s Preparing to unpack .../168-r-bioc-annotationdbi_1.64.1-1_all.deb ... 408s Unpacking r-bioc-annotationdbi (1.64.1-1) ... 408s Selecting previously unselected package r-cran-generics. 408s Preparing to unpack .../169-r-cran-generics_0.1.3-1_all.deb ... 408s Unpacking r-cran-generics (0.1.3-1) ... 408s Selecting previously unselected package r-cran-magrittr. 408s Preparing to unpack .../170-r-cran-magrittr_2.0.3-1_amd64.deb ... 408s Unpacking r-cran-magrittr (2.0.3-1) ... 408s Selecting previously unselected package r-cran-fansi. 408s Preparing to unpack .../171-r-cran-fansi_1.0.5-1_amd64.deb ... 408s Unpacking r-cran-fansi (1.0.5-1) ... 408s Selecting previously unselected package r-cran-utf8. 408s Preparing to unpack .../172-r-cran-utf8_1.2.4-1_amd64.deb ... 408s Unpacking r-cran-utf8 (1.2.4-1) ... 408s Selecting previously unselected package r-cran-pillar. 408s Preparing to unpack .../173-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 408s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 408s Selecting previously unselected package r-cran-tibble. 408s Preparing to unpack .../174-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 408s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 408s Selecting previously unselected package r-cran-withr. 408s Preparing to unpack .../175-r-cran-withr_2.5.0-1_all.deb ... 408s Unpacking r-cran-withr (2.5.0-1) ... 408s Selecting previously unselected package r-cran-tidyselect. 408s Preparing to unpack .../176-r-cran-tidyselect_1.2.0+dfsg-1_amd64.deb ... 408s Unpacking r-cran-tidyselect (1.2.0+dfsg-1) ... 408s Selecting previously unselected package r-cran-dplyr. 408s Preparing to unpack .../177-r-cran-dplyr_1.1.4-1_amd64.deb ... 408s Unpacking r-cran-dplyr (1.1.4-1) ... 408s Selecting previously unselected package r-cran-purrr. 408s Preparing to unpack .../178-r-cran-purrr_1.0.2-1_amd64.deb ... 408s Unpacking r-cran-purrr (1.0.2-1) ... 408s Selecting previously unselected package r-cran-stringi. 408s Preparing to unpack .../179-r-cran-stringi_1.8.3-1_amd64.deb ... 408s Unpacking r-cran-stringi (1.8.3-1) ... 408s Selecting previously unselected package r-cran-stringr. 408s Preparing to unpack .../180-r-cran-stringr_1.5.1-1_all.deb ... 408s Unpacking r-cran-stringr (1.5.1-1) ... 408s Selecting previously unselected package r-cran-tidyr. 408s Preparing to unpack .../181-r-cran-tidyr_1.3.1-1_amd64.deb ... 408s Unpacking r-cran-tidyr (1.3.1-1) ... 408s Selecting previously unselected package r-cran-dbplyr. 408s Preparing to unpack .../182-r-cran-dbplyr_2.4.0+dfsg-1_all.deb ... 408s Unpacking r-cran-dbplyr (2.4.0+dfsg-1) ... 408s Selecting previously unselected package r-cran-filelock. 408s Preparing to unpack .../183-r-cran-filelock_1.0.3-1_amd64.deb ... 408s Unpacking r-cran-filelock (1.0.3-1) ... 408s Selecting previously unselected package r-bioc-biocfilecache. 408s Preparing to unpack .../184-r-bioc-biocfilecache_2.10.1+dfsg-1_all.deb ... 408s Unpacking r-bioc-biocfilecache (2.10.1+dfsg-1) ... 408s Selecting previously unselected package r-cran-biocmanager. 408s Preparing to unpack .../185-r-cran-biocmanager_1.30.22+dfsg-2_all.deb ... 408s Unpacking r-cran-biocmanager (1.30.22+dfsg-2) ... 408s Selecting previously unselected package r-bioc-biocversion. 408s Preparing to unpack .../186-r-bioc-biocversion_3.18.1-1_all.deb ... 408s Unpacking r-bioc-biocversion (3.18.1-1) ... 408s Selecting previously unselected package r-cran-rappdirs. 408s Preparing to unpack .../187-r-cran-rappdirs_0.3.3-1_amd64.deb ... 408s Unpacking r-cran-rappdirs (0.3.3-1) ... 408s Selecting previously unselected package r-cran-yaml. 408s Preparing to unpack .../188-r-cran-yaml_2.3.8-1_amd64.deb ... 408s Unpacking r-cran-yaml (2.3.8-1) ... 409s Selecting previously unselected package r-cran-littler. 409s Preparing to unpack .../189-r-cran-littler_0.3.19-1_amd64.deb ... 409s Unpacking r-cran-littler (0.3.19-1) ... 409s Selecting previously unselected package r-cran-pkgkitten. 409s Preparing to unpack .../190-r-cran-pkgkitten_0.2.3-1_all.deb ... 409s Unpacking r-cran-pkgkitten (0.2.3-1) ... 409s Selecting previously unselected package r-cran-rcpp. 409s Preparing to unpack .../191-r-cran-rcpp_1.0.12-1_amd64.deb ... 409s Unpacking r-cran-rcpp (1.0.12-1) ... 409s Selecting previously unselected package r-cran-later. 409s Preparing to unpack .../192-r-cran-later_1.3.2+dfsg-1_amd64.deb ... 409s Unpacking r-cran-later (1.3.2+dfsg-1) ... 409s Selecting previously unselected package r-cran-promises. 409s Preparing to unpack .../193-r-cran-promises_1.2.1+dfsg-1_amd64.deb ... 409s Unpacking r-cran-promises (1.2.1+dfsg-1) ... 409s Selecting previously unselected package r-cran-httpuv. 409s Preparing to unpack .../194-r-cran-httpuv_1.6.14+dfsg-1build2_amd64.deb ... 409s Unpacking r-cran-httpuv (1.6.14+dfsg-1build2) ... 409s Selecting previously unselected package r-cran-xtable. 409s Preparing to unpack .../195-r-cran-xtable_1%3a1.8-4-2_all.deb ... 409s Unpacking r-cran-xtable (1:1.8-4-2) ... 409s Selecting previously unselected package r-cran-base64enc. 409s Preparing to unpack .../196-r-cran-base64enc_0.1-3-3_amd64.deb ... 409s Unpacking r-cran-base64enc (0.1-3-3) ... 409s Selecting previously unselected package r-cran-digest. 409s Preparing to unpack .../197-r-cran-digest_0.6.34-1_amd64.deb ... 409s Unpacking r-cran-digest (0.6.34-1) ... 409s Selecting previously unselected package r-cran-ellipsis. 409s Preparing to unpack .../198-r-cran-ellipsis_0.3.2-2_amd64.deb ... 409s Unpacking r-cran-ellipsis (0.3.2-2) ... 409s Selecting previously unselected package r-cran-htmltools. 409s Preparing to unpack .../199-r-cran-htmltools_0.5.7-1_amd64.deb ... 409s Unpacking r-cran-htmltools (0.5.7-1) ... 409s Selecting previously unselected package r-cran-fontawesome. 409s Preparing to unpack .../200-r-cran-fontawesome_0.5.2-1_all.deb ... 409s Unpacking r-cran-fontawesome (0.5.2-1) ... 409s Selecting previously unselected package r-cran-sourcetools. 409s Preparing to unpack .../201-r-cran-sourcetools_0.1.7-1-1_amd64.deb ... 409s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 409s Selecting previously unselected package r-cran-commonmark. 409s Preparing to unpack .../202-r-cran-commonmark_1.9.1-1_amd64.deb ... 409s Unpacking r-cran-commonmark (1.9.1-1) ... 409s Selecting previously unselected package r-cran-jquerylib. 409s Preparing to unpack .../203-r-cran-jquerylib_0.1.4+dfsg-4_all.deb ... 409s Unpacking r-cran-jquerylib (0.1.4+dfsg-4) ... 409s Selecting previously unselected package r-cran-fs. 409s Preparing to unpack .../204-r-cran-fs_1.6.3+dfsg-1build2_amd64.deb ... 409s Unpacking r-cran-fs (1.6.3+dfsg-1build2) ... 409s Selecting previously unselected package r-cran-sass. 409s Preparing to unpack .../205-r-cran-sass_0.4.8+dfsg-1_amd64.deb ... 409s Unpacking r-cran-sass (0.4.8+dfsg-1) ... 409s Selecting previously unselected package r-cran-bslib. 409s Preparing to unpack .../206-r-cran-bslib_0.6.1+dfsg-1_all.deb ... 409s Unpacking r-cran-bslib (0.6.1+dfsg-1) ... 409s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 409s Preparing to unpack .../207-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 409s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 409s Selecting previously unselected package r-cran-shiny. 409s Preparing to unpack .../208-r-cran-shiny_1.8.0+dfsg-1_all.deb ... 409s Unpacking r-cran-shiny (1.8.0+dfsg-1) ... 410s Selecting previously unselected package r-cran-evaluate. 410s Preparing to unpack .../209-r-cran-evaluate_0.23-1_all.deb ... 410s Unpacking r-cran-evaluate (0.23-1) ... 410s Selecting previously unselected package r-cran-xfun. 410s Preparing to unpack .../210-r-cran-xfun_0.41+dfsg-1_amd64.deb ... 410s Unpacking r-cran-xfun (0.41+dfsg-1) ... 410s Selecting previously unselected package r-cran-highr. 410s Preparing to unpack .../211-r-cran-highr_0.10+dfsg-1_all.deb ... 410s Unpacking r-cran-highr (0.10+dfsg-1) ... 410s Selecting previously unselected package libjs-mathjax. 410s Preparing to unpack .../212-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 410s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 410s Selecting previously unselected package r-cran-knitr. 410s Preparing to unpack .../213-r-cran-knitr_1.45+dfsg-1_all.deb ... 410s Unpacking r-cran-knitr (1.45+dfsg-1) ... 410s Selecting previously unselected package r-cran-tinytex. 410s Preparing to unpack .../214-r-cran-tinytex_0.49-1_all.deb ... 410s Unpacking r-cran-tinytex (0.49-1) ... 410s Selecting previously unselected package libjs-modernizr. 410s Preparing to unpack .../215-libjs-modernizr_2.6.2+ds1-5_all.deb ... 410s Unpacking libjs-modernizr (2.6.2+ds1-5) ... 410s Selecting previously unselected package r-cran-rmarkdown. 410s Preparing to unpack .../216-r-cran-rmarkdown_2.25+dfsg-3_all.deb ... 410s Unpacking r-cran-rmarkdown (2.25+dfsg-3) ... 411s Selecting previously unselected package r-cran-htmlwidgets. 411s Preparing to unpack .../217-r-cran-htmlwidgets_1.6.4+dfsg-1_all.deb ... 411s Unpacking r-cran-htmlwidgets (1.6.4+dfsg-1) ... 411s Selecting previously unselected package r-cran-lazyeval. 411s Preparing to unpack .../218-r-cran-lazyeval_0.2.2-1build1_amd64.deb ... 411s Unpacking r-cran-lazyeval (0.2.2-1build1) ... 411s Selecting previously unselected package r-cran-crosstalk. 411s Preparing to unpack .../219-r-cran-crosstalk_1.2.1+dfsg-1_all.deb ... 411s Unpacking r-cran-crosstalk (1.2.1+dfsg-1) ... 411s Selecting previously unselected package r-cran-dt. 411s Preparing to unpack .../220-r-cran-dt_0.31+dfsg-1_all.deb ... 411s Unpacking r-cran-dt (0.31+dfsg-1) ... 411s Selecting previously unselected package r-bioc-interactivedisplaybase. 411s Preparing to unpack .../221-r-bioc-interactivedisplaybase_1.40.0+dfsg-1_all.deb ... 411s Unpacking r-bioc-interactivedisplaybase (1.40.0+dfsg-1) ... 411s Selecting previously unselected package r-bioc-annotationhub. 411s Preparing to unpack .../222-r-bioc-annotationhub_3.10.0+dfsg-1_all.deb ... 411s Unpacking r-bioc-annotationhub (3.10.0+dfsg-1) ... 411s Selecting previously unselected package r-bioc-biocio. 411s Preparing to unpack .../223-r-bioc-biocio_1.12.0+dfsg-1_all.deb ... 411s Unpacking r-bioc-biocio (1.12.0+dfsg-1) ... 411s Selecting previously unselected package r-cran-formatr. 411s Preparing to unpack .../224-r-cran-formatr_1.14-1_all.deb ... 411s Unpacking r-cran-formatr (1.14-1) ... 411s Selecting previously unselected package r-cran-lambda.r. 411s Preparing to unpack .../225-r-cran-lambda.r_1.2.4-2build1_all.deb ... 411s Unpacking r-cran-lambda.r (1.2.4-2build1) ... 411s Selecting previously unselected package r-cran-futile.options. 411s Preparing to unpack .../226-r-cran-futile.options_1.0.1-3build1_all.deb ... 411s Unpacking r-cran-futile.options (1.0.1-3build1) ... 411s Selecting previously unselected package r-cran-futile.logger. 411s Preparing to unpack .../227-r-cran-futile.logger_1.4.3-4build1_all.deb ... 411s Unpacking r-cran-futile.logger (1.4.3-4build1) ... 411s Selecting previously unselected package r-cran-snow. 411s Preparing to unpack .../228-r-cran-snow_1%3a0.4.4-2_all.deb ... 411s Unpacking r-cran-snow (1:0.4.4-2) ... 411s Selecting previously unselected package r-cran-codetools. 411s Preparing to unpack .../229-r-cran-codetools_0.2-19-1_all.deb ... 411s Unpacking r-cran-codetools (0.2-19-1) ... 411s Selecting previously unselected package r-cran-bh. 411s Preparing to unpack .../230-r-cran-bh_1.84.0-1_all.deb ... 411s Unpacking r-cran-bh (1.84.0-1) ... 411s Selecting previously unselected package r-bioc-biocparallel. 411s Preparing to unpack .../231-r-bioc-biocparallel_1.36.0-1_amd64.deb ... 411s Unpacking r-bioc-biocparallel (1.36.0-1) ... 411s Selecting previously unselected package r-cran-bookdown. 411s Preparing to unpack .../232-r-cran-bookdown_0.37+dfsg-1_all.deb ... 411s Unpacking r-cran-bookdown (0.37+dfsg-1) ... 411s Selecting previously unselected package tex-common. 411s Preparing to unpack .../233-tex-common_6.18_all.deb ... 411s Unpacking tex-common (6.18) ... 411s Selecting previously unselected package t1utils. 411s Preparing to unpack .../234-t1utils_1.41-4build2_amd64.deb ... 411s Unpacking t1utils (1.41-4build2) ... 411s Selecting previously unselected package texlive-binaries. 411s Preparing to unpack .../235-texlive-binaries_2023.20230311.66589-9build3_amd64.deb ... 411s Unpacking texlive-binaries (2023.20230311.66589-9build3) ... 411s Selecting previously unselected package texlive-base. 411s Preparing to unpack .../236-texlive-base_2023.20240207-1_all.deb ... 411s Unpacking texlive-base (2023.20240207-1) ... 413s Selecting previously unselected package texlive-latex-base. 413s Preparing to unpack .../237-texlive-latex-base_2023.20240207-1_all.deb ... 413s Unpacking texlive-latex-base (2023.20240207-1) ... 413s Selecting previously unselected package texlive-bibtex-extra. 413s Preparing to unpack .../238-texlive-bibtex-extra_2023.20240207-1_all.deb ... 413s Unpacking texlive-bibtex-extra (2023.20240207-1) ... 415s Selecting previously unselected package r-bioc-biocstyle. 415s Preparing to unpack .../239-r-bioc-biocstyle_2.30.0+dfsg-1_all.deb ... 415s Unpacking r-bioc-biocstyle (2.30.0+dfsg-1) ... 415s Selecting previously unselected package r-cran-xml. 415s Preparing to unpack .../240-r-cran-xml_3.99-0.16.1-1_amd64.deb ... 415s Unpacking r-cran-xml (3.99-0.16.1-1) ... 415s Selecting previously unselected package r-cran-hms. 415s Preparing to unpack .../241-r-cran-hms_1.1.3-1_all.deb ... 415s Unpacking r-cran-hms (1.1.3-1) ... 415s Selecting previously unselected package r-cran-prettyunits. 415s Preparing to unpack .../242-r-cran-prettyunits_1.2.0-1_all.deb ... 415s Unpacking r-cran-prettyunits (1.2.0-1) ... 415s Selecting previously unselected package r-cran-progress. 415s Preparing to unpack .../243-r-cran-progress_1.2.3-1_all.deb ... 415s Unpacking r-cran-progress (1.2.3-1) ... 415s Selecting previously unselected package r-cran-xml2. 415s Preparing to unpack .../244-r-cran-xml2_1.3.6-1_amd64.deb ... 415s Unpacking r-cran-xml2 (1.3.6-1) ... 415s Selecting previously unselected package r-bioc-biomart. 415s Preparing to unpack .../245-r-bioc-biomart_2.58.2+dfsg-1_all.deb ... 415s Unpacking r-bioc-biomart (2.58.2+dfsg-1) ... 415s Selecting previously unselected package r-bioc-genomicranges. 415s Preparing to unpack .../246-r-bioc-genomicranges_1.54.1+dfsg-1_amd64.deb ... 415s Unpacking r-bioc-genomicranges (1.54.1+dfsg-1) ... 415s Selecting previously unselected package r-bioc-rhtslib. 415s Preparing to unpack .../247-r-bioc-rhtslib_2.4.1+dfsg-3build2_amd64.deb ... 415s Unpacking r-bioc-rhtslib (2.4.1+dfsg-3build2) ... 415s Selecting previously unselected package r-bioc-rsamtools. 415s Preparing to unpack .../248-r-bioc-rsamtools_2.18.0+dfsg-1_amd64.deb ... 415s Unpacking r-bioc-rsamtools (2.18.0+dfsg-1) ... 416s Selecting previously unselected package r-cran-matrixstats. 416s Preparing to unpack .../249-r-cran-matrixstats_1.2.0-1_amd64.deb ... 416s Unpacking r-cran-matrixstats (1.2.0-1) ... 416s Selecting previously unselected package r-bioc-matrixgenerics. 416s Preparing to unpack .../250-r-bioc-matrixgenerics_1.14.0-1_all.deb ... 416s Unpacking r-bioc-matrixgenerics (1.14.0-1) ... 416s Selecting previously unselected package r-cran-lattice. 416s Preparing to unpack .../251-r-cran-lattice_0.22-5-1_amd64.deb ... 416s Unpacking r-cran-lattice (0.22-5-1) ... 416s Selecting previously unselected package r-cran-matrix. 416s Preparing to unpack .../252-r-cran-matrix_1.6-5-1_amd64.deb ... 416s Unpacking r-cran-matrix (1.6-5-1) ... 416s Selecting previously unselected package r-cran-abind. 416s Preparing to unpack .../253-r-cran-abind_1.4-5-2_all.deb ... 416s Unpacking r-cran-abind (1.4-5-2) ... 416s Selecting previously unselected package r-bioc-s4arrays. 416s Preparing to unpack .../254-r-bioc-s4arrays_1.2.0+dfsg-1_amd64.deb ... 416s Unpacking r-bioc-s4arrays (1.2.0+dfsg-1) ... 416s Selecting previously unselected package r-bioc-sparsearray. 416s Preparing to unpack .../255-r-bioc-sparsearray_1.2.4+dfsg-1_amd64.deb ... 416s Unpacking r-bioc-sparsearray (1.2.4+dfsg-1) ... 416s Selecting previously unselected package r-bioc-delayedarray. 416s Preparing to unpack .../256-r-bioc-delayedarray_0.28.0+dfsg-1_amd64.deb ... 416s Unpacking r-bioc-delayedarray (0.28.0+dfsg-1) ... 416s Selecting previously unselected package r-bioc-summarizedexperiment. 416s Preparing to unpack .../257-r-bioc-summarizedexperiment_1.32.0+dfsg-1_all.deb ... 416s Unpacking r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... 416s Selecting previously unselected package r-bioc-genomicalignments. 416s Preparing to unpack .../258-r-bioc-genomicalignments_1.38.2-1_amd64.deb ... 416s Unpacking r-bioc-genomicalignments (1.38.2-1) ... 416s Selecting previously unselected package r-cran-rjson. 416s Preparing to unpack .../259-r-cran-rjson_0.2.21-1_amd64.deb ... 416s Unpacking r-cran-rjson (0.2.21-1) ... 416s Selecting previously unselected package r-cran-restfulr. 416s Preparing to unpack .../260-r-cran-restfulr_0.0.15-1_amd64.deb ... 416s Unpacking r-cran-restfulr (0.0.15-1) ... 416s Selecting previously unselected package r-bioc-rtracklayer. 416s Preparing to unpack .../261-r-bioc-rtracklayer_1.62.0-1_amd64.deb ... 416s Unpacking r-bioc-rtracklayer (1.62.0-1) ... 416s Selecting previously unselected package r-bioc-bsgenome. 416s Preparing to unpack .../262-r-bioc-bsgenome_1.70.2-1_all.deb ... 416s Unpacking r-bioc-bsgenome (1.70.2-1) ... 416s Selecting previously unselected package r-bioc-genomicfeatures. 416s Preparing to unpack .../263-r-bioc-genomicfeatures_1.54.3+dfsg-1_all.deb ... 416s Unpacking r-bioc-genomicfeatures (1.54.3+dfsg-1) ... 416s Selecting previously unselected package r-cran-survival. 416s Preparing to unpack .../264-r-cran-survival_3.5-8-1_amd64.deb ... 416s Unpacking r-cran-survival (3.5-8-1) ... 416s Selecting previously unselected package r-bioc-snpstats. 416s Preparing to unpack .../265-r-bioc-snpstats_1.52.0+dfsg-1_amd64.deb ... 416s Unpacking r-bioc-snpstats (1.52.0+dfsg-1) ... 416s Selecting previously unselected package r-bioc-variantannotation. 416s Preparing to unpack .../266-r-bioc-variantannotation_1.48.1-1_amd64.deb ... 416s Unpacking r-bioc-variantannotation (1.48.1-1) ... 416s Selecting previously unselected package r-cran-colorspace. 416s Preparing to unpack .../267-r-cran-colorspace_2.1-0+dfsg-1_amd64.deb ... 416s Unpacking r-cran-colorspace (2.1-0+dfsg-1) ... 417s Selecting previously unselected package r-cran-farver. 417s Preparing to unpack .../268-r-cran-farver_2.1.1-1_amd64.deb ... 417s Unpacking r-cran-farver (2.1.1-1) ... 417s Selecting previously unselected package r-cran-gtable. 417s Preparing to unpack .../269-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 417s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 417s Selecting previously unselected package r-cran-isoband. 417s Preparing to unpack .../270-r-cran-isoband_0.2.7-1_amd64.deb ... 417s Unpacking r-cran-isoband (0.2.7-1) ... 417s Selecting previously unselected package r-cran-mass. 417s Preparing to unpack .../271-r-cran-mass_7.3-60.0.1-1_amd64.deb ... 417s Unpacking r-cran-mass (7.3-60.0.1-1) ... 417s Selecting previously unselected package r-cran-nlme. 417s Preparing to unpack .../272-r-cran-nlme_3.1.164-1_amd64.deb ... 417s 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r-bioc-genomeinfodb (1.38.6+dfsg-1) ... 428s Setting up r-cran-httr (1.4.7+dfsg-1) ... 428s Setting up r-cran-hms (1.1.3-1) ... 428s Setting up r-cran-scales (1.3.0-1) ... 428s Setting up r-cran-memoise (2.0.1-1) ... 428s Setting up r-cran-promises (1.2.1+dfsg-1) ... 428s Setting up r-cran-purrr (1.0.2-1) ... 428s Setting up r-cran-blob (1.2.4-1) ... 428s Setting up r-cran-htmltools (0.5.7-1) ... 428s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 428s Setting up r-bioc-xvector (0.42.0-1) ... 428s Setting up r-cran-sass (0.4.8+dfsg-1) ... 428s Setting up r-cran-dplyr (1.1.4-1) ... 428s Setting up r-cran-rsqlite (2.3.4-1) ... 428s Setting up r-cran-progress (1.2.3-1) ... 428s Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ... 428s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 428s Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ... 428s Setting up r-cran-httpuv (1.6.14+dfsg-1build2) ... 428s Setting up r-bioc-biostrings (2.70.2+dfsg-1) ... 428s Setting up r-cran-fontawesome (0.5.2-1) ... 428s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ... 428s Setting up r-cran-bslib (0.6.1+dfsg-1) ... 428s Setting up r-cran-tidyr (1.3.1-1) ... 428s Setting up r-bioc-rsamtools (2.18.0+dfsg-1) ... 428s Setting up r-cran-dbplyr (2.4.0+dfsg-1) ... 428s Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ... 428s Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ... 428s Setting up r-bioc-biocfilecache (2.10.1+dfsg-1) ... 428s Setting up r-bioc-keggrest (1.42.0+dfsg-1) ... 428s Setting up r-bioc-annotationdbi (1.64.1-1) ... 428s Setting up r-cran-shiny (1.8.0+dfsg-1) ... 428s Setting up r-cran-rmarkdown (2.25+dfsg-3) ... 428s Setting up r-bioc-biomart (2.58.2+dfsg-1) ... 428s Setting up r-bioc-genomicalignments (1.38.2-1) ... 428s Setting up r-cran-bookdown (0.37+dfsg-1) ... 428s Setting up r-cran-crosstalk (1.2.1+dfsg-1) ... 428s Setting up r-bioc-rtracklayer (1.62.0-1) ... 428s Setting up r-bioc-genomicfeatures (1.54.3+dfsg-1) ... 428s Setting up r-cran-htmlwidgets (1.6.4+dfsg-1) ... 428s Setting up r-bioc-bsgenome (1.70.2-1) ... 428s Setting up r-bioc-biocstyle (2.30.0+dfsg-1) ... 428s Setting up r-cran-dt (0.31+dfsg-1) ... 428s Setting up r-bioc-variantannotation (1.48.1-1) ... 428s Setting up r-bioc-interactivedisplaybase (1.40.0+dfsg-1) ... 428s Setting up r-bioc-annotationhub (3.10.0+dfsg-1) ... 428s Setting up autopkgtest-satdep (0) ... 428s Processing triggers for man-db (2.12.0-4build1) ... 428s Processing triggers for install-info (7.1-3build2) ... 428s Processing triggers for libc-bin (2.39-0ubuntu8) ... 428s Processing triggers for tex-common (6.18) ... 428s Running updmap-sys. This may take some time... done. 428s Running mktexlsr /var/lib/texmf ... done. 428s Building format(s) --all. 468s This may take some time... done. 468s (Reading database ... 123552 files and directories currently installed.) 468s Removing autopkgtest-satdep (0) ... 468s autopkgtest [17:12:29]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 468s autopkgtest [17:12:29]: test pkg-r-autopkgtest: [----------------------- 468s Test: Try to load the R library VariantAnnotation 468s 468s R version 4.3.3 (2024-02-29) -- "Angel Food Cake" 468s Copyright (C) 2024 The R Foundation for Statistical Computing 468s Platform: x86_64-pc-linux-gnu (64-bit) 468s 468s R is free software and comes with ABSOLUTELY NO WARRANTY. 468s You are welcome to redistribute it under certain conditions. 468s Type 'license()' or 'licence()' for distribution details. 468s 468s R is a collaborative project with many contributors. 468s Type 'contributors()' for more information and 468s 'citation()' on how to cite R or R packages in publications. 468s 468s Type 'demo()' for some demos, 'help()' for on-line help, or 468s 'help.start()' for an HTML browser interface to help. 468s Type 'q()' to quit R. 468s 468s > library('VariantAnnotation') 468s Loading required package: BiocGenerics 468s 468s Attaching package: ‘BiocGenerics’ 468s 468s The following objects are masked from ‘package:stats’: 468s 468s IQR, mad, sd, var, xtabs 468s 468s The following objects are masked from ‘package:base’: 468s 468s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 468s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 468s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 468s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 468s Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, 468s table, tapply, union, unique, unsplit, which.max, which.min 468s 468s Loading required package: MatrixGenerics 468s Loading required package: matrixStats 468s 468s Attaching package: ‘MatrixGenerics’ 468s 468s The following objects are masked from ‘package:matrixStats’: 468s 468s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 468s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 468s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 468s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 468s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 468s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 468s colWeightedMeans, colWeightedMedians, colWeightedSds, 468s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 468s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 468s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 468s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 468s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 468s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 468s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 468s rowWeightedSds, rowWeightedVars 468s 468s Loading required package: GenomeInfoDb 468s Loading required package: S4Vectors 468s Loading required package: stats4 469s 469s Attaching package: ‘S4Vectors’ 469s 469s The following object is masked from ‘package:utils’: 469s 469s findMatches 469s 469s The following objects are masked from ‘package:base’: 469s 469s expand.grid, I, unname 469s 469s Loading required package: IRanges 470s Loading required package: GenomicRanges 470s Loading required package: SummarizedExperiment 470s Loading required package: Biobase 470s Welcome to Bioconductor 470s 470s Vignettes contain introductory material; view with 470s 'browseVignettes()'. To cite Bioconductor, see 470s 'citation("Biobase")', and for packages 'citation("pkgname")'. 470s 470s 470s Attaching package: ‘Biobase’ 470s 470s The following object is masked from ‘package:MatrixGenerics’: 470s 470s rowMedians 470s 470s The following objects are masked from ‘package:matrixStats’: 470s 470s anyMissing, rowMedians 470s 474s Loading required package: Rsamtools 474s Loading required package: Biostrings 474s Loading required package: XVector 474s 474s Attaching package: ‘Biostrings’ 474s 474s The following object is masked from ‘package:base’: 474s 474s strsplit 474s 482s > 482s > 482s 482s Attaching package: ‘VariantAnnotation’ 482s 482s The following object is masked from ‘package:base’: 482s 482s tabulate 482s 482s autopkgtest [17:12:40]: test pkg-r-autopkgtest: -----------------------] 482s Other tests are currently unsupported! 482s They will be progressively added. 482s pkg-r-autopkgtest PASS 482s autopkgtest [17:12:43]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 482s autopkgtest [17:12:43]: @@@@@@@@@@@@@@@@@@@@ summary 482s pkg-r-autopkgtest PASS 498s Creating nova instance adt-noble-amd64-r-bioc-variantannotation-20240409-170428-juju-7f2275-prod-proposed-migration-environment-2-84dc7795-9d5d-42a8-882a-82bb09dece97 from image adt/ubuntu-noble-amd64-server-20240409.img (UUID 3fc5ec4a-a752-4d16-a177-712062b74bd0)...