0s autopkgtest [11:12:24]: starting date and time: 2024-12-02 11:12:24+0000
  0s autopkgtest [11:12:24]: git checkout: be626eda Fix armhf LXD image generation for plucky
  0s autopkgtest [11:12:24]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dqf_i9jw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:hdf5,src:openmpi --apt-upgrade r-bioc-alabaster.base --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=hdf5/1.10.10+repack-5ubuntu1 openmpi/5.0.6-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-7.secgroup --name adt-plucky-amd64-r-bioc-alabaster.base-20241202-111223-juju-7f2275-prod-proposed-migration-environment-2-0239cf32-578d-448d-8ee9-912659c874f4 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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,keyserver.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/
351s autopkgtest [11:18:15]: testbed dpkg architecture: amd64
351s autopkgtest [11:18:15]: testbed apt version: 2.9.14ubuntu1
352s autopkgtest [11:18:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup
352s autopkgtest [11:18:16]: testbed release detected to be: None
352s autopkgtest [11:18:16]: updating testbed package index (apt update)
353s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
353s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
353s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
353s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
353s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.4 kB]
353s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B]
353s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [906 kB]
353s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.6 kB]
353s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [94.1 kB]
353s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [139 kB]
353s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB]
353s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B]
353s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB]
353s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [325 kB]
353s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6924 B]
353s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [22.7 kB]
354s Fetched 2546 kB in 1s (2810 kB/s)
355s Reading package lists...
355s Reading package lists...
355s Building dependency tree...
355s Reading state information...
355s Calculating upgrade...
356s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
356s Reading package lists...
356s Building dependency tree...
356s Reading state information...
356s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
356s autopkgtest [11:18:20]: upgrading testbed (apt dist-upgrade and autopurge)
356s Reading package lists...
357s Building dependency tree...
357s Reading state information...
357s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
357s Starting 2 pkgProblemResolver with broken count: 0
357s Done
357s Entering ResolveByKeep
357s 
358s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
358s Reading package lists...
358s Building dependency tree...
358s Reading state information...
358s Starting pkgProblemResolver with broken count: 0
358s Starting 2 pkgProblemResolver with broken count: 0
358s Done
359s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
361s autopkgtest [11:18:25]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
361s autopkgtest [11:18:25]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-alabaster.base
363s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-alabaster.base 1.4.2+ds-3 (dsc) [2319 B]
363s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-alabaster.base 1.4.2+ds-3 (tar) [133 kB]
363s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-alabaster.base 1.4.2+ds-3 (diff) [3896 B]
363s gpgv: Signature made Sat Aug 17 17:33:32 2024 UTC
363s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
363s gpgv: Can't check signature: No public key
363s dpkg-source: warning: cannot verify inline signature for ./r-bioc-alabaster.base_1.4.2+ds-3.dsc: no acceptable signature found
363s autopkgtest [11:18:27]: testing package r-bioc-alabaster.base version 1.4.2+ds-3
363s autopkgtest [11:18:27]: build not needed
365s autopkgtest [11:18:29]: test pkg-r-autopkgtest: preparing testbed
365s Reading package lists...
365s Building dependency tree...
365s Reading state information...
365s Starting pkgProblemResolver with broken count: 0
365s Starting 2 pkgProblemResolver with broken count: 0
365s Done
366s The following NEW packages will be installed:
366s   build-essential comerr-dev cpp cpp-14 cpp-14-x86-64-linux-gnu
366s   cpp-x86-64-linux-gnu dctrl-tools fontconfig fontconfig-config
366s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
366s   fonts-glyphicons-halflings fonts-lmodern fonts-mathjax g++ g++-14
366s   g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
366s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14
366s   gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu hdf5-helpers
366s   icu-devtools javascript-common krb5-multidev libaec-dev libaec0 libasan8
366s   libbibtex-parser-perl libblas-dev libblas3 libblosc1 libbrotli-dev
366s   libbz2-dev libcairo2 libcc1-0 libcurl4-openssl-dev libdatrie1 libdeflate-dev
366s   libdeflate0 libevent-2.1-7t64 libfontconfig1 libgcc-14-dev
366s   libgfortran-14-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64
366s   libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssrpc4t64
366s   libharfbuzz0b libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev
366s   libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64
366s   libhdf5-hl-fortran-100t64 libhwasan0 libice6 libicu-dev libidn2-dev
366s   libio-string-perl libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
366s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap libjs-bootstrap4
366s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
366s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
366s   libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr
366s   libjs-popper.js libjs-prettify libjs-sifter.js
366s   libjs-twitter-bootstrap-datepicker libkadm5clnt-mit12 libkadm5srv-mit12
366s   libkdb5-10t64 libkpathsea6 libkrb5-dev liblapack-dev liblapack3
366s   liblatex-tounicode-perl libldap-dev liblerc4 liblsan0 liblua5.4-0
366s   liblzma-dev libmpc3 libmpfi0 libncurses-dev libnghttp2-dev libp11-kit-dev
366s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
366s   libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
366s   libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libpsl-dev libptexenc1
366s   libquadmath0 libreadline-dev librtmp-dev libsharpyuv0 libsm6 libsnappy1v5
366s   libssh2-1-dev libssl-dev libstdc++-14-dev libsynctex2 libsz2 libtasn1-6-dev
366s   libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6
366s   libtirpc-dev libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libxaw7
366s   libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1
366s   libxss1 libxt6t64 libzstd-dev libzzip-0-13t64 littler nettle-dev
366s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
366s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
366s   r-bioc-alabaster.base r-bioc-alabaster.schemas r-bioc-biocgenerics
366s   r-bioc-biocstyle r-bioc-biocversion r-bioc-rhdf5 r-bioc-rhdf5filters
366s   r-bioc-rhdf5lib r-bioc-s4vectors r-cran-base64enc r-cran-biocmanager
366s   r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem r-cran-callr
366s   r-cran-cli r-cran-commonmark r-cran-crayon r-cran-desc r-cran-diffobj
366s   r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs
366s   r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-jquerylib
366s   r-cran-jsonlite r-cran-knitr r-cran-later r-cran-lattice r-cran-lifecycle
366s   r-cran-littler r-cran-magrittr r-cran-matrix r-cran-memoise r-cran-mime
366s   r-cran-pkgbuild r-cran-pkgkitten r-cran-pkgload r-cran-praise
366s   r-cran-processx r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs
366s   r-cran-rcpp r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-sass
366s   r-cran-shiny r-cran-sourcetools r-cran-testthat r-cran-tinytex r-cran-waldo
366s   r-cran-withr r-cran-xfun r-cran-xtable r-cran-yaml t1utils tex-common
366s   texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base unzip
366s   x11-common xdg-utils zip zlib1g-dev
366s 0 upgraded, 254 newly installed, 0 to remove and 0 not upgraded.
366s Need to get 354 MB of archives.
366s After this operation, 1122 MB of additional disk space will be used.
366s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
367s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
367s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB]
367s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B]
367s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B]
367s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB]
367s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB]
367s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
367s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB]
367s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB]
367s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB]
367s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB]
367s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB]
367s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB]
367s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB]
367s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB]
367s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB]
368s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB]
368s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B]
368s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B]
368s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB]
368s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB]
369s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB]
369s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B]
369s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B]
369s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
369s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB]
369s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
369s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
369s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
369s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
369s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
369s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
369s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
369s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lmodern all 2.005-1 [4799 kB]
369s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
369s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
369s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-8ubuntu1 [965 kB]
369s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [12.5 MB]
369s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-8ubuntu1 [11.9 kB]
369s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1022 B]
369s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.1.0-2ubuntu1 [1172 B]
369s Get:43 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 hdf5-helpers amd64 1.10.10+repack-5ubuntu1 [16.3 kB]
369s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 74.2-1ubuntu4 [213 kB]
369s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 javascript-common all 11+nmu1 [5936 B]
369s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 comerr-dev amd64 2.1-1.47.1-1ubuntu1 [44.5 kB]
369s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libgssrpc4t64 amd64 1.21.3-3 [57.5 kB]
369s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [40.0 kB]
369s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libkdb5-10t64 amd64 1.21.3-3 [40.6 kB]
369s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [52.8 kB]
369s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 krb5-multidev amd64 1.21.3-3 [125 kB]
369s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
369s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB]
369s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblatex-tounicode-perl all 0.55-1 [28.8 kB]
369s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 libbibtex-parser-perl all 1.05+dfsg-1 [16.5 kB]
369s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB]
369s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.0-4 [307 kB]
369s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libsnappy1v5 amd64 1.2.1-1 [30.4 kB]
369s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 libblosc1 amd64 1.21.5+ds-1build1 [36.2 kB]
369s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli-dev amd64 1.1.0-2build3 [381 kB]
369s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB]
370s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
370s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
370s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
370s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
370s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
370s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libidn2-dev amd64 2.3.7-2build2 [120 kB]
370s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libkrb5-dev amd64 1.21.3-3 [11.9 kB]
370s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libldap-dev amd64 2.6.8+dfsg-1~exp4ubuntu3 [308 kB]
370s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB]
370s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB]
370s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB]
370s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libnghttp2-dev amd64 1.64.0-1 [123 kB]
370s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libpsl-dev amd64 0.21.2-1.1build1 [76.4 kB]
370s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2ubuntu7 [10.0 kB]
370s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2ubuntu7 [341 kB]
370s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [144 kB]
370s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libunbound8 amd64 1.20.0-1ubuntu2.1 [447 kB]
370s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-dane0t64 amd64 3.8.8-2ubuntu1 [24.3 kB]
370s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2ubuntu1 [24.5 kB]
370s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit-dev amd64 0.25.5-2ubuntu1 [22.7 kB]
370s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6-dev amd64 4.19.0-3build1 [90.5 kB]
370s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 nettle-dev amd64 3.10-1 [1172 kB]
370s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libgnutls28-dev amd64 3.8.8-2ubuntu1 [1108 kB]
370s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
370s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2build7 [66.7 kB]
370s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libssl-dev amd64 3.3.1-2ubuntu2 [2686 kB]
370s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libssh2-1-dev amd64 1.11.1-1 [292 kB]
370s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [371 kB]
370s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4-openssl-dev amd64 8.11.0-1ubuntu2 [517 kB]
370s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
370s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.22-1 [64.5 kB]
370s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.22-1 [72.2 kB]
370s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
370s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.0.1-1 [540 kB]
370s Get:96 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
370s Get:97 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5ubuntu1 [1367 kB]
370s Get:98 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-5ubuntu1 [131 kB]
370s Get:99 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-5ubuntu1 [87.0 kB]
370s Get:100 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-5ubuntu1 [59.5 kB]
370s Get:101 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-5ubuntu1 [31.8 kB]
370s Get:102 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-5ubuntu1 [11.2 kB]
370s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
371s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB]
371s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
371s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
371s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
371s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec-dev amd64 1.1.3-1 [19.8 kB]
371s Get:109 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhdf5-dev amd64 1.10.10+repack-5ubuntu1 [2907 kB]
371s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
371s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
371s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 74.2-1ubuntu4 [11.9 MB]
371s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
371s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
371s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
371s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-d3 all 3.5.17-4 [132 kB]
371s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
371s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
371s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
371s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
371s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
371s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
371s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
371s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
371s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
371s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
371s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
371s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [66.8 kB]
371s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB]
372s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.0-4 [6486 kB]
372s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
372s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 liblua5.4-0 amd64 5.4.7-1 [196 kB]
372s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB]
372s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5-2 [384 kB]
372s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
372s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
372s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [252 kB]
372s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [51.6 kB]
372s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [29.1 kB]
372s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB]
372s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B]
372s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu3 [214 kB]
372s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu3 [201 kB]
372s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu3 [6768 B]
372s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.42-4ubuntu3 [747 kB]
372s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.44-2 [300 kB]
372s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpotrace0 amd64 1.16-2build1 [17.7 kB]
372s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [43.7 kB]
372s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-5 [169 kB]
372s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
372s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
372s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.3 kB]
372s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1085 kB]
372s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 libteckit0 amd64 2.5.12+ds1-1 [411 kB]
372s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [145 kB]
372s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
372s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
372s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
372s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
372s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
372s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.15-1 [862 kB]
372s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
372s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 libxmu6 amd64 2:1.1.3-3build2 [47.6 kB]
372s Get:164 http://ftpmaster.internal/ubuntu plucky/main amd64 libxpm4 amd64 1:3.5.17-1build2 [36.5 kB]
372s Get:165 http://ftpmaster.internal/ubuntu plucky/main amd64 libxaw7 amd64 2:1.0.16-1 [207 kB]
372s Get:166 http://ftpmaster.internal/ubuntu plucky/main amd64 libxi6 amd64 2:1.8.2-1 [32.4 kB]
372s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2build1 [28.1 kB]
372s Get:168 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu1 [185 kB]
372s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
372s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-0ubuntu1 [67.5 kB]
372s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1 [28.9 MB]
373s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-1 [96.0 kB]
374s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-1 [2486 B]
374s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
374s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
374s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB]
374s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
374s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 pandoc amd64 3.1.11.1+ds-2 [27.2 MB]
375s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.3-1 [189 kB]
375s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB]
375s Get:181 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.2-1 [4340 B]
375s Get:182 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
375s Get:183 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.50.0-2 [605 kB]
375s Get:184 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-alabaster.schemas all 1.4.0+ds-4 [24.7 kB]
375s Get:185 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4vectors amd64 0.42.1+dfsg-2 [1890 kB]
375s Get:186 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhdf5lib amd64 1.26.0+dfsg-1 [97.3 kB]
375s Get:187 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhdf5filters amd64 1.16.0+dfsg-1 [137 kB]
375s Get:188 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhdf5 amd64 2.48.0+dfsg-3 [818 kB]
375s Get:189 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.8.9+dfsg-1 [445 kB]
375s Get:190 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
375s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.13-1-1 [1993 kB]
375s Get:192 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-alabaster.base amd64 1.4.2+ds-3 [759 kB]
375s Get:193 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-base64enc amd64 0.1-3-3 [27.6 kB]
375s Get:194 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB]
375s Get:195 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
375s Get:196 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.4-1 [1708 kB]
375s Get:197 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
375s Get:198 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.0-1 [111 kB]
375s Get:199 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.49+dfsg-1 [545 kB]
375s Get:200 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
375s Get:201 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
375s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
376s Get:203 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB]
376s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
376s Get:205 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
376s Get:206 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.3-1 [1348 kB]
376s Get:207 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB]
376s Get:208 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
376s Get:209 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
376s Get:210 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
376s Get:211 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fs amd64 1.6.4+dfsg-1 [245 kB]
376s Get:212 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB]
376s Get:213 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rappdirs amd64 0.3.3-1 [47.5 kB]
376s Get:214 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
376s Get:215 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bslib all 0.7.0+dfsg-1 [4255 kB]
376s Get:216 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fontawesome all 0.5.2-1 [1300 kB]
376s Get:217 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-tinytex all 0.53-1 [145 kB]
376s Get:218 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-modernizr all 3.13.0-0.1 [101 kB]
376s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-later amd64 1.3.2+dfsg-1 [123 kB]
376s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
376s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-promises amd64 1.3.0+dfsg-1 [287 kB]
376s Get:222 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
376s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
376s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
376s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
376s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
376s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.1-1 [131 kB]
376s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
376s Get:229 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-shiny all 1.9.1+dfsg-1 [3111 kB]
377s Get:230 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rmarkdown all 2.28+dfsg-1 [1501 kB]
377s Get:231 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bookdown all 0.41+dfsg-1 [1408 kB]
377s Get:232 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB]
377s Get:233 http://ftpmaster.internal/ubuntu plucky/universe amd64 tex-common all 6.18 [32.8 kB]
377s Get:234 http://ftpmaster.internal/ubuntu plucky/main amd64 t1utils amd64 1.41-4build3 [61.3 kB]
377s Get:235 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [9801 kB]
377s Get:236 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-base all 2024.20241115-1 [22.5 MB]
378s Get:237 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-latex-base all 2024.20241115-1 [1260 kB]
378s Get:238 http://ftpmaster.internal/ubuntu plucky/universe amd64 texlive-bibtex-extra all 2024.20241115-1 [79.9 MB]
381s Get:239 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocversion all 3.19.1-1 [11.2 kB]
381s Get:240 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocstyle all 2.32.1+dfsg-1 [452 kB]
381s Get:241 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB]
381s Get:242 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ps amd64 1.8.0-1 [395 kB]
381s Get:243 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-processx amd64 3.8.4-1 [353 kB]
381s Get:244 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
381s Get:245 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
381s Get:246 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-diffobj amd64 0.3.5-1 [1117 kB]
381s Get:247 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
381s Get:248 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-1-1 [4199 kB]
381s Get:249 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgbuild all 1.4.4-1 [212 kB]
381s Get:250 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rprojroot all 2.0.4-1 [124 kB]
381s Get:251 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgload all 1.4.0-1 [247 kB]
381s Get:252 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-praise all 1.0.0-4build1 [20.3 kB]
381s Get:253 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-waldo all 0.6.1-1 [150 kB]
381s Get:254 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-testthat amd64 3.2.1.1-1 [1636 kB]
382s Preconfiguring packages ...
382s Fetched 354 MB in 16s (22.8 MB/s)
382s Selecting previously unselected package libisl23:amd64.
382s (Reading database ... 
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(Reading database ... 75952 files and directories currently installed.)
382s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ...
382s Unpacking libisl23:amd64 (0.27-1) ...
383s Selecting previously unselected package libmpc3:amd64.
383s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ...
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383s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
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383s Selecting previously unselected package libcc1-0:amd64.
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383s Selecting previously unselected package libquadmath0:amd64.
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384s Selecting previously unselected package libstdc++-14-dev:amd64.
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384s Selecting previously unselected package fonts-dejavu-mono.
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384s Selecting previously unselected package fonts-glyphicons-halflings.
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385s Selecting previously unselected package fonts-lmodern.
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385s Selecting previously unselected package libgfortran5:amd64.
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385s Selecting previously unselected package gfortran-14.
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385s Selecting previously unselected package hdf5-helpers.
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385s Selecting previously unselected package icu-devtools.
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385s Selecting previously unselected package javascript-common.
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385s Selecting previously unselected package comerr-dev:amd64.
385s Preparing to unpack .../045-comerr-dev_2.1-1.47.1-1ubuntu1_amd64.deb ...
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385s Selecting previously unselected package libgssrpc4t64:amd64.
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385s Selecting previously unselected package libkadm5clnt-mit12:amd64.
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385s Selecting previously unselected package libaec0:amd64.
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385s Selecting previously unselected package libio-string-perl.
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385s Selecting previously unselected package liblatex-tounicode-perl.
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385s Selecting previously unselected package libbibtex-parser-perl.
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385s Selecting previously unselected package libblas3:amd64.
385s Preparing to unpack .../055-libblas3_3.12.0-4_amd64.deb ...
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385s Selecting previously unselected package libblas-dev:amd64.
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385s Selecting previously unselected package libsnappy1v5:amd64.
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385s Preparing to unpack .../058-libblosc1_1.21.5+ds-1build1_amd64.deb ...
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385s Selecting previously unselected package libbrotli-dev:amd64.
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385s Selecting previously unselected package libbz2-dev:amd64.
385s Preparing to unpack .../060-libbz2-dev_1.0.8-6_amd64.deb ...
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386s Selecting previously unselected package libpixman-1-0:amd64.
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386s Selecting previously unselected package libcairo2:amd64.
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386s Selecting previously unselected package libldap-dev:amd64.
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386s Selecting previously unselected package libpkgconf3:amd64.
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386s Selecting previously unselected package libgmp-dev:amd64.
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386s Selecting previously unselected package libevent-2.1-7t64:amd64.
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386s Selecting previously unselected package libgnutls-openssl27t64:amd64.
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386s Selecting previously unselected package libp11-kit-dev:amd64.
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386s Selecting previously unselected package nettle-dev:amd64.
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386s Selecting previously unselected package zlib1g-dev:amd64.
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386s Selecting previously unselected package librtmp-dev:amd64.
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386s Selecting previously unselected package libssl-dev:amd64.
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386s Selecting previously unselected package libssh2-1-dev:amd64.
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386s Selecting previously unselected package libzstd-dev:amd64.
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386s Selecting previously unselected package libcurl4-openssl-dev:amd64.
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386s Selecting previously unselected package libdatrie1:amd64.
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386s Selecting previously unselected package libgraphite2-3:amd64.
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386s Selecting previously unselected package libharfbuzz0b:amd64.
387s Preparing to unpack .../094-libharfbuzz0b_10.0.1-1_amd64.deb ...
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387s Selecting previously unselected package libsz2:amd64.
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387s Selecting previously unselected package libhdf5-103-1t64:amd64.
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387s Selecting previously unselected package libhdf5-cpp-103-1t64:amd64.
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387s Selecting previously unselected package libhdf5-fortran-102t64:amd64.
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387s Selecting previously unselected package libhdf5-hl-100t64:amd64.
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387s Selecting previously unselected package libhdf5-hl-fortran-100t64:amd64.
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398s Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-5ubuntu1) ...
398s Setting up libkrb5-dev:amd64 (1.21.3-3) ...
398s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
398s Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2build7) ...
398s Setting up cpp (4:14.1.0-2ubuntu1) ...
398s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
398s Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-5ubuntu1) ...
398s Setting up libxmu6:amd64 (2:1.1.3-3build2) ...
398s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
398s Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-5ubuntu1) ...
398s Setting up libxaw7:amd64 (2:1.0.16-1) ...
398s Setting up gcc-14 (14.2.0-8ubuntu1) ...
398s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
398s Setting up libcurl4-openssl-dev:amd64 (8.11.0-1ubuntu2) ...
398s Setting up libhdf5-dev (1.10.10+repack-5ubuntu1) ...
398s update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
398s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ...
398s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
398s Setting up g++-14 (14.2.0-8ubuntu1) ...
398s Setting up gfortran-14 (14.2.0-8ubuntu1) ...
398s Setting up gfortran-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ...
398s Setting up gcc (4:14.1.0-2ubuntu1) ...
398s Setting up g++ (4:14.1.0-2ubuntu1) ...
398s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
398s Setting up build-essential (12.10ubuntu1) ...
398s Setting up gfortran (4:14.1.0-2ubuntu1) ...
398s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
398s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
398s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
398s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
399s Processing triggers for sgml-base (1.31) ...
399s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
399s Processing triggers for install-info (7.1.1-1) ...
399s Setting up fontconfig (2.15.0-1.1ubuntu2) ...
401s Regenerating fonts cache... done.
401s Setting up libxft2:amd64 (2.3.6-1build1) ...
401s Setting up libtk8.6:amd64 (8.6.15-1) ...
401s Processing triggers for libc-bin (2.40-1ubuntu3) ...
401s Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ...
401s Processing triggers for man-db (2.13.0-1) ...
402s Setting up libcairo2:amd64 (1.18.2-2) ...
402s Setting up texlive-binaries (2024.20240313.70630+ds-5) ...
402s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
402s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
402s Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ...
403s Setting up texlive-base (2024.20241115-1) ...
403s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
403s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
403s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
404s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
404s Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ...
404s Setting up texlive-latex-base (2024.20241115-1) ...
404s Setting up r-base-core (4.4.2-1) ...
404s 
404s Creating config file /etc/R/Renviron with new version
404s Setting up r-cran-crayon (1.5.2-1) ...
404s Setting up r-cran-sourcetools (0.1.7-1-1) ...
404s Setting up r-cran-lattice (0.22-6-1) ...
404s Setting up r-cran-ps (1.8.0-1) ...
404s Setting up r-cran-commonmark (1.9.1-1) ...
404s Setting up r-cran-r6 (2.5.1-1) ...
404s Setting up r-cran-pkgkitten (0.2.4-1) ...
404s Setting up r-cran-magrittr (2.0.3-1) ...
404s Setting up r-cran-rappdirs (0.3.3-1) ...
404s Setting up r-cran-littler (0.3.20-1) ...
404s Setting up r-cran-fs (1.6.4+dfsg-1) ...
404s Setting up r-cran-rcpp (1.0.13-1-1) ...
404s Setting up r-cran-brio (1.1.5-1) ...
404s Setting up r-cran-diffobj (0.3.5-1) ...
404s Setting up r-bioc-biocgenerics (0.50.0-2) ...
404s Setting up r-cran-rlang (1.1.4-1) ...
404s Setting up r-base-dev (4.4.2-1) ...
404s Setting up littler (0.3.20-1) ...
404s Setting up r-cran-xfun (0.49+dfsg-1) ...
404s Setting up r-cran-withr (3.0.2+dfsg-1) ...
404s Setting up r-cran-processx (3.8.4-1) ...
404s Setting up r-cran-mime (0.12-2) ...
404s Setting up r-cran-praise (1.0.0-4build1) ...
404s Setting up r-cran-base64enc (0.1-3-3) ...
404s Setting up r-cran-digest (0.6.37-1) ...
404s Setting up r-cran-yaml (2.3.10-1) ...
404s Setting up r-cran-evaluate (1.0.0-1) ...
404s Setting up r-cran-highr (0.11+dfsg-1) ...
404s Setting up r-bioc-rhdf5lib (1.26.0+dfsg-1) ...
404s Setting up r-cran-glue (1.7.0-1) ...
404s Setting up r-bioc-rhdf5filters (1.16.0+dfsg-1) ...
404s Setting up r-cran-xtable (1:1.8-4-2) ...
404s Setting up r-cran-cli (3.6.3-1) ...
404s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
404s Setting up r-bioc-biocversion (3.19.1-1) ...
404s Setting up r-cran-rprojroot (2.0.4-1) ...
404s Setting up r-cran-biocmanager (1.30.25+dfsg-1) ...
404s Setting up texlive-bibtex-extra (2024.20241115-1) ...
404s Setting up r-cran-fastmap (1.2.0-1) ...
404s Setting up r-cran-jsonlite (1.8.9+dfsg-1) ...
404s Setting up r-bioc-s4vectors (0.42.1+dfsg-2) ...
404s Setting up r-cran-waldo (0.6.1-1) ...
404s Setting up r-cran-later (1.3.2+dfsg-1) ...
404s Setting up r-cran-matrix (1.7-1-1) ...
404s Setting up r-cran-htmltools (0.5.8.1-1) ...
404s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
404s Setting up r-cran-tinytex (0.53-1) ...
404s Setting up r-cran-knitr (1.49+dfsg-1) ...
404s Setting up r-cran-cachem (1.1.0-1) ...
404s Setting up r-cran-sass (0.4.9+dfsg-1) ...
404s Setting up r-bioc-alabaster.schemas (1.4.0+ds-4) ...
404s Setting up r-cran-callr (3.7.6-1) ...
404s Setting up r-cran-desc (1.4.3-1) ...
404s Setting up r-bioc-rhdf5 (2.48.0+dfsg-3) ...
404s Setting up r-cran-fontawesome (0.5.2-1) ...
404s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
404s Setting up r-bioc-alabaster.base (1.4.2+ds-3) ...
404s Setting up r-cran-memoise (2.0.1-1) ...
404s Setting up r-cran-promises (1.3.0+dfsg-1) ...
404s Setting up r-cran-pkgbuild (1.4.4-1) ...
404s Setting up r-cran-pkgload (1.4.0-1) ...
404s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
404s Setting up r-cran-testthat (3.2.1.1-1) ...
404s Setting up r-cran-bslib (0.7.0+dfsg-1) ...
404s Setting up r-cran-shiny (1.9.1+dfsg-1) ...
404s Setting up r-cran-rmarkdown (2.28+dfsg-1) ...
404s Setting up r-cran-bookdown (0.41+dfsg-1) ...
404s Setting up r-bioc-biocstyle (2.32.1+dfsg-1) ...
404s Processing triggers for libc-bin (2.40-1ubuntu3) ...
404s Processing triggers for tex-common (6.18) ...
405s Running updmap-sys. This may take some time... done.
405s Running mktexlsr /var/lib/texmf ... done.
405s Building format(s) --all.
426s 	This may take some time... done.
427s autopkgtest [11:19:31]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
427s autopkgtest [11:19:31]: test pkg-r-autopkgtest: [-----------------------
427s Test: Try to load the R library alabaster.base
427s 
427s R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
427s Copyright (C) 2024 The R Foundation for Statistical Computing
427s Platform: x86_64-pc-linux-gnu
427s 
427s R is free software and comes with ABSOLUTELY NO WARRANTY.
427s You are welcome to redistribute it under certain conditions.
427s Type 'license()' or 'licence()' for distribution details.
427s 
427s R is a collaborative project with many contributors.
427s Type 'contributors()' for more information and
427s 'citation()' on how to cite R or R packages in publications.
427s 
427s Type 'demo()' for some demos, 'help()' for on-line help, or
427s 'help.start()' for an HTML browser interface to help.
427s Type 'q()' to quit R.
427s 
427s > library('alabaster.base')
428s > 
428s > 
428s Other tests are currently unsupported!
428s They will be progressively added.
428s autopkgtest [11:19:32]: test pkg-r-autopkgtest: -----------------------]
429s pkg-r-autopkgtest    PASS
429s autopkgtest [11:19:33]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
429s autopkgtest [11:19:33]: @@@@@@@@@@@@@@@@@@@@ summary
429s pkg-r-autopkgtest    PASS
441s nova [W] Skipping flock for amd64
441s Creating nova instance adt-plucky-amd64-r-bioc-alabaster.base-20241202-111223-juju-7f2275-prod-proposed-migration-environment-2-0239cf32-578d-448d-8ee9-912659c874f4 from image adt/ubuntu-plucky-amd64-server-20241202.img (UUID e2dd381a-9f8d-4c68-9282-8ccd9f59e142)...
441s nova [W] nova quota exceeded (attempt #0)