0s autopkgtest [00:42:25]: starting date and time: 2024-03-22 00:42:25+0000
  0s autopkgtest [00:42:25]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [00:42:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ruzc60el/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base --apt-upgrade r-bioc-annotate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-58.secgroup --name adt-noble-i386-r-bioc-annotate-20240322-004224-juju-7f2275-prod-proposed-migration-environment-2 --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/
453s autopkgtest [00:49:58]: testbed dpkg architecture: amd64
453s autopkgtest [00:49:58]: testbed apt version: 2.7.12
453s autopkgtest [00:49:58]: test architecture: i386
453s autopkgtest [00:49:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup
454s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
454s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3765 kB]
454s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB]
454s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
454s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB]
454s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [703 kB]
454s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [467 kB]
454s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
454s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
454s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
454s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
454s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4237 kB]
454s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1271 kB]
454s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
454s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB]
454s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB]
454s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
457s Fetched 11.3 MB in 1s (7704 kB/s)
457s Reading package lists...
459s Reading package lists...
459s Building dependency tree...
459s Reading state information...
460s Calculating upgrade...
460s The following packages will be upgraded:
460s   cloud-init fonts-ubuntu-console python3-markupsafe
460s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
460s Need to get 629 kB of archives.
460s After this operation, 11.3 kB disk space will be freed.
460s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB]
460s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 python3-markupsafe amd64 2.1.5-1build1 [12.6 kB]
460s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 cloud-init all 24.1.2-0ubuntu1 [597 kB]
460s Preconfiguring packages ...
460s Fetched 629 kB in 0s (20.2 MB/s)
460s (Reading database ... 
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(Reading database ... 15%
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(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 ... 71865 files and directories currently installed.)
460s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ...
460s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ...
460s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_amd64.deb ...
460s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
461s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ...
461s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ...
461s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ...
461s Setting up cloud-init (24.1.2-0ubuntu1) ...
462s Setting up python3-markupsafe (2.1.5-1build1) ...
462s Processing triggers for man-db (2.12.0-3) ...
463s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
463s Reading package lists...
463s Building dependency tree...
463s Reading state information...
464s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
464s sh: Attempting to set up Debian/Ubuntu apt sources automatically
464s sh: Distribution appears to be Ubuntu
466s Reading package lists...
466s Building dependency tree...
466s Reading state information...
466s eatmydata is already the newest version (131-1).
466s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
466s Reading package lists...
466s Building dependency tree...
466s Reading state information...
466s dbus is already the newest version (1.14.10-4ubuntu1).
466s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
466s Reading package lists...
467s Building dependency tree...
467s Reading state information...
467s rng-tools-debian is already the newest version (2.4).
467s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
467s Reading package lists...
467s Building dependency tree...
467s Reading state information...
467s The following packages will be REMOVED:
467s   cloud-init* python3-configobj* python3-debconf*
468s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
468s After this operation, 3256 kB disk space will be freed.
468s (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 ... 71864 files and directories currently installed.)
468s Removing cloud-init (24.1.2-0ubuntu1) ...
469s Removing python3-configobj (5.0.8-3) ...
469s Removing python3-debconf (1.5.86) ...
469s Processing triggers for man-db (2.12.0-3) ...
469s (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 ... 71475 files and directories currently installed.)
469s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
470s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
470s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
470s invoke-rc.d: policy-rc.d denied execution of try-restart.
470s Reading package lists...
470s Building dependency tree...
470s Reading state information...
470s linux-generic is already the newest version (6.8.0-11.11+1).
470s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
470s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
470s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
470s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
473s Reading package lists...
473s Reading package lists...
473s Building dependency tree...
473s Reading state information...
474s Calculating upgrade...
474s autopkgtest [00:50:19]: rebooting testbed after setup commands that affected boot
474s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
474s Reading package lists...
474s Building dependency tree...
474s Reading state information...
474s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
501s autopkgtest [00:50:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
502s autopkgtest [00:50:47]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-annotate
502s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-annotate 1.80.0+dfsg-1 (dsc) [2217 B]
502s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-annotate 1.80.0+dfsg-1 (tar) [1410 kB]
502s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-annotate 1.80.0+dfsg-1 (diff) [4908 B]
503s gpgv: Signature made Thu Nov 30 13:33:47 2023 UTC
503s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
503s gpgv:                issuer "tillea@rki.de"
503s gpgv: Can't check signature: No public key
503s dpkg-source: warning: cannot verify inline signature for ./r-bioc-annotate_1.80.0+dfsg-1.dsc: no acceptable signature found
503s autopkgtest [00:50:48]: testing package r-bioc-annotate version 1.80.0+dfsg-1
503s autopkgtest [00:50:48]: build not needed
505s autopkgtest [00:50:50]: test pkg-r-autopkgtest: preparing testbed
509s Note, using file '/tmp/autopkgtest.MUZIFx/1-autopkgtest-satdep.dsc' to get the build dependencies
509s Reading package lists...
509s Building dependency tree...
509s Reading state information...
509s Starting pkgProblemResolver with broken count: 0
509s Starting 2 pkgProblemResolver with broken count: 0
509s Done
510s The following NEW packages will be installed:
510s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
510s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
510s   g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13
510s   gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13
510s   gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
510s   libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2
510s   libcc1-0 libcrypt-dev libdatrie1 libdeflate0 libfontconfig1 libgcc-13-dev
510s   libgfortran-13-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
510s   libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev
510s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev
510s   liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev libnsl-dev
510s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
510s   libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
510s   libpixman-1-0 libpkgconf3 libpng-dev libquadmath0 libreadline-dev
510s   libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6 libthai-data libthai0
510s   libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0
510s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev pkg-config
510s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-bioc-annotate
510s   r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biostrings
510s   r-bioc-genefilter r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-go.db
510s   r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-org.hs.eg.db
510s   r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-bit
510s   r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli r-cran-cpp11
510s   r-cran-crayon r-cran-curl r-cran-dbi r-cran-fastmap r-cran-glue r-cran-httr
510s   r-cran-jsonlite r-cran-lattice r-cran-lifecycle r-cran-matrix
510s   r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-openssl
510s   r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6 r-cran-rcurl r-cran-rlang
510s   r-cran-rsqlite r-cran-runit r-cran-survival r-cran-sys r-cran-vctrs
510s   r-cran-xml r-cran-xtable rpcsvc-proto unzip x11-common xdg-utils zip
510s   zlib1g-dev
510s 0 upgraded, 157 newly installed, 0 to remove and 0 not upgraded.
510s Need to get 293 MB of archives.
510s After this operation, 1025 MB of additional disk space will be used.
510s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB]
510s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
510s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
510s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB]
510s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB]
510s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
510s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB]
510s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
510s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
510s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
510s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
510s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
510s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
510s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
510s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
510s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
510s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
510s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
510s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
510s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
510s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
510s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
510s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
510s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
510s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
510s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
510s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
510s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
510s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
510s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
510s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
510s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
510s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
510s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
510s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB]
510s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
510s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
510s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
510s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
510s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB]
510s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
510s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB]
510s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB]
510s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB]
510s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B]
510s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B]
510s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB]
510s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
510s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB]
510s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB]
510s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
510s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
510s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
510s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
510s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
510s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB]
510s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
510s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
510s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
510s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
510s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB]
510s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB]
511s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
511s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB]
511s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
511s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
511s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
511s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
511s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB]
511s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
511s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB]
511s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB]
511s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB]
511s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB]
511s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB]
511s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB]
511s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB]
511s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B]
511s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB]
511s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB]
511s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B]
511s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB]
511s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB]
511s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB]
511s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB]
511s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB]
511s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
511s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB]
511s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB]
511s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
511s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
511s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
511s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB]
511s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B]
511s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB]
511s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB]
511s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB]
511s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB]
511s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B]
511s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB]
511s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB]
511s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
511s Get:103 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB]
511s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB]
511s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B]
511s Get:106 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
511s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
511s Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biobase amd64 2.62.0-1 [2136 kB]
511s Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2056 kB]
511s Get:110 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-iranges amd64 2.36.0-1 [2252 kB]
511s Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-dbi all 1.2.2-1 [823 kB]
511s Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit amd64 4.0.5-1 [1063 kB]
511s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bit64 amd64 4.0.5-1 [465 kB]
511s Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB]
511s Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB]
511s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB]
511s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
511s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
511s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
511s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fastmap amd64 1.1.1-1 [70.5 kB]
511s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cachem amd64 1.0.8-1 [72.1 kB]
511s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
511s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
511s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
511s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB]
511s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rsqlite amd64 2.3.4-1 [1364 kB]
511s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-curl amd64 5.2.0+dfsg-1 [188 kB]
511s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-jsonlite amd64 1.8.8+dfsg-1 [441 kB]
511s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mime amd64 0.12-1 [35.8 kB]
511s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-sys amd64 3.4.2-1 [44.6 kB]
511s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-askpass amd64 1.2.0-1 [24.6 kB]
511s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-openssl amd64 2.1.1+dfsg-2 [402 kB]
511s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB]
511s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
511s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-png amd64 0.1-8-1 [40.5 kB]
511s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9596 B]
511s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-xvector amd64 0.42.0-1 [621 kB]
511s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB]
511s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1 [793 kB]
511s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB]
511s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3886 kB]
511s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
511s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.6 MB]
511s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-keggrest all 1.42.0+dfsg-1 [188 kB]
511s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-annotationdbi all 1.64.1-1 [4897 kB]
511s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xml amd64 3.99-0.16.1-1 [1733 kB]
511s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
511s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-annotate all 1.80.0+dfsg-1 [1730 kB]
511s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixstats amd64 1.2.0-1 [488 kB]
511s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB]
511s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB]
511s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB]
511s Get:153 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB]
511s Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genefilter amd64 1.84.0-1 [1123 kB]
511s Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-go.db all 3.18.0-1 [18.7 MB]
512s Get:156 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-org.hs.eg.db all 3.18.0-1 [64.1 MB]
512s Get:157 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-runit all 0.4.33-1 [377 kB]
513s Preconfiguring packages ...
513s Fetched 293 MB in 2s (129 MB/s)
513s Selecting previously unselected package libc-dev-bin.
513s (Reading database ... 
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(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 ... 71420 files and directories currently installed.)
513s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_amd64.deb ...
513s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
513s Selecting previously unselected package linux-libc-dev:amd64.
513s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ...
513s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
513s Selecting previously unselected package libcrypt-dev:amd64.
513s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
513s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
513s Selecting previously unselected package libtirpc-dev:amd64.
513s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ...
513s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
513s Selecting previously unselected package libnsl-dev:amd64.
513s Preparing to unpack .../004-libnsl-dev_1.3.0-3_amd64.deb ...
513s Unpacking libnsl-dev:amd64 (1.3.0-3) ...
513s Selecting previously unselected package rpcsvc-proto.
513s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
513s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
513s Selecting previously unselected package libc6-dev:amd64.
513s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_amd64.deb ...
513s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ...
513s Selecting previously unselected package libisl23:amd64.
513s Preparing to unpack .../007-libisl23_0.26-3_amd64.deb ...
513s Unpacking libisl23:amd64 (0.26-3) ...
513s Selecting previously unselected package libmpc3:amd64.
513s Preparing to unpack .../008-libmpc3_1.3.1-1_amd64.deb ...
513s Unpacking libmpc3:amd64 (1.3.1-1) ...
513s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
513s Preparing to unpack .../009-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
513s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
514s Selecting previously unselected package cpp-13.
514s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_amd64.deb ...
514s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
514s Selecting previously unselected package cpp-x86-64-linux-gnu.
514s Preparing to unpack .../011-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
514s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
514s Selecting previously unselected package cpp.
514s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ...
514s Unpacking cpp (4:13.2.0-7ubuntu1) ...
514s Selecting previously unselected package libcc1-0:amd64.
514s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libgomp1:amd64.
514s Preparing to unpack .../014-libgomp1_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libitm1:amd64.
514s Preparing to unpack .../015-libitm1_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libatomic1:amd64.
514s Preparing to unpack .../016-libatomic1_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libasan8:amd64.
514s Preparing to unpack .../017-libasan8_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package liblsan0:amd64.
514s Preparing to unpack .../018-liblsan0_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libtsan2:amd64.
514s Preparing to unpack .../019-libtsan2_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libubsan1:amd64.
514s Preparing to unpack .../020-libubsan1_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libhwasan0:amd64.
514s Preparing to unpack .../021-libhwasan0_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libquadmath0:amd64.
514s Preparing to unpack .../022-libquadmath0_14-20240303-1ubuntu1_amd64.deb ...
514s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ...
514s Selecting previously unselected package libgcc-13-dev:amd64.
514s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ...
514s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
514s Selecting previously unselected package gcc-13-x86-64-linux-gnu.
514s Preparing to unpack .../024-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
514s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
515s Selecting previously unselected package gcc-13.
515s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_amd64.deb ...
515s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
515s Selecting previously unselected package gcc-x86-64-linux-gnu.
515s Preparing to unpack .../026-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
515s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
515s Selecting previously unselected package gcc.
515s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
515s Unpacking gcc (4:13.2.0-7ubuntu1) ...
515s Selecting previously unselected package libstdc++-13-dev:amd64.
515s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ...
515s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
515s Selecting previously unselected package g++-13-x86-64-linux-gnu.
515s Preparing to unpack .../029-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
515s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
515s Selecting previously unselected package g++-13.
515s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_amd64.deb ...
515s Unpacking g++-13 (13.2.0-17ubuntu2) ...
515s Selecting previously unselected package g++-x86-64-linux-gnu.
515s Preparing to unpack .../031-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
515s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
515s Selecting previously unselected package g++.
515s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
515s Unpacking g++ (4:13.2.0-7ubuntu1) ...
515s Selecting previously unselected package build-essential.
515s Preparing to unpack .../033-build-essential_12.10ubuntu1_amd64.deb ...
515s Unpacking build-essential (12.10ubuntu1) ...
515s Selecting previously unselected package dctrl-tools.
515s Preparing to unpack .../034-dctrl-tools_2.24-3build2_amd64.deb ...
515s Unpacking dctrl-tools (2.24-3build2) ...
515s Selecting previously unselected package fonts-dejavu-mono.
515s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
515s Unpacking fonts-dejavu-mono (2.37-8) ...
515s Selecting previously unselected package fonts-dejavu-core.
515s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
515s Unpacking fonts-dejavu-core (2.37-8) ...
515s Selecting previously unselected package fontconfig-config.
515s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ...
516s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
516s Selecting previously unselected package libfontconfig1:amd64.
516s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ...
516s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
516s Selecting previously unselected package fontconfig.
516s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_amd64.deb ...
516s Unpacking fontconfig (2.15.0-1ubuntu1) ...
516s Selecting previously unselected package libgfortran5:amd64.
516s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_amd64.deb ...
516s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ...
516s Selecting previously unselected package libgfortran-13-dev:amd64.
516s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_amd64.deb ...
516s Unpacking libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
516s Selecting previously unselected package gfortran-13-x86-64-linux-gnu.
516s Preparing to unpack .../042-gfortran-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
516s Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
516s Selecting previously unselected package gfortran-13.
516s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_amd64.deb ...
516s Unpacking gfortran-13 (13.2.0-17ubuntu2) ...
516s Selecting previously unselected package gfortran-x86-64-linux-gnu.
516s Preparing to unpack .../044-gfortran-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
516s Unpacking gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
516s Selecting previously unselected package gfortran.
516s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ...
516s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
516s Selecting previously unselected package icu-devtools.
516s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_amd64.deb ...
516s Unpacking icu-devtools (74.2-1ubuntu1) ...
516s Selecting previously unselected package libblas3:amd64.
516s Preparing to unpack .../047-libblas3_3.12.0-3_amd64.deb ...
516s Unpacking libblas3:amd64 (3.12.0-3) ...
516s Selecting previously unselected package libblas-dev:amd64.
516s Preparing to unpack .../048-libblas-dev_3.12.0-3_amd64.deb ...
516s Unpacking libblas-dev:amd64 (3.12.0-3) ...
516s Selecting previously unselected package libbz2-dev:amd64.
516s Preparing to unpack .../049-libbz2-dev_1.0.8-5ubuntu1_amd64.deb ...
516s Unpacking libbz2-dev:amd64 (1.0.8-5ubuntu1) ...
516s Selecting previously unselected package libpixman-1-0:amd64.
516s Preparing to unpack .../050-libpixman-1-0_0.42.2-1_amd64.deb ...
516s Unpacking libpixman-1-0:amd64 (0.42.2-1) ...
516s Selecting previously unselected package libxcb-render0:amd64.
516s Preparing to unpack .../051-libxcb-render0_1.15-1_amd64.deb ...
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523s Unpacking r-cran-runit (0.4.33-1) ...
523s Setting up libgraphite2-3:amd64 (1.3.14-2) ...
523s Setting up libpixman-1-0:amd64 (0.42.2-1) ...
523s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ...
523s Setting up libpaper1:amd64 (1.1.29) ...
523s 
523s Creating config file /etc/papersize with new version
523s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
523s Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
523s Setting up libdatrie1:amd64 (0.2.13-3) ...
523s Setting up libxcb-render0:amd64 (1.15-1) ...
523s Setting up unzip (6.0-28ubuntu3) ...
523s Setting up x11-common (1:7.7+23ubuntu2) ...
523s Setting up libdeflate0:amd64 (1.19-1) ...
523s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ...
523s Setting up libxcb-shm0:amd64 (1.15-1) ...
523s Setting up libpaper-utils (1.1.29) ...
523s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ...
523s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu1) ...
523s Setting up zip (3.0-13) ...
523s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu1) ...
523s Setting up libblas3:amd64 (3.12.0-3) ...
523s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
523s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
523s Setting up libpkgconf3:amd64 (1.8.1-2) ...
523s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
523s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ...
523s Setting up fonts-dejavu-mono (2.37-8) ...
523s Setting up libmpc3:amd64 (1.3.1-1) ...
523s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ...
523s Setting up icu-devtools (74.2-1ubuntu1) ...
523s Setting up fonts-dejavu-core (2.37-8) ...
523s Setting up pkgconf-bin (1.8.1-2) ...
523s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ...
523s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libwebp7:amd64 (1.3.2-0.4) ...
523s Setting up liblzma-dev:amd64 (5.4.5-0.3) ...
523s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu1) ...
523s Setting up libnsl-dev:amd64 (1.3.0-3) ...
523s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ...
523s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libharfbuzz0b:amd64 (8.3.0-2) ...
523s Setting up libthai-data (0.1.29-2) ...
523s Setting up libxss1:amd64 (1:1.2.3-1build2) ...
523s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libisl23:amd64 (0.26-3) ...
523s Setting up libc-dev-bin (2.39-0ubuntu2) ...
523s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
523s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
523s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ...
523s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ...
523s Setting up libblas-dev:amd64 (3.12.0-3) ...
523s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
523s Setting up dctrl-tools (2.24-3build2) ...
524s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ...
524s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
524s Setting up libice6:amd64 (2:1.0.10-1build2) ...
524s Setting up liblapack3:amd64 (3.12.0-3) ...
524s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
524s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
524s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
524s Setting up pkgconf:amd64 (1.8.1-2) ...
524s Setting up libthai0:amd64 (0.1.29-2) ...
524s Setting up liblapack-dev:amd64 (3.12.0-3) ...
524s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
524s Setting up pkg-config:amd64 (1.8.1-2) ...
524s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
524s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
524s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ...
524s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
524s Setting up libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
524s Setting up libsm6:amd64 (2:1.2.3-1build2) ...
524s Setting up libicu-dev:amd64 (74.2-1ubuntu1) ...
524s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
524s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ...
524s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
524s Setting up fontconfig (2.15.0-1ubuntu1) ...
526s Regenerating fonts cache... done.
526s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ...
526s Setting up libxft2:amd64 (2.3.6-1) ...
526s Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ...
526s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ...
526s Setting up cpp-13 (13.2.0-17ubuntu2) ...
526s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
526s Setting up libtk8.6:amd64 (8.6.13-2) ...
526s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ...
526s Setting up libreadline-dev:amd64 (8.2-3) ...
526s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
526s Setting up libcairo2:amd64 (1.18.0-1) ...
526s Setting up gcc-13 (13.2.0-17ubuntu2) ...
526s Setting up libxt6:amd64 (1:1.2.1-1.1) ...
526s Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ...
526s Setting up cpp (4:13.2.0-7ubuntu1) ...
526s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ...
526s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
526s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ...
526s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
526s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
526s Setting up libpng-dev:amd64 (1.6.43-1) ...
526s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
526s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
526s Setting up gcc (4:13.2.0-7ubuntu1) ...
526s Setting up gfortran-13 (13.2.0-17ubuntu2) ...
526s Setting up r-base-core (4.3.2-1build1) ...
526s 
526s Creating config file /etc/R/Renviron with new version
526s Setting up r-cran-crayon (1.5.2-1) ...
526s Setting up r-cran-lattice (0.22-5-1) ...
526s Setting up r-cran-xml (3.99-0.16.1-1) ...
526s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
526s Setting up r-cran-r6 (2.5.1-1) ...
526s Setting up r-bioc-genomeinfodbdata (1.2.11-2) ...
526s Setting up r-cran-curl (5.2.0+dfsg-1) ...
526s Setting up g++-13 (13.2.0-17ubuntu2) ...
526s Setting up r-bioc-biocgenerics (0.48.1-2) ...
526s Setting up r-cran-rlang (1.1.3-1) ...
526s Setting up r-cran-matrixstats (1.2.0-1) ...
526s Setting up r-bioc-matrixgenerics (1.14.0-1) ...
526s Setting up r-cran-sys (3.4.2-1) ...
526s Setting up r-cran-plogr (0.2.0-3build1) ...
526s Setting up r-cran-mime (0.12-1) ...
526s Setting up r-cran-dbi (1.2.2-1) ...
526s Setting up r-cran-glue (1.7.0-1) ...
526s Setting up r-cran-bit (4.0.5-1) ...
526s Setting up r-cran-xtable (1:1.8-4-2) ...
526s Setting up r-cran-cli (3.6.2-1) ...
526s Setting up gfortran (4:13.2.0-7ubuntu1) ...
526s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
526s 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
526s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
526s 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
526s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
526s Setting up r-cran-bitops (1.0-7-1) ...
526s Setting up r-cran-bit64 (4.0.5-1) ...
526s Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ...
526s Setting up r-cran-askpass (1.2.0-1) ...
526s Setting up r-cran-fastmap (1.1.1-1) ...
526s Setting up r-cran-png (0.1-8-1) ...
526s Setting up r-bioc-biobase (2.62.0-1) ...
526s Setting up r-cran-jsonlite (1.8.8+dfsg-1) ...
526s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
526s Setting up r-cran-cpp11 (0.4.7-1) ...
526s Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ...
526s Setting up r-cran-runit (0.4.33-1) ...
526s Setting up r-cran-matrix (1.6-5-1) ...
526s Setting up g++ (4:13.2.0-7ubuntu1) ...
526s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
526s Setting up r-cran-cachem (1.0.8-1) ...
526s Setting up build-essential (12.10ubuntu1) ...
526s Setting up r-bioc-iranges (2.36.0-1) ...
526s Setting up r-cran-rcurl (1.98-1.14+dfsg-1) ...
526s Setting up r-cran-vctrs (0.6.5-1) ...
526s Setting up r-cran-openssl (2.1.1+dfsg-2) ...
526s Setting up r-base-dev (4.3.2-1build1) ...
526s Setting up r-cran-survival (3.5-8-1) ...
526s Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ...
526s Setting up r-cran-httr (1.4.7+dfsg-1) ...
526s Setting up r-cran-memoise (2.0.1-1) ...
526s Setting up r-cran-blob (1.2.4-1) ...
526s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
526s Setting up r-bioc-xvector (0.42.0-1) ...
526s Setting up r-cran-rsqlite (2.3.4-1) ...
526s Setting up r-bioc-biostrings (2.70.2+dfsg-1) ...
526s Setting up r-bioc-keggrest (1.42.0+dfsg-1) ...
526s Setting up r-bioc-annotationdbi (1.64.1-1) ...
526s Setting up r-bioc-go.db (3.18.0-1) ...
526s Setting up r-bioc-annotate (1.80.0+dfsg-1) ...
526s Setting up r-bioc-genefilter (1.84.0-1) ...
526s Setting up r-bioc-org.hs.eg.db (3.18.0-1) ...
526s Processing triggers for man-db (2.12.0-3) ...
527s Processing triggers for install-info (7.1-3) ...
528s Processing triggers for libc-bin (2.39-0ubuntu2) ...
530s Reading package lists...
530s Building dependency tree...
530s Reading state information...
530s Starting pkgProblemResolver with broken count: 0
530s Starting 2 pkgProblemResolver with broken count: 0
530s Done
531s The following NEW packages will be installed:
531s   autopkgtest-satdep
531s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
531s Need to get 0 B/696 B of archives.
531s After this operation, 0 B of additional disk space will be used.
531s Get:1 /tmp/autopkgtest.MUZIFx/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
531s Selecting previously unselected package autopkgtest-satdep.
531s (Reading database ... 
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531s Preparing to unpack .../2-autopkgtest-satdep.deb ...
531s Unpacking autopkgtest-satdep (0) ...
531s Setting up autopkgtest-satdep (0) ...
532s (Reading database ... 81291 files and directories currently installed.)
532s Removing autopkgtest-satdep (0) ...
533s autopkgtest [00:51:18]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
533s autopkgtest [00:51:18]: test pkg-r-autopkgtest: [-----------------------
533s Test: Try to load the R library annotate
533s 
533s R version 4.3.2 (2023-10-31) -- "Eye Holes"
533s Copyright (C) 2023 The R Foundation for Statistical Computing
533s Platform: x86_64-pc-linux-gnu (64-bit)
533s 
533s R is free software and comes with ABSOLUTELY NO WARRANTY.
533s You are welcome to redistribute it under certain conditions.
533s Type 'license()' or 'licence()' for distribution details.
533s 
533s R is a collaborative project with many contributors.
533s Type 'contributors()' for more information and
533s 'citation()' on how to cite R or R packages in publications.
533s 
533s Type 'demo()' for some demos, 'help()' for on-line help, or
533s 'help.start()' for an HTML browser interface to help.
533s Type 'q()' to quit R.
533s 
533s > library('annotate')
533s Loading required package: AnnotationDbi
533s Loading required package: stats4
533s Loading required package: BiocGenerics
533s 
533s Attaching package: ‘BiocGenerics’
533s 
533s The following objects are masked from ‘package:stats’:
533s 
533s     IQR, mad, sd, var, xtabs
533s 
533s The following objects are masked from ‘package:base’:
533s 
533s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
533s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
533s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
533s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
533s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
533s     table, tapply, union, unique, unsplit, which.max, which.min
533s 
533s Loading required package: Biobase
533s Welcome to Bioconductor
533s 
533s     Vignettes contain introductory material; view with
533s     'browseVignettes()'. To cite Bioconductor, see
533s     'citation("Biobase")', and for packages 'citation("pkgname")'.
533s 
533s Loading required package: IRanges
533s Loading required package: S4Vectors
534s 
534s Attaching package: ‘S4Vectors’
534s 
534s The following object is masked from ‘package:utils’:
534s 
534s     findMatches
534s 
534s The following objects are masked from ‘package:base’:
534s 
534s     expand.grid, I, unname
534s 
536s Loading required package: XML
536s > 
536s > 
536s Other tests are currently unsupported!
536s They will be progressively added.
537s autopkgtest [00:51:22]: test pkg-r-autopkgtest: -----------------------]
537s pkg-r-autopkgtest    PASS
537s autopkgtest [00:51:22]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
537s autopkgtest [00:51:22]: @@@@@@@@@@@@@@@@@@@@ summary
537s pkg-r-autopkgtest    PASS
548s Creating nova instance adt-noble-i386-r-bioc-annotate-20240322-004224-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240321.img (UUID 6f9effbc-61d8-4d0a-a7e9-883547f42ac1)...