0s autopkgtest [01:50:46]: starting date and time: 2024-03-22 01:50:46+0000
  0s autopkgtest [01:50:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [01:50:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.klqvr_67/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-bsgenome --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@lcy02-29.secgroup --name adt-noble-i386-r-bioc-bsgenome-20240322-015046-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/
329s autopkgtest [01:56:15]: testbed dpkg architecture: amd64
329s autopkgtest [01:56:15]: testbed apt version: 2.7.12
329s autopkgtest [01:56:15]: test architecture: i386
329s autopkgtest [01:56:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup
329s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
329s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB]
329s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB]
329s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
329s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3801 kB]
329s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [467 kB]
329s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [703 kB]
329s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
329s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
329s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
329s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
329s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4251 kB]
329s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1280 kB]
329s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
329s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB]
329s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB]
329s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
333s Fetched 11.3 MB in 2s (7364 kB/s)
333s Reading package lists...
335s Reading package lists...
335s Building dependency tree...
335s Reading state information...
336s Calculating upgrade...
336s The following packages will be upgraded:
336s   cloud-init fonts-ubuntu-console python3-markupsafe
336s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
336s Need to get 629 kB of archives.
336s After this operation, 11.3 kB disk space will be freed.
336s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB]
336s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 python3-markupsafe amd64 2.1.5-1build1 [12.6 kB]
336s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 cloud-init all 24.1.2-0ubuntu1 [597 kB]
336s Preconfiguring packages ...
336s Fetched 629 kB in 0s (26.2 MB/s)
337s (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 ... 71865 files and directories currently installed.)
337s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ...
337s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ...
337s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_amd64.deb ...
337s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ...
337s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ...
337s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ...
337s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ...
337s Setting up cloud-init (24.1.2-0ubuntu1) ...
340s Setting up python3-markupsafe (2.1.5-1build1) ...
340s Processing triggers for man-db (2.12.0-3) ...
340s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
340s Reading package lists...
340s Building dependency tree...
340s Reading state information...
341s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
341s sh: Attempting to set up Debian/Ubuntu apt sources automatically
341s sh: Distribution appears to be Ubuntu
342s Reading package lists...
342s Building dependency tree...
342s Reading state information...
343s eatmydata is already the newest version (131-1).
343s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
343s Reading package lists...
343s Building dependency tree...
343s Reading state information...
344s dbus is already the newest version (1.14.10-4ubuntu1).
344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
344s Reading package lists...
344s Building dependency tree...
344s Reading state information...
344s rng-tools-debian is already the newest version (2.4).
344s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
344s Reading package lists...
345s Building dependency tree...
345s Reading state information...
345s The following packages will be REMOVED:
345s   cloud-init* python3-configobj* python3-debconf*
346s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
346s After this operation, 3256 kB disk space will be freed.
346s (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.)
346s Removing cloud-init (24.1.2-0ubuntu1) ...
346s Removing python3-configobj (5.0.8-3) ...
346s Removing python3-debconf (1.5.86) ...
346s Processing triggers for man-db (2.12.0-3) ...
347s (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.)
347s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
347s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
347s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
347s invoke-rc.d: policy-rc.d denied execution of try-restart.
348s Reading package lists...
348s Building dependency tree...
348s Reading state information...
348s linux-generic is already the newest version (6.8.0-11.11+1).
348s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
348s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
348s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
348s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
351s Reading package lists...
351s Reading package lists...
351s Building dependency tree...
351s Reading state information...
352s Calculating upgrade...
352s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
352s Reading package lists...
352s Building dependency tree...
352s Reading state information...
353s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
353s autopkgtest [01:56:39]: rebooting testbed after setup commands that affected boot
394s autopkgtest [01:57:20]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
395s autopkgtest [01:57:21]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-bsgenome
396s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (dsc) [2284 B]
396s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (tar) [5909 kB]
396s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (diff) [10.1 kB]
396s gpgv: Signature made Tue Feb 13 12:40:36 2024 UTC
396s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
396s gpgv:                issuer "tille@debian.org"
396s gpgv: Can't check signature: No public key
396s dpkg-source: warning: cannot verify inline signature for ./r-bioc-bsgenome_1.70.2-1.dsc: no acceptable signature found
396s autopkgtest [01:57:22]: testing package r-bioc-bsgenome version 1.70.2-1
397s autopkgtest [01:57:23]: build not needed
399s autopkgtest [01:57:25]: test pkg-r-autopkgtest: preparing testbed
401s Note, using file '/tmp/autopkgtest.K8bJqT/1-autopkgtest-satdep.dsc' to get the build dependencies
401s Reading package lists...
402s Building dependency tree...
402s Reading state information...
402s Starting pkgProblemResolver with broken count: 0
402s Starting 2 pkgProblemResolver with broken count: 0
402s Done
402s The following NEW packages will be installed:
402s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
402s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
402s   g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13
402s   gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13
402s   gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
402s   libatomic1 libblas-dev libblas3 libboost-dev libboost1.83-dev libbz2-dev
402s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1
402s   libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5
402s   libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23
402s   libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
402s   libjpeg8-dev liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
402s   libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0
402s   libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0
402s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev
402s   libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6
402s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
402s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
402s   linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core
402s   r-base-dev r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio
402s   r-bioc-biocparallel r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
402s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
402s   r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib
402s   r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors
402s   r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-xvector
402s   r-bioc-zlibbioc r-cran-abind r-cran-bh r-cran-biocmanager r-cran-bitops
402s   r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-formatr
402s   r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-lattice
402s   r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-rcurl r-cran-restfulr
402s   r-cran-rjson r-cran-runit r-cran-snow r-cran-xml r-cran-yaml rpcsvc-proto
402s   unzip x11-common xdg-utils zip zlib1g-dev
402s 0 upgraded, 152 newly installed, 0 to remove and 0 not upgraded.
402s Need to get 229 MB of archives.
402s After this operation, 726 MB of additional disk space will be used.
402s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB]
402s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
402s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
402s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB]
402s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB]
402s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
402s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB]
402s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
402s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
402s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
402s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
402s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
402s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
402s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
402s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
402s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
402s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
402s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
402s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
402s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
402s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
402s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
403s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
403s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
403s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
403s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
403s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
403s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
403s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
403s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
403s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
403s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
403s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
403s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
403s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB]
403s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
403s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
403s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
403s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
403s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB]
403s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
403s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB]
403s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB]
403s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB]
403s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B]
403s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B]
403s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB]
403s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
403s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB]
403s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libboost1.83-dev amd64 1.83.0-2ubuntu1 [15.3 MB]
403s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libboost-dev amd64 1.83.0.1ubuntu2 [4308 B]
403s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB]
403s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
403s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
403s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
403s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
403s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
403s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB]
403s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
403s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
403s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
403s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
403s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB]
403s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB]
403s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
403s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB]
403s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
403s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
403s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
403s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
403s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB]
403s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
403s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB]
403s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB]
403s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB]
403s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB]
403s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB]
403s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB]
403s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB]
403s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B]
403s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB]
403s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB]
403s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B]
403s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB]
403s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB]
403s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB]
403s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB]
403s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB]
403s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
403s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB]
403s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB]
403s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
403s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
403s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
403s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB]
403s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B]
403s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB]
403s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB]
403s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB]
403s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB]
403s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B]
403s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB]
403s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB]
403s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
403s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB]
403s Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB]
403s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B]
403s Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
403s Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
403s Get:110 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biobase amd64 2.62.0-1 [2136 kB]
403s Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2056 kB]
403s Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocio all 1.12.0+dfsg-1 [213 kB]
403s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-formatr all 1.14-1 [152 kB]
403s Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
403s Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
403s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
403s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
403s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB]
403s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
403s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB]
404s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocparallel amd64 1.36.0-1 [1347 kB]
404s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-iranges amd64 2.36.0-1 [2252 kB]
404s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9596 B]
404s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-xvector amd64 0.42.0-1 [621 kB]
404s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB]
404s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1 [793 kB]
404s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB]
404s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3886 kB]
404s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
404s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.6 MB]
404s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1823 kB]
404s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xml amd64 3.99-0.16.1-1 [1733 kB]
404s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-1 [1361 kB]
404s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1 [3640 kB]
404s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixstats amd64 1.2.0-1 [488 kB]
404s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB]
404s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB]
404s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB]
404s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB]
404s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [501 kB]
404s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1195 kB]
404s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1787 kB]
404s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1134 kB]
404s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2133 kB]
404s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB]
404s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rjson amd64 0.2.21-1 [143 kB]
404s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-yaml amd64 2.3.8-1 [108 kB]
404s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
404s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5108 kB]
404s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-bsgenome all 1.70.2-1 [6975 kB]
404s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB]
404s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-runit all 0.4.33-1 [377 kB]
405s Preconfiguring packages ...
405s Fetched 229 MB in 2s (125 MB/s)
405s Selecting previously unselected package libc-dev-bin.
405s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
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(Reading database ... 71420 files and directories currently installed.)
405s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_amd64.deb ...
405s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
405s Selecting previously unselected package linux-libc-dev:amd64.
405s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ...
405s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
405s Selecting previously unselected package libcrypt-dev:amd64.
405s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
405s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
405s Selecting previously unselected package libtirpc-dev:amd64.
405s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ...
405s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
405s Selecting previously unselected package libnsl-dev:amd64.
405s Preparing to unpack .../004-libnsl-dev_1.3.0-3_amd64.deb ...
405s Unpacking libnsl-dev:amd64 (1.3.0-3) ...
405s Selecting previously unselected package rpcsvc-proto.
405s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
405s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
405s Selecting previously unselected package libc6-dev:amd64.
405s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_amd64.deb ...
405s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ...
405s Selecting previously unselected package libisl23:amd64.
405s Preparing to unpack .../007-libisl23_0.26-3_amd64.deb ...
405s Unpacking libisl23:amd64 (0.26-3) ...
405s Selecting previously unselected package libmpc3:amd64.
405s Preparing to unpack .../008-libmpc3_1.3.1-1_amd64.deb ...
405s Unpacking libmpc3:amd64 (1.3.1-1) ...
405s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
405s Preparing to unpack .../009-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
405s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
406s Selecting previously unselected package cpp-13.
406s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_amd64.deb ...
406s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
406s Selecting previously unselected package cpp-x86-64-linux-gnu.
406s Preparing to unpack .../011-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
406s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
406s Selecting previously unselected package cpp.
406s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ...
406s Unpacking cpp (4:13.2.0-7ubuntu1) ...
406s Selecting previously unselected package libcc1-0:amd64.
406s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libgomp1:amd64.
406s Preparing to unpack .../014-libgomp1_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libitm1:amd64.
406s Preparing to unpack .../015-libitm1_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libatomic1:amd64.
406s Preparing to unpack .../016-libatomic1_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libasan8:amd64.
406s Preparing to unpack .../017-libasan8_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package liblsan0:amd64.
406s Preparing to unpack .../018-liblsan0_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libtsan2:amd64.
406s Preparing to unpack .../019-libtsan2_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libubsan1:amd64.
406s Preparing to unpack .../020-libubsan1_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libhwasan0:amd64.
406s Preparing to unpack .../021-libhwasan0_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libquadmath0:amd64.
406s Preparing to unpack .../022-libquadmath0_14-20240303-1ubuntu1_amd64.deb ...
406s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ...
406s Selecting previously unselected package libgcc-13-dev:amd64.
406s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ...
406s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
406s Selecting previously unselected package gcc-13-x86-64-linux-gnu.
406s Preparing to unpack .../024-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
406s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
407s Selecting previously unselected package gcc-13.
407s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_amd64.deb ...
407s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
407s Selecting previously unselected package gcc-x86-64-linux-gnu.
407s Preparing to unpack .../026-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
407s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
407s Selecting previously unselected package gcc.
407s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
407s Unpacking gcc (4:13.2.0-7ubuntu1) ...
407s Selecting previously unselected package libstdc++-13-dev:amd64.
407s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ...
407s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
407s Selecting previously unselected package g++-13-x86-64-linux-gnu.
407s Preparing to unpack .../029-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
407s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
407s Selecting previously unselected package g++-13.
407s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_amd64.deb ...
407s Unpacking g++-13 (13.2.0-17ubuntu2) ...
407s Selecting previously unselected package g++-x86-64-linux-gnu.
407s Preparing to unpack .../031-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
407s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
407s Selecting previously unselected package g++.
407s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
407s Unpacking g++ (4:13.2.0-7ubuntu1) ...
407s Selecting previously unselected package build-essential.
407s Preparing to unpack .../033-build-essential_12.10ubuntu1_amd64.deb ...
407s Unpacking build-essential (12.10ubuntu1) ...
407s Selecting previously unselected package dctrl-tools.
407s Preparing to unpack .../034-dctrl-tools_2.24-3build2_amd64.deb ...
407s Unpacking dctrl-tools (2.24-3build2) ...
407s Selecting previously unselected package fonts-dejavu-mono.
407s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
407s Unpacking fonts-dejavu-mono (2.37-8) ...
407s Selecting previously unselected package fonts-dejavu-core.
407s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
407s Unpacking fonts-dejavu-core (2.37-8) ...
407s Selecting previously unselected package fontconfig-config.
407s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ...
407s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
408s Selecting previously unselected package libfontconfig1:amd64.
408s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ...
408s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
408s Selecting previously unselected package fontconfig.
408s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_amd64.deb ...
408s Unpacking fontconfig (2.15.0-1ubuntu1) ...
408s Selecting previously unselected package libgfortran5:amd64.
408s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_amd64.deb ...
408s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ...
408s Selecting previously unselected package libgfortran-13-dev:amd64.
408s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_amd64.deb ...
408s Unpacking libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
408s Selecting previously unselected package gfortran-13-x86-64-linux-gnu.
408s Preparing to unpack .../042-gfortran-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
408s Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
408s Selecting previously unselected package gfortran-13.
408s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_amd64.deb ...
408s Unpacking gfortran-13 (13.2.0-17ubuntu2) ...
408s Selecting previously unselected package gfortran-x86-64-linux-gnu.
408s Preparing to unpack .../044-gfortran-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
408s Unpacking gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
408s Selecting previously unselected package gfortran.
408s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ...
408s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
408s Selecting previously unselected package icu-devtools.
408s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_amd64.deb ...
408s Unpacking icu-devtools (74.2-1ubuntu1) ...
408s Selecting previously unselected package libblas3:amd64.
408s Preparing to unpack .../047-libblas3_3.12.0-3_amd64.deb ...
408s Unpacking libblas3:amd64 (3.12.0-3) ...
408s Selecting previously unselected package libblas-dev:amd64.
408s Preparing to unpack .../048-libblas-dev_3.12.0-3_amd64.deb ...
408s Unpacking libblas-dev:amd64 (3.12.0-3) ...
408s Selecting previously unselected package libboost1.83-dev:amd64.
408s Preparing to unpack .../049-libboost1.83-dev_1.83.0-2ubuntu1_amd64.deb ...
408s Unpacking libboost1.83-dev:amd64 (1.83.0-2ubuntu1) ...
410s Selecting previously unselected package libboost-dev:amd64.
410s Preparing to unpack .../050-libboost-dev_1.83.0.1ubuntu2_amd64.deb ...
410s Unpacking libboost-dev:amd64 (1.83.0.1ubuntu2) ...
410s Selecting previously unselected package libbz2-dev:amd64.
410s Preparing to unpack .../051-libbz2-dev_1.0.8-5ubuntu1_amd64.deb ...
410s Unpacking libbz2-dev:amd64 (1.0.8-5ubuntu1) ...
410s Selecting previously unselected package libpixman-1-0:amd64.
410s Preparing to unpack .../052-libpixman-1-0_0.42.2-1_amd64.deb ...
410s Unpacking libpixman-1-0:amd64 (0.42.2-1) ...
410s Selecting previously unselected package libxcb-render0:amd64.
410s Preparing to unpack .../053-libxcb-render0_1.15-1_amd64.deb ...
410s Unpacking libxcb-render0:amd64 (1.15-1) ...
411s Selecting previously unselected package libxcb-shm0:amd64.
411s Preparing to unpack .../054-libxcb-shm0_1.15-1_amd64.deb ...
411s Unpacking libxcb-shm0:amd64 (1.15-1) ...
411s Selecting previously unselected package libxrender1:amd64.
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411s Selecting previously unselected package libgraphite2-3:amd64.
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411s Selecting previously unselected package libharfbuzz0b:amd64.
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411s Selecting previously unselected package libjpeg-turbo8:amd64.
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412s Selecting previously unselected package libpango-1.0-0:amd64.
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412s Selecting previously unselected package libpangocairo-1.0-0:amd64.
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412s Selecting previously unselected package libpaper1:amd64.
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412s Selecting previously unselected package libpcre2-16-0:amd64.
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412s Selecting previously unselected package libpcre2-posix3:amd64.
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421s Selecting previously unselected package libpng-dev:amd64.
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421s Selecting previously unselected package libreadline-dev:amd64.
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421s Selecting previously unselected package libjbig0:amd64.
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421s Selecting previously unselected package libwebp7:amd64.
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421s Selecting previously unselected package libtiff6:amd64.
421s Preparing to unpack .../093-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ...
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421s Selecting previously unselected package libxft2:amd64.
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421s Selecting previously unselected package libxss1:amd64.
421s Preparing to unpack .../095-libxss1_1%3a1.2.3-1build2_amd64.deb ...
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421s Selecting previously unselected package libtk8.6:amd64.
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421s Selecting previously unselected package pkgconf-bin.
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421s Selecting previously unselected package pkgconf:amd64.
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421s Selecting previously unselected package zip.
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421s Selecting previously unselected package xdg-utils.
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421s Selecting previously unselected package r-base-core.
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421s Selecting previously unselected package liblzma-dev:amd64.
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421s Selecting previously unselected package r-bioc-biocgenerics.
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421s Selecting previously unselected package r-bioc-biocio.
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421s Selecting previously unselected package r-cran-formatr.
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421s Selecting previously unselected package r-bioc-biocparallel.
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421s Selecting previously unselected package r-bioc-zlibbioc.
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421s Selecting previously unselected package r-bioc-xvector.
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421s Selecting previously unselected package r-cran-bitops.
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421s Selecting previously unselected package r-cran-rcurl.
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421s Selecting previously unselected package r-bioc-genomeinfodbdata.
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421s Selecting previously unselected package r-cran-crayon.
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421s Selecting previously unselected package r-bioc-biostrings.
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421s Selecting previously unselected package r-bioc-genomicranges.
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421s Selecting previously unselected package r-cran-xml.
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421s Selecting previously unselected package r-bioc-rhtslib.
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421s Selecting previously unselected package r-cran-matrixstats.
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421s Selecting previously unselected package r-bioc-matrixgenerics.
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421s Selecting previously unselected package r-cran-lattice.
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421s Setting up libgraphite2-3:amd64 (1.3.14-2) ...
421s Setting up libpixman-1-0:amd64 (0.42.2-1) ...
421s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ...
421s Setting up libpaper1:amd64 (1.1.29) ...
421s 
421s Creating config file /etc/papersize with new version
421s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
421s Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
421s Setting up libdatrie1:amd64 (0.2.13-3) ...
421s Setting up libxcb-render0:amd64 (1.15-1) ...
421s Setting up unzip (6.0-28ubuntu3) ...
421s Setting up x11-common (1:7.7+23ubuntu2) ...
421s Setting up libdeflate0:amd64 (1.19-1) ...
421s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ...
421s Setting up libxcb-shm0:amd64 (1.15-1) ...
421s Setting up libpaper-utils (1.1.29) ...
421s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ...
421s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu1) ...
421s Setting up zip (3.0-13) ...
421s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu1) ...
421s Setting up libblas3:amd64 (3.12.0-3) ...
421s 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
421s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
421s Setting up libpkgconf3:amd64 (1.8.1-2) ...
421s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
421s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ...
421s Setting up fonts-dejavu-mono (2.37-8) ...
421s Setting up libmpc3:amd64 (1.3.1-1) ...
421s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ...
421s Setting up icu-devtools (74.2-1ubuntu1) ...
421s Setting up fonts-dejavu-core (2.37-8) ...
421s Setting up pkgconf-bin (1.8.1-2) ...
421s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ...
421s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libwebp7:amd64 (1.3.2-0.4) ...
421s Setting up liblzma-dev:amd64 (5.4.5-0.3) ...
421s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu1) ...
421s Setting up libnsl-dev:amd64 (1.3.0-3) ...
421s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ...
421s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libharfbuzz0b:amd64 (8.3.0-2) ...
421s Setting up libthai-data (0.1.29-2) ...
421s Setting up libxss1:amd64 (1:1.2.3-1build2) ...
421s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libisl23:amd64 (0.26-3) ...
421s Setting up libc-dev-bin (2.39-0ubuntu2) ...
421s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
421s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
421s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ...
421s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libblas-dev:amd64 (3.12.0-3) ...
421s 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
421s Setting up dctrl-tools (2.24-3build2) ...
421s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ...
421s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
421s Setting up libice6:amd64 (2:1.0.10-1build2) ...
421s Setting up liblapack3:amd64 (3.12.0-3) ...
421s 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
421s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
421s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
421s Setting up pkgconf:amd64 (1.8.1-2) ...
421s Setting up libthai0:amd64 (0.1.29-2) ...
421s Setting up liblapack-dev:amd64 (3.12.0-3) ...
421s 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
421s Setting up pkg-config:amd64 (1.8.1-2) ...
421s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
421s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
421s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ...
421s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
421s Setting up libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
421s Setting up libsm6:amd64 (2:1.2.3-1build2) ...
421s Setting up libicu-dev:amd64 (74.2-1ubuntu1) ...
421s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
421s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ...
421s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
421s Setting up fontconfig (2.15.0-1ubuntu1) ...
421s Regenerating fonts cache... done.
421s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ...
421s Setting up libxft2:amd64 (2.3.6-1) ...
421s Setting up libboost1.83-dev:amd64 (1.83.0-2ubuntu1) ...
421s Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ...
421s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ...
421s Setting up cpp-13 (13.2.0-17ubuntu2) ...
421s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
421s Setting up libtk8.6:amd64 (8.6.13-2) ...
421s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ...
421s Setting up libreadline-dev:amd64 (8.2-3) ...
421s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
421s Setting up libcairo2:amd64 (1.18.0-1) ...
421s Setting up gcc-13 (13.2.0-17ubuntu2) ...
421s Setting up libxt6:amd64 (1:1.2.1-1.1) ...
421s Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ...
421s Setting up cpp (4:13.2.0-7ubuntu1) ...
421s Setting up libboost-dev:amd64 (1.83.0.1ubuntu2) ...
421s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ...
421s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
421s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ...
421s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
421s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
421s Setting up libpng-dev:amd64 (1.6.43-1) ...
421s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
421s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
421s Setting up gcc (4:13.2.0-7ubuntu1) ...
421s Setting up gfortran-13 (13.2.0-17ubuntu2) ...
421s Setting up r-base-core (4.3.2-1build1) ...
421s 
421s Creating config file /etc/R/Renviron with new version
421s Setting up r-cran-crayon (1.5.2-1) ...
421s Setting up r-cran-futile.options (1.0.1-3build1) ...
421s Setting up r-cran-lattice (0.22-5-1) ...
421s Setting up r-cran-formatr (1.14-1) ...
421s Setting up r-cran-xml (3.99-0.16.1-1) ...
421s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
421s Setting up r-bioc-genomeinfodbdata (1.2.11-2) ...
421s Setting up r-cran-littler (0.3.19-1) ...
421s Setting up r-cran-bh (1.84.0-1) ...
421s Setting up r-cran-codetools (0.2-19-1) ...
421s Setting up g++-13 (13.2.0-17ubuntu2) ...
421s Setting up r-bioc-biocgenerics (0.48.1-2) ...
421s Setting up r-cran-matrixstats (1.2.0-1) ...
421s Setting up r-bioc-matrixgenerics (1.14.0-1) ...
421s Setting up r-cran-abind (1.4-5-2) ...
421s Setting up r-cran-yaml (2.3.8-1) ...
421s Setting up r-cran-lambda.r (1.2.4-2build1) ...
421s Setting up r-cran-snow (1:0.4.4-2) ...
421s Setting up gfortran (4:13.2.0-7ubuntu1) ...
421s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
421s 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
421s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
421s 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
421s Setting up r-cran-bitops (1.0-7-1) ...
421s Setting up r-cran-biocmanager (1.30.22+dfsg-2) ...
421s Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ...
421s Setting up r-bioc-biobase (2.62.0-1) ...
421s Setting up r-cran-cpp11 (0.4.7-1) ...
421s Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ...
421s Setting up r-cran-runit (0.4.33-1) ...
421s Setting up r-cran-futile.logger (1.4.3-4build1) ...
421s Setting up r-cran-matrix (1.6-5-1) ...
421s Setting up g++ (4:13.2.0-7ubuntu1) ...
421s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
421s Setting up build-essential (12.10ubuntu1) ...
421s Setting up r-bioc-iranges (2.36.0-1) ...
421s Setting up r-cran-rjson (0.2.21-1) ...
421s Setting up r-cran-rcurl (1.98-1.14+dfsg-1) ...
421s Setting up r-cran-restfulr (0.0.15-1) ...
421s Setting up r-base-dev (4.3.2-1build1) ...
421s Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ...
421s Setting up r-bioc-biocparallel (1.36.0-1) ...
421s Setting up r-bioc-rhtslib (2.4.1+dfsg-1) ...
421s Setting up r-bioc-biocio (1.12.0+dfsg-1) ...
421s Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ...
421s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
421s Setting up r-bioc-xvector (0.42.0-1) ...
421s Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ...
421s Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ...
421s Setting up r-bioc-biostrings (2.70.2+dfsg-1) ...
421s Setting up r-bioc-rsamtools (2.18.0+dfsg-1) ...
421s Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ...
421s Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ...
421s Setting up r-bioc-genomicalignments (1.38.2-1) ...
421s Setting up r-bioc-rtracklayer (1.62.0-1) ...
421s Setting up r-bioc-bsgenome (1.70.2-1) ...
421s Processing triggers for libc-bin (2.39-0ubuntu2) ...
421s Processing triggers for man-db (2.12.0-3) ...
421s Processing triggers for install-info (7.1-3) ...
427s Reading package lists...
428s Building dependency tree...
428s Reading state information...
428s Starting pkgProblemResolver with broken count: 0
428s Starting 2 pkgProblemResolver with broken count: 0
428s Done
428s The following NEW packages will be installed:
428s   autopkgtest-satdep
428s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
428s Need to get 0 B/696 B of archives.
428s After this operation, 0 B of additional disk space will be used.
428s Get:1 /tmp/autopkgtest.K8bJqT/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
429s Selecting previously unselected package autopkgtest-satdep.
429s (Reading database ... 
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429s Preparing to unpack .../2-autopkgtest-satdep.deb ...
429s Unpacking autopkgtest-satdep (0) ...
429s Setting up autopkgtest-satdep (0) ...
430s (Reading database ... 97514 files and directories currently installed.)
430s Removing autopkgtest-satdep (0) ...
431s autopkgtest [01:57:57]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
431s autopkgtest [01:57:57]: test pkg-r-autopkgtest: [-----------------------
431s Test: Try to load the R library BSgenome
431s 
431s R version 4.3.2 (2023-10-31) -- "Eye Holes"
431s Copyright (C) 2023 The R Foundation for Statistical Computing
431s Platform: x86_64-pc-linux-gnu (64-bit)
431s 
431s R is free software and comes with ABSOLUTELY NO WARRANTY.
431s You are welcome to redistribute it under certain conditions.
431s Type 'license()' or 'licence()' for distribution details.
431s 
431s R is a collaborative project with many contributors.
431s Type 'contributors()' for more information and
431s 'citation()' on how to cite R or R packages in publications.
431s 
431s Type 'demo()' for some demos, 'help()' for on-line help, or
431s 'help.start()' for an HTML browser interface to help.
431s Type 'q()' to quit R.
431s 
431s > library('BSgenome')
431s Loading required package: BiocGenerics
431s 
431s Attaching package: ‘BiocGenerics’
431s 
431s The following objects are masked from ‘package:stats’:
431s 
431s     IQR, mad, sd, var, xtabs
431s 
431s The following objects are masked from ‘package:base’:
431s 
431s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
431s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
431s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
431s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
431s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
431s     table, tapply, union, unique, unsplit, which.max, which.min
431s 
431s Loading required package: S4Vectors
431s Loading required package: stats4
432s 
432s Attaching package: ‘S4Vectors’
432s 
432s The following object is masked from ‘package:utils’:
432s 
432s     findMatches
432s 
432s The following objects are masked from ‘package:base’:
432s 
432s     expand.grid, I, unname
432s 
432s Loading required package: IRanges
432s Loading required package: GenomeInfoDb
433s Loading required package: GenomicRanges
433s Loading required package: Biostrings
433s Loading required package: XVector
434s 
434s Attaching package: ‘Biostrings’
434s 
434s The following object is masked from ‘package:base’:
434s 
434s     strsplit
434s 
434s Loading required package: BiocIO
434s Loading required package: rtracklayer
439s 
439s Attaching package: ‘rtracklayer’
439s 
439s The following object is masked from ‘package:BiocIO’:
439s 
439s     FileForFormat
439s 
441s > 
441s > 
441s autopkgtest [01:58:06]: test pkg-r-autopkgtest: -----------------------]
441s Other tests are currently unsupported!
441s They will be progressively added.
441s pkg-r-autopkgtest    PASS
441s autopkgtest [01:58:07]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
441s autopkgtest [01:58:07]: @@@@@@@@@@@@@@@@@@@@ summary
441s pkg-r-autopkgtest    PASS
451s Creating nova instance adt-noble-i386-r-bioc-bsgenome-20240322-015046-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240321.img (UUID 6f9effbc-61d8-4d0a-a7e9-883547f42ac1)...