0s autopkgtest [12:57:12]: starting date and time: 2024-03-21 12:57:12+0000
  0s autopkgtest [12:57:12]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [12:57:12]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a34_pnku/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-bioc-rsamtools --apt-upgrade r-bioc-bsgenome --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-bioc-rsamtools/2.18.0+dfsg-1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-47.secgroup --name adt-noble-i386-r-bioc-bsgenome-20240321-125712-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/
1051s autopkgtest [13:14:43]: testbed dpkg architecture: amd64
1051s autopkgtest [13:14:43]: testbed apt version: 2.7.12
1051s autopkgtest [13:14:43]: test architecture: i386
1051s autopkgtest [13:14:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup
1052s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
1052s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3818 kB]
1055s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [53.9 kB]
1055s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
1055s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB]
1055s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [460 kB]
1055s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [697 kB]
1055s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
1055s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB]
1055s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
1055s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
1055s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4242 kB]
1055s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1281 kB]
1055s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
1055s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [93.7 kB]
1055s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [26.8 kB]
1055s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
1055s Fetched 11.3 MB in 1s (7923 kB/s)
1055s Reading package lists...
1057s Reading package lists...
1057s Building dependency tree...
1057s Reading state information...
1057s Calculating upgrade...
1058s The following packages will be upgraded:
1058s   debianutils linux-firmware
1058s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1058s Need to get 476 MB of archives.
1058s After this operation, 5724 kB of additional disk space will be used.
1058s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.17 [89.8 kB]
1058s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-firmware amd64 20240318.git3b128b60-0ubuntu1 [475 MB]
1062s Fetched 476 MB in 4s (134 MB/s)
1062s (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 ... 71803 files and directories currently installed.)
1062s Preparing to unpack .../debianutils_5.17_amd64.deb ...
1062s Unpacking debianutils (5.17) over (5.16) ...
1062s Setting up debianutils (5.17) ...
1062s (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 ... 71803 files and directories currently installed.)
1062s Preparing to unpack .../linux-firmware_20240318.git3b128b60-0ubuntu1_amd64.deb ...
1062s Unpacking linux-firmware (20240318.git3b128b60-0ubuntu1) over (20240202.git36777504-0ubuntu1) ...
1065s Setting up linux-firmware (20240318.git3b128b60-0ubuntu1) ...
1065s Processing triggers for man-db (2.12.0-3) ...
1066s Processing triggers for initramfs-tools (0.142ubuntu20) ...
1066s update-initramfs: Generating /boot/initrd.img-6.8.0-11-generic
1066s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
1074s Reading package lists...
1074s Building dependency tree...
1074s Reading state information...
1074s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1075s sh: Attempting to set up Debian/Ubuntu apt sources automatically
1075s sh: Distribution appears to be Ubuntu
1075s Reading package lists...
1076s Building dependency tree...
1076s Reading state information...
1076s eatmydata is already the newest version (131-1).
1076s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1076s Reading package lists...
1076s Building dependency tree...
1076s Reading state information...
1076s dbus is already the newest version (1.14.10-4ubuntu1).
1076s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1076s Reading package lists...
1077s Building dependency tree...
1077s Reading state information...
1077s rng-tools-debian is already the newest version (2.4).
1077s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1077s Reading package lists...
1077s Building dependency tree...
1077s Reading state information...
1078s The following packages will be REMOVED:
1078s   cloud-init* python3-configobj* python3-debconf*
1078s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
1078s After this operation, 3252 kB disk space will be freed.
1078s (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 ... 71865 files and directories currently installed.)
1078s Removing cloud-init (24.1.1-0ubuntu1) ...
1078s Removing python3-configobj (5.0.8-3) ...
1078s Removing python3-debconf (1.5.86) ...
1079s Processing triggers for man-db (2.12.0-3) ...
1079s (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 ... 71476 files and directories currently installed.)
1079s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ...
1079s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
1079s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
1079s invoke-rc.d: policy-rc.d denied execution of try-restart.
1080s Reading package lists...
1080s Building dependency tree...
1080s Reading state information...
1080s linux-generic is already the newest version (6.8.0-11.11+1).
1080s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1080s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
1080s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
1080s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
1082s Reading package lists...
1082s Reading package lists...
1083s Building dependency tree...
1083s Reading state information...
1083s Calculating upgrade...
1083s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1083s Reading package lists...
1083s Building dependency tree...
1083s Reading state information...
1083s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1083s autopkgtest [13:15:15]: rebooting testbed after setup commands that affected boot
1126s autopkgtest [13:15:58]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
1127s autopkgtest [13:15:59]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-bsgenome
1128s Get:1 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (dsc) [2284 B]
1128s Get:2 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (tar) [5909 kB]
1128s Get:3 http://ftpmaster.internal/ubuntu noble/universe r-bioc-bsgenome 1.70.2-1 (diff) [10.1 kB]
1129s gpgv: Signature made Tue Feb 13 12:40:36 2024 UTC
1129s gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
1129s gpgv:                issuer "tille@debian.org"
1129s gpgv: Can't check signature: No public key
1129s dpkg-source: warning: cannot verify inline signature for ./r-bioc-bsgenome_1.70.2-1.dsc: no acceptable signature found
1129s autopkgtest [13:16:01]: testing package r-bioc-bsgenome version 1.70.2-1
1129s autopkgtest [13:16:01]: build not needed
1131s autopkgtest [13:16:03]: test pkg-r-autopkgtest: preparing testbed
1134s Note, using file '/tmp/autopkgtest.ReAMhr/1-autopkgtest-satdep.dsc' to get the build dependencies
1134s Reading package lists...
1134s Building dependency tree...
1134s Reading state information...
1134s Starting pkgProblemResolver with broken count: 0
1134s Starting 2 pkgProblemResolver with broken count: 0
1134s Done
1135s The following NEW packages will be installed:
1135s   build-essential cpp cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu
1135s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
1135s   g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-13
1135s   gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-13
1135s   gfortran-13-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
1135s   libatomic1 libblas-dev libblas3 libboost-dev libboost1.83-dev libbz2-dev
1135s   libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1
1135s   libdeflate0 libfontconfig1 libgcc-13-dev libgfortran-13-dev libgfortran5
1135s   libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23
1135s   libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
1135s   libjpeg8-dev liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
1135s   libncurses-dev libnsl-dev libpango-1.0-0 libpangocairo-1.0-0
1135s   libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0
1135s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev
1135s   libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-13-dev libtcl8.6
1135s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
1135s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6
1135s   linux-libc-dev pkg-config pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core
1135s   r-base-dev r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio
1135s   r-bioc-biocparallel r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
1135s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
1135s   r-bioc-genomicranges r-bioc-iranges r-bioc-matrixgenerics r-bioc-rhtslib
1135s   r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors
1135s   r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-xvector
1135s   r-bioc-zlibbioc r-cran-abind r-cran-bh r-cran-biocmanager r-cran-bitops
1135s   r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-formatr
1135s   r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-lattice
1135s   r-cran-littler r-cran-matrix r-cran-matrixstats r-cran-rcurl r-cran-restfulr
1135s   r-cran-rjson r-cran-runit r-cran-snow r-cran-xml r-cran-yaml rpcsvc-proto
1135s   unzip x11-common xdg-utils zip zlib1g-dev
1135s 0 upgraded, 152 newly installed, 0 to remove and 0 not upgraded.
1135s Need to get 229 MB of archives.
1135s After this operation, 726 MB of additional disk space will be used.
1135s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu2 [20.4 kB]
1135s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB]
1135s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB]
1135s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB]
1135s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB]
1135s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB]
1135s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu2 [2126 kB]
1135s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB]
1135s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB]
1135s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB]
1135s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B]
1135s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
1135s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
1135s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB]
1135s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
1135s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB]
1135s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB]
1135s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB]
1135s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB]
1135s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB]
1135s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB]
1135s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB]
1135s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB]
1135s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB]
1135s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB]
1135s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB]
1135s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
1135s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
1135s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB]
1135s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB]
1135s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB]
1135s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
1135s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
1135s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
1135s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 dctrl-tools amd64 2.24-3build2 [66.9 kB]
1135s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
1135s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
1135s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB]
1135s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB]
1135s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB]
1135s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
1135s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran-13-dev amd64 13.2.0-17ubuntu2 [942 kB]
1135s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.6 MB]
1135s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-13 amd64 13.2.0-17ubuntu2 [10.3 kB]
1135s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1024 B]
1135s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 gfortran amd64 4:13.2.0-7ubuntu1 [1176 B]
1135s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB]
1135s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
1135s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.12.0-3 [170 kB]
1135s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libboost1.83-dev amd64 1.83.0-2ubuntu1 [15.3 MB]
1135s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libboost-dev amd64 1.83.0.1ubuntu2 [4308 B]
1135s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB]
1135s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB]
1135s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB]
1135s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B]
1135s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB]
1135s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB]
1135s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB]
1135s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB]
1135s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB]
1135s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB]
1135s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB]
1135s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB]
1135s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB]
1135s Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB]
1135s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB]
1135s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
1135s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
1135s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
1135s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
1135s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.12.0-3 [5196 kB]
1135s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB]
1135s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB]
1135s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB]
1135s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB]
1135s Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB]
1135s Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB]
1135s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB]
1135s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB]
1135s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B]
1135s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu1 [211 kB]
1135s Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu1 [198 kB]
1135s Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu1 [6808 B]
1135s Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-dev amd64 10.42-4ubuntu1 [743 kB]
1135s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB]
1135s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB]
1135s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libpng-dev amd64 1.6.43-1 [264 kB]
1135s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline-dev amd64 8.2-3 [167 kB]
1135s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB]
1135s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB]
1135s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB]
1136s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB]
1136s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB]
1136s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB]
1136s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB]
1136s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B]
1136s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.13-2 [776 kB]
1136s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB]
1136s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB]
1136s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB]
1136s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 pkg-config amd64 1.8.1-2 [7170 B]
1136s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB]
1136s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB]
1136s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
1136s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB]
1136s Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.3 [205 kB]
1136s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-dev all 4.3.2-1build1 [4336 B]
1136s Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
1136s Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocgenerics all 0.48.1-2 [595 kB]
1136s Get:110 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biobase amd64 2.62.0-1 [2136 kB]
1136s Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4vectors amd64 0.40.2+dfsg-1 [2056 kB]
1136s Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocio all 1.12.0+dfsg-1 [213 kB]
1136s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-formatr all 1.14-1 [152 kB]
1136s Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
1136s Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
1136s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
1136s Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
1136s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB]
1136s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
1136s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cpp11 all 0.4.7-1 [266 kB]
1136s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biocparallel amd64 1.36.0-1 [1347 kB]
1136s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-iranges amd64 2.36.0-1 [2252 kB]
1136s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-zlibbioc all 1.48.0+dfsg-1 [9596 B]
1136s Get:124 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-xvector amd64 0.42.0-1 [621 kB]
1136s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-bitops amd64 1.0-7-1 [29.8 kB]
1136s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcurl amd64 1.98-1.14+dfsg-1 [793 kB]
1136s Get:127 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodbdata all 1.2.11-2 [12.3 MB]
1136s Get:128 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomeinfodb all 1.38.6+dfsg-1 [3886 kB]
1136s Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-crayon all 1.5.2-1 [164 kB]
1136s Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-biostrings amd64 2.70.2+dfsg-1 [13.6 MB]
1136s Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicranges amd64 1.54.1+dfsg-1 [1823 kB]
1136s Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-xml amd64 3.99-0.16.1-1 [1733 kB]
1136s Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rhtslib amd64 2.4.1+dfsg-1 [1361 kB]
1136s Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rsamtools amd64 2.18.0+dfsg-1 [3640 kB]
1136s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrixstats amd64 1.2.0-1 [488 kB]
1136s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-matrixgenerics all 1.14.0-1 [407 kB]
1136s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB]
1136s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB]
1136s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-abind all 1.4-5-2 [63.6 kB]
1136s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-s4arrays amd64 1.2.0+dfsg-1 [501 kB]
1136s Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-sparsearray amd64 1.2.4+dfsg-1 [1195 kB]
1136s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-delayedarray amd64 0.28.0+dfsg-1 [1787 kB]
1136s Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-summarizedexperiment all 1.32.0+dfsg-1 [1134 kB]
1136s Get:144 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-genomicalignments amd64 1.38.2-1 [2133 kB]
1136s Get:145 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-littler amd64 0.3.19-1 [94.1 kB]
1136s Get:146 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rjson amd64 0.2.21-1 [143 kB]
1136s Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-yaml amd64 2.3.8-1 [108 kB]
1136s Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
1136s Get:149 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-rtracklayer amd64 1.62.0-1 [5108 kB]
1136s Get:150 http://ftpmaster.internal/ubuntu noble/universe amd64 r-bioc-bsgenome all 1.70.2-1 [6975 kB]
1136s Get:151 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-biocmanager all 1.30.22+dfsg-2 [125 kB]
1136s Get:152 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-runit all 0.4.32-3 [283 kB]
1137s Preconfiguring packages ...
1137s Fetched 229 MB in 2s (134 MB/s)
1137s Selecting previously unselected package libc-dev-bin.
1137s (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 ... 71421 files and directories currently installed.)
1137s Preparing to unpack .../000-libc-dev-bin_2.39-0ubuntu2_amd64.deb ...
1137s Unpacking libc-dev-bin (2.39-0ubuntu2) ...
1137s Selecting previously unselected package linux-libc-dev:amd64.
1137s Preparing to unpack .../001-linux-libc-dev_6.8.0-11.11_amd64.deb ...
1137s Unpacking linux-libc-dev:amd64 (6.8.0-11.11) ...
1137s Selecting previously unselected package libcrypt-dev:amd64.
1137s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
1137s Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
1137s Selecting previously unselected package libtirpc-dev:amd64.
1137s Preparing to unpack .../003-libtirpc-dev_1.3.4+ds-1build1_amd64.deb ...
1137s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
1137s Selecting previously unselected package libnsl-dev:amd64.
1137s Preparing to unpack .../004-libnsl-dev_1.3.0-3_amd64.deb ...
1137s Unpacking libnsl-dev:amd64 (1.3.0-3) ...
1137s Selecting previously unselected package rpcsvc-proto.
1137s Preparing to unpack .../005-rpcsvc-proto_1.4.2-0ubuntu6_amd64.deb ...
1137s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
1137s Selecting previously unselected package libc6-dev:amd64.
1137s Preparing to unpack .../006-libc6-dev_2.39-0ubuntu2_amd64.deb ...
1137s Unpacking libc6-dev:amd64 (2.39-0ubuntu2) ...
1138s Selecting previously unselected package libisl23:amd64.
1138s Preparing to unpack .../007-libisl23_0.26-3_amd64.deb ...
1138s Unpacking libisl23:amd64 (0.26-3) ...
1138s Selecting previously unselected package libmpc3:amd64.
1138s Preparing to unpack .../008-libmpc3_1.3.1-1_amd64.deb ...
1138s Unpacking libmpc3:amd64 (1.3.1-1) ...
1138s Selecting previously unselected package cpp-13-x86-64-linux-gnu.
1138s Preparing to unpack .../009-cpp-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1138s Unpacking cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1138s Selecting previously unselected package cpp-13.
1138s Preparing to unpack .../010-cpp-13_13.2.0-17ubuntu2_amd64.deb ...
1138s Unpacking cpp-13 (13.2.0-17ubuntu2) ...
1138s Selecting previously unselected package cpp-x86-64-linux-gnu.
1138s Preparing to unpack .../011-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1138s Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1138s Selecting previously unselected package cpp.
1138s Preparing to unpack .../012-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ...
1138s Unpacking cpp (4:13.2.0-7ubuntu1) ...
1138s Selecting previously unselected package libcc1-0:amd64.
1138s Preparing to unpack .../013-libcc1-0_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libcc1-0:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libgomp1:amd64.
1138s Preparing to unpack .../014-libgomp1_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libitm1:amd64.
1138s Preparing to unpack .../015-libitm1_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libitm1:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libatomic1:amd64.
1138s Preparing to unpack .../016-libatomic1_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libatomic1:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libasan8:amd64.
1138s Preparing to unpack .../017-libasan8_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libasan8:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package liblsan0:amd64.
1138s Preparing to unpack .../018-liblsan0_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking liblsan0:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libtsan2:amd64.
1138s Preparing to unpack .../019-libtsan2_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libtsan2:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libubsan1:amd64.
1138s Preparing to unpack .../020-libubsan1_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libubsan1:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libhwasan0:amd64.
1138s Preparing to unpack .../021-libhwasan0_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libhwasan0:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libquadmath0:amd64.
1138s Preparing to unpack .../022-libquadmath0_14-20240303-1ubuntu1_amd64.deb ...
1138s Unpacking libquadmath0:amd64 (14-20240303-1ubuntu1) ...
1138s Selecting previously unselected package libgcc-13-dev:amd64.
1138s Preparing to unpack .../023-libgcc-13-dev_13.2.0-17ubuntu2_amd64.deb ...
1138s Unpacking libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
1138s Selecting previously unselected package gcc-13-x86-64-linux-gnu.
1138s Preparing to unpack .../024-gcc-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1138s Unpacking gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1139s Selecting previously unselected package gcc-13.
1139s Preparing to unpack .../025-gcc-13_13.2.0-17ubuntu2_amd64.deb ...
1139s Unpacking gcc-13 (13.2.0-17ubuntu2) ...
1139s Selecting previously unselected package gcc-x86-64-linux-gnu.
1139s Preparing to unpack .../026-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1139s Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1139s Selecting previously unselected package gcc.
1139s Preparing to unpack .../027-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
1139s Unpacking gcc (4:13.2.0-7ubuntu1) ...
1139s Selecting previously unselected package libstdc++-13-dev:amd64.
1139s Preparing to unpack .../028-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ...
1139s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
1139s Selecting previously unselected package g++-13-x86-64-linux-gnu.
1139s Preparing to unpack .../029-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1139s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1139s Selecting previously unselected package g++-13.
1139s Preparing to unpack .../030-g++-13_13.2.0-17ubuntu2_amd64.deb ...
1139s Unpacking g++-13 (13.2.0-17ubuntu2) ...
1139s Selecting previously unselected package g++-x86-64-linux-gnu.
1139s Preparing to unpack .../031-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1139s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1139s Selecting previously unselected package g++.
1139s Preparing to unpack .../032-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
1139s Unpacking g++ (4:13.2.0-7ubuntu1) ...
1139s Selecting previously unselected package build-essential.
1139s Preparing to unpack .../033-build-essential_12.10ubuntu1_amd64.deb ...
1139s Unpacking build-essential (12.10ubuntu1) ...
1139s Selecting previously unselected package dctrl-tools.
1139s Preparing to unpack .../034-dctrl-tools_2.24-3build2_amd64.deb ...
1139s Unpacking dctrl-tools (2.24-3build2) ...
1139s Selecting previously unselected package fonts-dejavu-mono.
1139s Preparing to unpack .../035-fonts-dejavu-mono_2.37-8_all.deb ...
1139s Unpacking fonts-dejavu-mono (2.37-8) ...
1139s Selecting previously unselected package fonts-dejavu-core.
1139s Preparing to unpack .../036-fonts-dejavu-core_2.37-8_all.deb ...
1139s Unpacking fonts-dejavu-core (2.37-8) ...
1139s Selecting previously unselected package fontconfig-config.
1139s Preparing to unpack .../037-fontconfig-config_2.15.0-1ubuntu1_amd64.deb ...
1140s Unpacking fontconfig-config (2.15.0-1ubuntu1) ...
1140s Selecting previously unselected package libfontconfig1:amd64.
1140s Preparing to unpack .../038-libfontconfig1_2.15.0-1ubuntu1_amd64.deb ...
1140s Unpacking libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
1140s Selecting previously unselected package fontconfig.
1140s Preparing to unpack .../039-fontconfig_2.15.0-1ubuntu1_amd64.deb ...
1140s Unpacking fontconfig (2.15.0-1ubuntu1) ...
1140s Selecting previously unselected package libgfortran5:amd64.
1140s Preparing to unpack .../040-libgfortran5_14-20240303-1ubuntu1_amd64.deb ...
1140s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ...
1140s Selecting previously unselected package libgfortran-13-dev:amd64.
1140s Preparing to unpack .../041-libgfortran-13-dev_13.2.0-17ubuntu2_amd64.deb ...
1140s Unpacking libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
1140s Selecting previously unselected package gfortran-13-x86-64-linux-gnu.
1140s Preparing to unpack .../042-gfortran-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ...
1140s Unpacking gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1140s Selecting previously unselected package gfortran-13.
1140s Preparing to unpack .../043-gfortran-13_13.2.0-17ubuntu2_amd64.deb ...
1140s Unpacking gfortran-13 (13.2.0-17ubuntu2) ...
1140s Selecting previously unselected package gfortran-x86-64-linux-gnu.
1140s Preparing to unpack .../044-gfortran-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
1140s Unpacking gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1140s Selecting previously unselected package gfortran.
1140s Preparing to unpack .../045-gfortran_4%3a13.2.0-7ubuntu1_amd64.deb ...
1140s Unpacking gfortran (4:13.2.0-7ubuntu1) ...
1140s Selecting previously unselected package icu-devtools.
1140s Preparing to unpack .../046-icu-devtools_74.2-1ubuntu1_amd64.deb ...
1140s Unpacking icu-devtools (74.2-1ubuntu1) ...
1140s Selecting previously unselected package libblas3:amd64.
1140s Preparing to unpack .../047-libblas3_3.12.0-3_amd64.deb ...
1140s Unpacking libblas3:amd64 (3.12.0-3) ...
1140s Selecting previously unselected package libblas-dev:amd64.
1140s Preparing to unpack .../048-libblas-dev_3.12.0-3_amd64.deb ...
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1140s Selecting previously unselected package libboost1.83-dev:amd64.
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1142s Selecting previously unselected package libboost-dev:amd64.
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1143s Selecting previously unselected package libbz2-dev:amd64.
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1143s Selecting previously unselected package libpixman-1-0:amd64.
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1143s Selecting previously unselected package libxcb-render0:amd64.
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1143s Selecting previously unselected package libxcb-shm0:amd64.
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1143s Selecting previously unselected package libxrender1:amd64.
1143s Preparing to unpack .../055-libxrender1_1%3a0.9.10-1.1_amd64.deb ...
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1143s Selecting previously unselected package libcairo2:amd64.
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1143s Selecting previously unselected package libdatrie1:amd64.
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1143s Selecting previously unselected package libdeflate0:amd64.
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1143s Selecting previously unselected package libgraphite2-3:amd64.
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1143s Selecting previously unselected package libharfbuzz0b:amd64.
1143s Preparing to unpack .../060-libharfbuzz0b_8.3.0-2_amd64.deb ...
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1143s Selecting previously unselected package x11-common.
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1143s Selecting previously unselected package libice6:amd64.
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1143s Selecting previously unselected package libicu-dev:amd64.
1143s Preparing to unpack .../063-libicu-dev_74.2-1ubuntu1_amd64.deb ...
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1143s Selecting previously unselected package libjpeg-turbo8:amd64.
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1143s Selecting previously unselected package libjpeg8:amd64.
1143s Preparing to unpack .../066-libjpeg8_8c-2ubuntu11_amd64.deb ...
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1143s Selecting previously unselected package libjpeg8-dev:amd64.
1143s Preparing to unpack .../067-libjpeg8-dev_8c-2ubuntu11_amd64.deb ...
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1143s Selecting previously unselected package libjpeg-dev:amd64.
1143s Preparing to unpack .../068-libjpeg-dev_8c-2ubuntu11_amd64.deb ...
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1143s Selecting previously unselected package liblapack3:amd64.
1143s Preparing to unpack .../069-liblapack3_3.12.0-3_amd64.deb ...
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1143s Selecting previously unselected package liblapack-dev:amd64.
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1144s Selecting previously unselected package liblerc4:amd64.
1144s Preparing to unpack .../071-liblerc4_4.0.0+ds-4ubuntu1_amd64.deb ...
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1144s Selecting previously unselected package libncurses-dev:amd64.
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1144s Selecting previously unselected package libthai-data.
1144s Preparing to unpack .../073-libthai-data_0.1.29-2_all.deb ...
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1144s Selecting previously unselected package libthai0:amd64.
1144s Preparing to unpack .../074-libthai0_0.1.29-2_amd64.deb ...
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1144s Selecting previously unselected package libpango-1.0-0:amd64.
1144s Preparing to unpack .../075-libpango-1.0-0_1.51.0+ds-4_amd64.deb ...
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1144s Selecting previously unselected package libpangoft2-1.0-0:amd64.
1144s Preparing to unpack .../076-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ...
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1144s Selecting previously unselected package libpangocairo-1.0-0:amd64.
1144s Preparing to unpack .../077-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ...
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1144s Selecting previously unselected package libpaper1:amd64.
1144s Preparing to unpack .../078-libpaper1_1.1.29_amd64.deb ...
1144s Unpacking libpaper1:amd64 (1.1.29) ...
1144s Selecting previously unselected package libpaper-utils.
1144s Preparing to unpack .../079-libpaper-utils_1.1.29_amd64.deb ...
1144s Unpacking libpaper-utils (1.1.29) ...
1144s Selecting previously unselected package libpcre2-16-0:amd64.
1144s Preparing to unpack .../080-libpcre2-16-0_10.42-4ubuntu1_amd64.deb ...
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1144s Selecting previously unselected package libpcre2-32-0:amd64.
1144s Preparing to unpack .../081-libpcre2-32-0_10.42-4ubuntu1_amd64.deb ...
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1144s Selecting previously unselected package libpcre2-posix3:amd64.
1144s Preparing to unpack .../082-libpcre2-posix3_10.42-4ubuntu1_amd64.deb ...
1144s Unpacking libpcre2-posix3:amd64 (10.42-4ubuntu1) ...
1144s Selecting previously unselected package libpcre2-dev:amd64.
1144s Preparing to unpack .../083-libpcre2-dev_10.42-4ubuntu1_amd64.deb ...
1144s Unpacking libpcre2-dev:amd64 (10.42-4ubuntu1) ...
1144s Selecting previously unselected package libpkgconf3:amd64.
1144s Preparing to unpack .../084-libpkgconf3_1.8.1-2_amd64.deb ...
1144s Unpacking libpkgconf3:amd64 (1.8.1-2) ...
1144s Selecting previously unselected package zlib1g-dev:amd64.
1144s Preparing to unpack .../085-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_amd64.deb ...
1144s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ...
1144s Selecting previously unselected package libpng-dev:amd64.
1144s Preparing to unpack .../086-libpng-dev_1.6.43-1_amd64.deb ...
1144s Unpacking libpng-dev:amd64 (1.6.43-1) ...
1144s Selecting previously unselected package libreadline-dev:amd64.
1144s Preparing to unpack .../087-libreadline-dev_8.2-3_amd64.deb ...
1144s Unpacking libreadline-dev:amd64 (8.2-3) ...
1144s Selecting previously unselected package libsharpyuv0:amd64.
1144s Preparing to unpack .../088-libsharpyuv0_1.3.2-0.4_amd64.deb ...
1144s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ...
1144s Selecting previously unselected package libsm6:amd64.
1144s Preparing to unpack .../089-libsm6_2%3a1.2.3-1build2_amd64.deb ...
1144s Unpacking libsm6:amd64 (2:1.2.3-1build2) ...
1144s Selecting previously unselected package libtcl8.6:amd64.
1144s Preparing to unpack .../090-libtcl8.6_8.6.13+dfsg-2_amd64.deb ...
1144s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ...
1144s Selecting previously unselected package libjbig0:amd64.
1144s Preparing to unpack .../091-libjbig0_2.1-6.1ubuntu1_amd64.deb ...
1144s Unpacking libjbig0:amd64 (2.1-6.1ubuntu1) ...
1144s Selecting previously unselected package libwebp7:amd64.
1144s Preparing to unpack .../092-libwebp7_1.3.2-0.4_amd64.deb ...
1144s Unpacking libwebp7:amd64 (1.3.2-0.4) ...
1144s Selecting previously unselected package libtiff6:amd64.
1144s Preparing to unpack .../093-libtiff6_4.5.1+git230720-3ubuntu1_amd64.deb ...
1144s Unpacking libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
1144s Selecting previously unselected package libxft2:amd64.
1144s Preparing to unpack .../094-libxft2_2.3.6-1_amd64.deb ...
1144s Unpacking libxft2:amd64 (2.3.6-1) ...
1144s Selecting previously unselected package libxss1:amd64.
1144s Preparing to unpack .../095-libxss1_1%3a1.2.3-1build2_amd64.deb ...
1144s Unpacking libxss1:amd64 (1:1.2.3-1build2) ...
1144s Selecting previously unselected package libtk8.6:amd64.
1144s Preparing to unpack .../096-libtk8.6_8.6.13-2_amd64.deb ...
1144s Unpacking libtk8.6:amd64 (8.6.13-2) ...
1144s Selecting previously unselected package libxt6:amd64.
1144s Preparing to unpack .../097-libxt6_1%3a1.2.1-1.1_amd64.deb ...
1144s Unpacking libxt6:amd64 (1:1.2.1-1.1) ...
1144s Selecting previously unselected package pkgconf-bin.
1144s Preparing to unpack .../098-pkgconf-bin_1.8.1-2_amd64.deb ...
1144s Unpacking pkgconf-bin (1.8.1-2) ...
1144s Selecting previously unselected package pkgconf:amd64.
1144s Preparing to unpack .../099-pkgconf_1.8.1-2_amd64.deb ...
1144s Unpacking pkgconf:amd64 (1.8.1-2) ...
1144s Selecting previously unselected package pkg-config:amd64.
1144s Preparing to unpack .../100-pkg-config_1.8.1-2_amd64.deb ...
1144s Unpacking pkg-config:amd64 (1.8.1-2) ...
1144s Selecting previously unselected package zip.
1144s Preparing to unpack .../101-zip_3.0-13_amd64.deb ...
1144s Unpacking zip (3.0-13) ...
1145s Selecting previously unselected package unzip.
1145s Preparing to unpack .../102-unzip_6.0-28ubuntu3_amd64.deb ...
1145s Unpacking unzip (6.0-28ubuntu3) ...
1145s Selecting previously unselected package xdg-utils.
1145s Preparing to unpack .../103-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
1145s Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
1145s Selecting previously unselected package r-base-core.
1145s Preparing to unpack .../104-r-base-core_4.3.2-1build1_amd64.deb ...
1145s Unpacking r-base-core (4.3.2-1build1) ...
1145s Selecting previously unselected package liblzma-dev:amd64.
1145s Preparing to unpack .../105-liblzma-dev_5.4.5-0.3_amd64.deb ...
1145s Unpacking liblzma-dev:amd64 (5.4.5-0.3) ...
1145s Selecting previously unselected package r-base-dev.
1145s Preparing to unpack .../106-r-base-dev_4.3.2-1build1_all.deb ...
1145s Unpacking r-base-dev (4.3.2-1build1) ...
1145s Selecting previously unselected package pkg-r-autopkgtest.
1145s Preparing to unpack .../107-pkg-r-autopkgtest_20231212ubuntu1_all.deb ...
1145s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ...
1145s Selecting previously unselected package r-bioc-biocgenerics.
1145s Preparing to unpack .../108-r-bioc-biocgenerics_0.48.1-2_all.deb ...
1145s Unpacking r-bioc-biocgenerics (0.48.1-2) ...
1145s Selecting previously unselected package r-bioc-biobase.
1145s Preparing to unpack .../109-r-bioc-biobase_2.62.0-1_amd64.deb ...
1145s Unpacking r-bioc-biobase (2.62.0-1) ...
1145s Selecting previously unselected package r-bioc-s4vectors.
1145s Preparing to unpack .../110-r-bioc-s4vectors_0.40.2+dfsg-1_amd64.deb ...
1145s Unpacking r-bioc-s4vectors (0.40.2+dfsg-1) ...
1145s Selecting previously unselected package r-bioc-biocio.
1145s Preparing to unpack .../111-r-bioc-biocio_1.12.0+dfsg-1_all.deb ...
1145s Unpacking r-bioc-biocio (1.12.0+dfsg-1) ...
1145s Selecting previously unselected package r-cran-formatr.
1145s Preparing to unpack .../112-r-cran-formatr_1.14-1_all.deb ...
1145s Unpacking r-cran-formatr (1.14-1) ...
1145s Selecting previously unselected package r-cran-lambda.r.
1145s Preparing to unpack .../113-r-cran-lambda.r_1.2.4-2build1_all.deb ...
1145s Unpacking r-cran-lambda.r (1.2.4-2build1) ...
1145s Selecting previously unselected package r-cran-futile.options.
1145s Preparing to unpack .../114-r-cran-futile.options_1.0.1-3build1_all.deb ...
1145s Unpacking r-cran-futile.options (1.0.1-3build1) ...
1145s Selecting previously unselected package r-cran-futile.logger.
1145s Preparing to unpack .../115-r-cran-futile.logger_1.4.3-4build1_all.deb ...
1145s Unpacking r-cran-futile.logger (1.4.3-4build1) ...
1145s Selecting previously unselected package r-cran-snow.
1145s Preparing to unpack .../116-r-cran-snow_1%3a0.4.4-2_all.deb ...
1145s Unpacking r-cran-snow (1:0.4.4-2) ...
1145s Selecting previously unselected package r-cran-codetools.
1145s Preparing to unpack .../117-r-cran-codetools_0.2-19-1_all.deb ...
1145s Unpacking r-cran-codetools (0.2-19-1) ...
1145s Selecting previously unselected package r-cran-bh.
1145s Preparing to unpack .../118-r-cran-bh_1.84.0-1_all.deb ...
1145s Unpacking r-cran-bh (1.84.0-1) ...
1145s Selecting previously unselected package r-cran-cpp11.
1145s Preparing to unpack .../119-r-cran-cpp11_0.4.7-1_all.deb ...
1145s Unpacking r-cran-cpp11 (0.4.7-1) ...
1145s Selecting previously unselected package r-bioc-biocparallel.
1145s Preparing to unpack .../120-r-bioc-biocparallel_1.36.0-1_amd64.deb ...
1145s Unpacking r-bioc-biocparallel (1.36.0-1) ...
1145s Selecting previously unselected package r-bioc-iranges.
1145s Preparing to unpack .../121-r-bioc-iranges_2.36.0-1_amd64.deb ...
1145s Unpacking r-bioc-iranges (2.36.0-1) ...
1146s Selecting previously unselected package r-bioc-zlibbioc.
1146s Preparing to unpack .../122-r-bioc-zlibbioc_1.48.0+dfsg-1_all.deb ...
1146s Unpacking r-bioc-zlibbioc (1.48.0+dfsg-1) ...
1146s Selecting previously unselected package r-bioc-xvector.
1146s Preparing to unpack .../123-r-bioc-xvector_0.42.0-1_amd64.deb ...
1146s Unpacking r-bioc-xvector (0.42.0-1) ...
1146s Selecting previously unselected package r-cran-bitops.
1146s Preparing to unpack .../124-r-cran-bitops_1.0-7-1_amd64.deb ...
1146s Unpacking r-cran-bitops (1.0-7-1) ...
1146s Selecting previously unselected package r-cran-rcurl.
1146s Preparing to unpack .../125-r-cran-rcurl_1.98-1.14+dfsg-1_amd64.deb ...
1146s Unpacking r-cran-rcurl (1.98-1.14+dfsg-1) ...
1146s Selecting previously unselected package r-bioc-genomeinfodbdata.
1146s Preparing to unpack .../126-r-bioc-genomeinfodbdata_1.2.11-2_all.deb ...
1146s Unpacking r-bioc-genomeinfodbdata (1.2.11-2) ...
1146s Selecting previously unselected package r-bioc-genomeinfodb.
1146s Preparing to unpack .../127-r-bioc-genomeinfodb_1.38.6+dfsg-1_all.deb ...
1146s Unpacking r-bioc-genomeinfodb (1.38.6+dfsg-1) ...
1146s Selecting previously unselected package r-cran-crayon.
1146s Preparing to unpack .../128-r-cran-crayon_1.5.2-1_all.deb ...
1146s Unpacking r-cran-crayon (1.5.2-1) ...
1146s Selecting previously unselected package r-bioc-biostrings.
1146s Preparing to unpack .../129-r-bioc-biostrings_2.70.2+dfsg-1_amd64.deb ...
1146s Unpacking r-bioc-biostrings (2.70.2+dfsg-1) ...
1146s Selecting previously unselected package r-bioc-genomicranges.
1146s Preparing to unpack .../130-r-bioc-genomicranges_1.54.1+dfsg-1_amd64.deb ...
1146s Unpacking r-bioc-genomicranges (1.54.1+dfsg-1) ...
1146s Selecting previously unselected package r-cran-xml.
1146s Preparing to unpack .../131-r-cran-xml_3.99-0.16.1-1_amd64.deb ...
1146s Unpacking r-cran-xml (3.99-0.16.1-1) ...
1146s Selecting previously unselected package r-bioc-rhtslib.
1146s Preparing to unpack .../132-r-bioc-rhtslib_2.4.1+dfsg-1_amd64.deb ...
1146s Unpacking r-bioc-rhtslib (2.4.1+dfsg-1) ...
1146s Selecting previously unselected package r-bioc-rsamtools.
1146s Preparing to unpack .../133-r-bioc-rsamtools_2.18.0+dfsg-1_amd64.deb ...
1146s Unpacking r-bioc-rsamtools (2.18.0+dfsg-1) ...
1146s Selecting previously unselected package r-cran-matrixstats.
1146s Preparing to unpack .../134-r-cran-matrixstats_1.2.0-1_amd64.deb ...
1146s Unpacking r-cran-matrixstats (1.2.0-1) ...
1146s Selecting previously unselected package r-bioc-matrixgenerics.
1146s Preparing to unpack .../135-r-bioc-matrixgenerics_1.14.0-1_all.deb ...
1146s Unpacking r-bioc-matrixgenerics (1.14.0-1) ...
1146s Selecting previously unselected package r-cran-lattice.
1146s Preparing to unpack .../136-r-cran-lattice_0.22-5-1_amd64.deb ...
1146s Unpacking r-cran-lattice (0.22-5-1) ...
1146s Selecting previously unselected package r-cran-matrix.
1146s Preparing to unpack .../137-r-cran-matrix_1.6-5-1_amd64.deb ...
1146s Unpacking r-cran-matrix (1.6-5-1) ...
1147s Selecting previously unselected package r-cran-abind.
1147s Preparing to unpack .../138-r-cran-abind_1.4-5-2_all.deb ...
1147s Unpacking r-cran-abind (1.4-5-2) ...
1147s Selecting previously unselected package r-bioc-s4arrays.
1147s Preparing to unpack .../139-r-bioc-s4arrays_1.2.0+dfsg-1_amd64.deb ...
1147s Unpacking r-bioc-s4arrays (1.2.0+dfsg-1) ...
1147s Selecting previously unselected package r-bioc-sparsearray.
1147s Preparing to unpack .../140-r-bioc-sparsearray_1.2.4+dfsg-1_amd64.deb ...
1147s Unpacking r-bioc-sparsearray (1.2.4+dfsg-1) ...
1147s Selecting previously unselected package r-bioc-delayedarray.
1147s Preparing to unpack .../141-r-bioc-delayedarray_0.28.0+dfsg-1_amd64.deb ...
1147s Unpacking r-bioc-delayedarray (0.28.0+dfsg-1) ...
1147s Selecting previously unselected package r-bioc-summarizedexperiment.
1147s Preparing to unpack .../142-r-bioc-summarizedexperiment_1.32.0+dfsg-1_all.deb ...
1147s Unpacking r-bioc-summarizedexperiment (1.32.0+dfsg-1) ...
1147s Selecting previously unselected package r-bioc-genomicalignments.
1147s Preparing to unpack .../143-r-bioc-genomicalignments_1.38.2-1_amd64.deb ...
1147s Unpacking r-bioc-genomicalignments (1.38.2-1) ...
1147s Selecting previously unselected package r-cran-littler.
1147s Preparing to unpack .../144-r-cran-littler_0.3.19-1_amd64.deb ...
1147s Unpacking r-cran-littler (0.3.19-1) ...
1147s Selecting previously unselected package r-cran-rjson.
1147s Preparing to unpack .../145-r-cran-rjson_0.2.21-1_amd64.deb ...
1147s Unpacking r-cran-rjson (0.2.21-1) ...
1147s Selecting previously unselected package r-cran-yaml.
1147s Preparing to unpack .../146-r-cran-yaml_2.3.8-1_amd64.deb ...
1147s Unpacking r-cran-yaml (2.3.8-1) ...
1147s Selecting previously unselected package r-cran-restfulr.
1147s Preparing to unpack .../147-r-cran-restfulr_0.0.15-1_amd64.deb ...
1147s Unpacking r-cran-restfulr (0.0.15-1) ...
1147s Selecting previously unselected package r-bioc-rtracklayer.
1147s Preparing to unpack .../148-r-bioc-rtracklayer_1.62.0-1_amd64.deb ...
1147s Unpacking r-bioc-rtracklayer (1.62.0-1) ...
1147s Selecting previously unselected package r-bioc-bsgenome.
1147s Preparing to unpack .../149-r-bioc-bsgenome_1.70.2-1_all.deb ...
1147s Unpacking r-bioc-bsgenome (1.70.2-1) ...
1147s Selecting previously unselected package r-cran-biocmanager.
1147s Preparing to unpack .../150-r-cran-biocmanager_1.30.22+dfsg-2_all.deb ...
1147s Unpacking r-cran-biocmanager (1.30.22+dfsg-2) ...
1147s Selecting previously unselected package r-cran-runit.
1147s Preparing to unpack .../151-r-cran-runit_0.4.32-3_all.deb ...
1147s Unpacking r-cran-runit (0.4.32-3) ...
1147s Setting up libgraphite2-3:amd64 (1.3.14-2) ...
1147s Setting up libpixman-1-0:amd64 (0.42.2-1) ...
1147s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ...
1147s Setting up libpaper1:amd64 (1.1.29) ...
1147s 
1147s Creating config file /etc/papersize with new version
1147s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ...
1147s Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
1147s Setting up libdatrie1:amd64 (0.2.13-3) ...
1147s Setting up libxcb-render0:amd64 (1.15-1) ...
1147s Setting up unzip (6.0-28ubuntu3) ...
1147s Setting up x11-common (1:7.7+23ubuntu2) ...
1148s Setting up libdeflate0:amd64 (1.19-1) ...
1148s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ...
1148s Setting up libxcb-shm0:amd64 (1.15-1) ...
1148s Setting up libpaper-utils (1.1.29) ...
1148s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ...
1148s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu1) ...
1148s Setting up zip (3.0-13) ...
1148s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu1) ...
1148s Setting up libblas3:amd64 (3.12.0-3) ...
1148s 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
1148s Setting up libtirpc-dev:amd64 (1.3.4+ds-1build1) ...
1148s Setting up libpkgconf3:amd64 (1.8.1-2) ...
1148s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
1148s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up fonts-dejavu-mono (2.37-8) ...
1148s Setting up libmpc3:amd64 (1.3.1-1) ...
1148s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ...
1148s Setting up icu-devtools (74.2-1ubuntu1) ...
1148s Setting up fonts-dejavu-core (2.37-8) ...
1148s Setting up pkgconf-bin (1.8.1-2) ...
1148s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ...
1148s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libwebp7:amd64 (1.3.2-0.4) ...
1148s Setting up liblzma-dev:amd64 (5.4.5-0.3) ...
1148s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu1) ...
1148s Setting up libnsl-dev:amd64 (1.3.0-3) ...
1148s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ...
1148s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libharfbuzz0b:amd64 (8.3.0-2) ...
1148s Setting up libthai-data (0.1.29-2) ...
1148s Setting up libxss1:amd64 (1:1.2.3-1build2) ...
1148s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libisl23:amd64 (0.26-3) ...
1148s Setting up libc-dev-bin (2.39-0ubuntu2) ...
1148s Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
1148s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
1148s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libblas-dev:amd64 (3.12.0-3) ...
1148s 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
1148s Setting up dctrl-tools (2.24-3build2) ...
1148s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ...
1148s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
1148s Setting up libice6:amd64 (2:1.0.10-1build2) ...
1148s Setting up liblapack3:amd64 (3.12.0-3) ...
1148s 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
1148s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1148s Setting up fontconfig-config (2.15.0-1ubuntu1) ...
1148s Setting up pkgconf:amd64 (1.8.1-2) ...
1148s Setting up libthai0:amd64 (0.1.29-2) ...
1148s Setting up liblapack-dev:amd64 (3.12.0-3) ...
1148s 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
1148s Setting up pkg-config:amd64 (1.8.1-2) ...
1148s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ...
1148s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ...
1148s Setting up libc6-dev:amd64 (2.39-0ubuntu2) ...
1148s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ...
1148s Setting up libgfortran-13-dev:amd64 (13.2.0-17ubuntu2) ...
1148s Setting up libsm6:amd64 (2:1.2.3-1build2) ...
1148s Setting up libicu-dev:amd64 (74.2-1ubuntu1) ...
1148s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ...
1148s Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ...
1148s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1148s Setting up fontconfig (2.15.0-1ubuntu1) ...
1150s Regenerating fonts cache... done.
1150s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ...
1150s Setting up libxft2:amd64 (2.3.6-1) ...
1150s Setting up libboost1.83-dev:amd64 (1.83.0-2ubuntu1) ...
1150s Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ...
1150s Setting up libpcre2-dev:amd64 (10.42-4ubuntu1) ...
1150s Setting up cpp-13 (13.2.0-17ubuntu2) ...
1150s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1150s Setting up libtk8.6:amd64 (8.6.13-2) ...
1150s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ...
1150s Setting up libreadline-dev:amd64 (8.2-3) ...
1150s Setting up gfortran-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1150s Setting up libcairo2:amd64 (1.18.0-1) ...
1150s Setting up gcc-13 (13.2.0-17ubuntu2) ...
1150s Setting up libxt6:amd64 (1:1.2.1-1.1) ...
1150s Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ...
1150s Setting up cpp (4:13.2.0-7ubuntu1) ...
1150s Setting up libboost-dev:amd64 (1.83.0.1ubuntu2) ...
1150s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ...
1150s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
1150s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ...
1150s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ...
1150s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1150s Setting up libpng-dev:amd64 (1.6.43-1) ...
1150s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
1150s Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1150s Setting up gcc (4:13.2.0-7ubuntu1) ...
1150s Setting up gfortran-13 (13.2.0-17ubuntu2) ...
1150s Setting up r-base-core (4.3.2-1build1) ...
1151s 
1151s Creating config file /etc/R/Renviron with new version
1151s Setting up r-cran-crayon (1.5.2-1) ...
1151s Setting up r-cran-futile.options (1.0.1-3build1) ...
1151s Setting up r-cran-lattice (0.22-5-1) ...
1151s Setting up r-cran-formatr (1.14-1) ...
1151s Setting up r-cran-xml (3.99-0.16.1-1) ...
1151s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
1151s Setting up r-bioc-genomeinfodbdata (1.2.11-2) ...
1151s Setting up r-cran-littler (0.3.19-1) ...
1151s Setting up r-cran-bh (1.84.0-1) ...
1151s Setting up r-cran-codetools (0.2-19-1) ...
1151s Setting up g++-13 (13.2.0-17ubuntu2) ...
1151s Setting up r-bioc-biocgenerics (0.48.1-2) ...
1151s Setting up r-cran-matrixstats (1.2.0-1) ...
1151s Setting up r-bioc-matrixgenerics (1.14.0-1) ...
1151s Setting up r-cran-abind (1.4-5-2) ...
1151s Setting up r-cran-yaml (2.3.8-1) ...
1151s Setting up r-cran-lambda.r (1.2.4-2build1) ...
1151s Setting up r-cran-snow (1:0.4.4-2) ...
1151s Setting up gfortran (4:13.2.0-7ubuntu1) ...
1151s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
1151s 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
1151s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
1151s 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
1151s Setting up r-cran-bitops (1.0-7-1) ...
1151s Setting up r-cran-biocmanager (1.30.22+dfsg-2) ...
1151s Setting up r-bioc-zlibbioc (1.48.0+dfsg-1) ...
1151s Setting up r-bioc-biobase (2.62.0-1) ...
1151s Setting up r-cran-cpp11 (0.4.7-1) ...
1151s Setting up r-bioc-s4vectors (0.40.2+dfsg-1) ...
1151s Setting up r-cran-runit (0.4.32-3) ...
1151s Setting up r-cran-futile.logger (1.4.3-4build1) ...
1151s Setting up r-cran-matrix (1.6-5-1) ...
1151s Setting up g++ (4:13.2.0-7ubuntu1) ...
1151s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
1151s Setting up build-essential (12.10ubuntu1) ...
1151s Setting up r-bioc-iranges (2.36.0-1) ...
1151s Setting up r-cran-rjson (0.2.21-1) ...
1151s Setting up r-cran-rcurl (1.98-1.14+dfsg-1) ...
1151s Setting up r-cran-restfulr (0.0.15-1) ...
1151s Setting up r-base-dev (4.3.2-1build1) ...
1151s Setting up r-bioc-s4arrays (1.2.0+dfsg-1) ...
1151s Setting up r-bioc-biocparallel (1.36.0-1) ...
1151s Setting up r-bioc-rhtslib (2.4.1+dfsg-1) ...
1151s Setting up r-bioc-biocio (1.12.0+dfsg-1) ...
1151s Setting up r-bioc-genomeinfodb (1.38.6+dfsg-1) ...
1151s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
1151s Setting up r-bioc-xvector (0.42.0-1) ...
1151s Setting up r-bioc-sparsearray (1.2.4+dfsg-1) ...
1151s Setting up r-bioc-genomicranges (1.54.1+dfsg-1) ...
1151s Setting up r-bioc-biostrings (2.70.2+dfsg-1) ...
1151s Setting up r-bioc-rsamtools (2.18.0+dfsg-1) ...
1151s Setting up r-bioc-delayedarray (0.28.0+dfsg-1) ...
1151s Setting up r-bioc-summarizedexperiment (1.32.0+dfsg-1) ...
1151s Setting up r-bioc-genomicalignments (1.38.2-1) ...
1151s Setting up r-bioc-rtracklayer (1.62.0-1) ...
1151s Setting up r-bioc-bsgenome (1.70.2-1) ...
1151s Processing triggers for libc-bin (2.39-0ubuntu2) ...
1151s Processing triggers for man-db (2.12.0-3) ...
1152s Processing triggers for install-info (7.1-3) ...
1160s Reading package lists...
1160s Building dependency tree...
1160s Reading state information...
1160s Starting pkgProblemResolver with broken count: 0
1160s Starting 2 pkgProblemResolver with broken count: 0
1160s Done
1160s The following NEW packages will be installed:
1160s   autopkgtest-satdep
1161s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
1161s Need to get 0 B/696 B of archives.
1161s After this operation, 0 B of additional disk space will be used.
1161s Get:1 /tmp/autopkgtest.ReAMhr/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B]
1161s Selecting previously unselected package autopkgtest-satdep.
1161s (Reading database ... 
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(Reading database ... 97515 files and directories currently installed.)
1161s Preparing to unpack .../2-autopkgtest-satdep.deb ...
1161s Unpacking autopkgtest-satdep (0) ...
1161s Setting up autopkgtest-satdep (0) ...
1162s (Reading database ... 97515 files and directories currently installed.)
1162s Removing autopkgtest-satdep (0) ...
1163s autopkgtest [13:16:35]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
1163s autopkgtest [13:16:35]: test pkg-r-autopkgtest: [-----------------------
1163s Test: Try to load the R library BSgenome
1163s 
1163s R version 4.3.2 (2023-10-31) -- "Eye Holes"
1163s Copyright (C) 2023 The R Foundation for Statistical Computing
1163s Platform: x86_64-pc-linux-gnu (64-bit)
1163s 
1163s R is free software and comes with ABSOLUTELY NO WARRANTY.
1163s You are welcome to redistribute it under certain conditions.
1163s Type 'license()' or 'licence()' for distribution details.
1163s 
1163s R is a collaborative project with many contributors.
1163s Type 'contributors()' for more information and
1163s 'citation()' on how to cite R or R packages in publications.
1163s 
1163s Type 'demo()' for some demos, 'help()' for on-line help, or
1163s 'help.start()' for an HTML browser interface to help.
1163s Type 'q()' to quit R.
1163s 
1163s > library('BSgenome')
1163s Loading required package: BiocGenerics
1163s 
1163s Attaching package: ‘BiocGenerics’
1163s 
1163s The following objects are masked from ‘package:stats’:
1163s 
1163s     IQR, mad, sd, var, xtabs
1163s 
1163s The following objects are masked from ‘package:base’:
1163s 
1163s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
1163s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
1163s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
1163s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
1163s     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
1163s     table, tapply, union, unique, unsplit, which.max, which.min
1163s 
1163s Loading required package: S4Vectors
1163s Loading required package: stats4
1164s 
1164s Attaching package: ‘S4Vectors’
1164s 
1164s The following object is masked from ‘package:utils’:
1164s 
1164s     findMatches
1164s 
1164s The following objects are masked from ‘package:base’:
1164s 
1164s     expand.grid, I, unname
1164s 
1164s Loading required package: IRanges
1164s Loading required package: GenomeInfoDb
1165s Loading required package: GenomicRanges
1165s Loading required package: Biostrings
1165s Loading required package: XVector
1166s 
1166s Attaching package: ‘Biostrings’
1166s 
1166s The following object is masked from ‘package:base’:
1166s 
1166s     strsplit
1166s 
1166s Loading required package: BiocIO
1166s Loading required package: rtracklayer
1171s 
1171s Attaching package: ‘rtracklayer’
1171s 
1171s The following object is masked from ‘package:BiocIO’:
1171s 
1171s     FileForFormat
1171s 
1172s > 
1172s > 
1172s Other tests are currently unsupported!
1172s They will be progressively added.
1172s autopkgtest [13:16:44]: test pkg-r-autopkgtest: -----------------------]
1172s autopkgtest [13:16:44]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
1172s pkg-r-autopkgtest    PASS
1172s autopkgtest [13:16:44]: @@@@@@@@@@@@@@@@@@@@ summary
1172s pkg-r-autopkgtest    PASS
1188s Creating nova instance adt-noble-i386-r-bioc-bsgenome-20240321-125712-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240320.img (UUID 3219a3f4-90ea-47d9-8dfb-3912f2ae9f95)...