0s autopkgtest [15:13:26]: starting date and time: 2025-03-15 15:13:26+0000
  0s autopkgtest [15:13:26]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [15:13:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u5ebfuii/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-bioc-xvector --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-29.secgroup --name adt-plucky-arm64-r-bioc-xvector-20250315-151326-juju-7f2275-prod-proposed-migration-environment-2-152e67d0-704d-45e6-91ba-726f89d34925 --image adt/ubuntu-plucky-arm64-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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
128s autopkgtest [15:15:34]: testbed dpkg architecture: arm64
128s autopkgtest [15:15:34]: testbed apt version: 2.9.33
129s autopkgtest [15:15:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup
129s autopkgtest [15:15:35]: testbed release detected to be: None
130s autopkgtest [15:15:36]: updating testbed package index (apt update)
130s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
130s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
130s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
130s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
131s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
131s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
131s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
131s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
131s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
131s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
131s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
131s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
132s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
132s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
132s Fetched 1094 kB in 2s (651 kB/s)
133s Reading package lists...
133s Reading package lists...
133s Building dependency tree...
133s Reading state information...
134s Calculating upgrade...
134s Calculating upgrade...
135s The following packages will be upgraded:
135s   python3-jinja2 strace
135s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
135s Need to get 608 kB of archives.
135s After this operation, 11.3 kB of additional disk space will be used.
135s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
136s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
136s Fetched 608 kB in 1s (569 kB/s)
136s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
136s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
136s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
136s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
137s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
137s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
137s Setting up strace (6.13+ds-1ubuntu1) ...
137s Processing triggers for man-db (2.13.0-1) ...
138s Reading package lists...
138s Building dependency tree...
138s Reading state information...
138s Solving dependencies...
139s The following packages will be REMOVED:
139s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
139s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
139s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
139s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
139s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
139s After this operation, 267 MB disk space will be freed.
139s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
139s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
139s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
139s Removing libpython3.12t64:arm64 (3.12.9-1) ...
139s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
139s Removing libnsl2:arm64 (1.3.0-3build3) ...
139s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
139s Removing libunwind8:arm64 (1.6.2-3.1) ...
139s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
140s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
141s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
142s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
142s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
142s /etc/kernel/postrm.d/initramfs-tools:
142s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
142s /etc/kernel/postrm.d/zz-flash-kernel:
142s flash-kernel: Kernel 6.11.0-8-generic has been removed.
142s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
142s /etc/kernel/postrm.d/zz-update-grub:
142s Sourcing file `/etc/default/grub'
142s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
142s Generating grub configuration file ...
142s Found linux image: /boot/vmlinuz-6.14.0-10-generic
142s Found initrd image: /boot/initrd.img-6.14.0-10-generic
143s Warning: os-prober will not be executed to detect other bootable partitions.
143s Systems on them will not be added to the GRUB boot configuration.
143s Check GRUB_DISABLE_OS_PROBER documentation entry.
143s Adding boot menu entry for UEFI Firmware Settings ...
143s done
143s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
143s Processing triggers for libc-bin (2.41-1ubuntu1) ...
143s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81650 files and directories currently installed.)
143s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
143s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
143s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
143s autopkgtest [15:15:49]: upgrading testbed (apt dist-upgrade and autopurge)
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
144s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
144s Starting 2 pkgProblemResolver with broken count: 0
144s Done
145s Entering ResolveByKeep
145s 
146s Calculating upgrade...
146s The following packages will be upgraded:
146s   libc-bin libc-dev-bin libc6 libc6-dev locales
146s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
146s Need to get 9530 kB of archives.
146s After this operation, 0 B of additional disk space will be used.
146s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
148s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
148s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
150s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
151s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
154s Preconfiguring packages ...
154s Fetched 9530 kB in 8s (1181 kB/s)
155s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
155s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
155s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
155s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
155s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
155s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
155s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
155s Setting up libc6:arm64 (2.41-1ubuntu2) ...
155s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
155s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
155s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
155s Setting up libc-bin (2.41-1ubuntu2) ...
156s (Reading database ... 
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(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 ... 81647 files and directories currently installed.)
156s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
156s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
156s Setting up locales (2.41-1ubuntu2) ...
156s Generating locales (this might take a while)...
158s   en_US.UTF-8... done
158s Generation complete.
158s Setting up libc-dev-bin (2.41-1ubuntu2) ...
158s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
158s Processing triggers for man-db (2.13.0-1) ...
160s Processing triggers for systemd (257.3-1ubuntu3) ...
160s Reading package lists...
161s Building dependency tree...
161s Reading state information...
161s Starting pkgProblemResolver with broken count: 0
161s Starting 2 pkgProblemResolver with broken count: 0
161s Done
161s Solving dependencies...
162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
162s autopkgtest [15:16:08]: rebooting testbed after setup commands that affected boot
185s autopkgtest [15:16:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
188s autopkgtest [15:16:34]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-xvector
190s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-xvector 0.46.0-2 (dsc) [2200 B]
190s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-xvector 0.46.0-2 (tar) [70.2 kB]
190s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-xvector 0.46.0-2 (diff) [4820 B]
191s gpgv: Signature made Sun Jan 12 11:46:10 2025 UTC
191s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
191s gpgv:                issuer "crusoe@debian.org"
191s gpgv: Can't check signature: No public key
191s dpkg-source: warning: cannot verify inline signature for ./r-bioc-xvector_0.46.0-2.dsc: no acceptable signature found
191s autopkgtest [15:16:37]: testing package r-bioc-xvector version 0.46.0-2
191s autopkgtest [15:16:37]: build not needed
193s autopkgtest [15:16:39]: test pkg-r-autopkgtest: preparing testbed
193s Reading package lists...
193s Building dependency tree...
193s Reading state information...
193s Starting pkgProblemResolver with broken count: 0
193s Starting 2 pkgProblemResolver with broken count: 0
193s Done
194s The following NEW packages will be installed:
194s   build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
194s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
194s   g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
194s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14
194s   gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools
194s   libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1
194s   libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev
194s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
194s   libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
194s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4
194s   liblsan0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0
194s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0
194s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
194s   libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6
194s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
194s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
194s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
194s   r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
194s   r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-s4vectors r-bioc-ucsc.utils
194s   r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-crayon r-cran-curl
194s   r-cran-httr r-cran-jsonlite r-cran-mime r-cran-openssl r-cran-r6
194s   r-cran-runit r-cran-sys unzip x11-common xdg-utils zip zlib1g-dev
194s 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded.
194s Need to get 169 MB of archives.
194s After this operation, 459 MB of additional disk space will be used.
194s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
195s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
195s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB]
202s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B]
202s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B]
202s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB]
202s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB]
202s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
202s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
202s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
204s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
205s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
207s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
207s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
208s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
210s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB]
224s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB]
224s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B]
224s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B]
224s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
227s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB]
236s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB]
236s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B]
236s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B]
236s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
236s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
236s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
237s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
237s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
237s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
238s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
238s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
238s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB]
239s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB]
247s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB]
247s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B]
247s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B]
248s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB]
248s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
248s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB]
248s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB]
248s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
249s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
249s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
249s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
249s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
249s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
250s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
250s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB]
250s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
250s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
250s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
251s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
251s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB]
259s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
260s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB]
260s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
260s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
260s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
260s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
262s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB]
265s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
265s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB]
265s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
266s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
266s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB]
266s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB]
266s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB]
266s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB]
266s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB]
266s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
267s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
267s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B]
267s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB]
268s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB]
268s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
269s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB]
269s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB]
270s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
270s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
270s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
271s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
271s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
271s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
272s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
272s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
272s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
273s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
273s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB]
273s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
273s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
273s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB]
290s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB]
290s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB]
290s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB]
290s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB]
290s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B]
290s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
290s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
291s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB]
292s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-iranges arm64 2.40.1-2 [2303 kB]
293s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
293s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB]
293s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB]
294s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB]
294s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB]
294s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB]
294s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB]
294s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB]
295s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB]
295s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
295s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
295s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
302s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
304s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB]
304s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB]
309s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-runit all 0.4.33-1 [377 kB]
310s Preconfiguring packages ...
310s Fetched 169 MB in 1min 55s (1472 kB/s)
310s Selecting previously unselected package libisl23:arm64.
310s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
310s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ...
310s Unpacking libisl23:arm64 (0.27-1) ...
310s Selecting previously unselected package libmpc3:arm64.
310s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ...
310s Unpacking libmpc3:arm64 (1.3.1-1build2) ...
310s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
310s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
310s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
310s Selecting previously unselected package cpp-14.
310s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ...
310s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
310s Selecting previously unselected package cpp-aarch64-linux-gnu.
310s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
310s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
310s Selecting previously unselected package cpp.
310s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ...
310s Unpacking cpp (4:14.2.0-1ubuntu1) ...
311s Selecting previously unselected package libcc1-0:arm64.
311s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libgomp1:arm64.
311s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libitm1:arm64.
311s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libasan8:arm64.
311s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package liblsan0:arm64.
311s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libtsan2:arm64.
311s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libubsan1:arm64.
311s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libhwasan0:arm64.
311s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
311s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ...
311s Selecting previously unselected package libgcc-14-dev:arm64.
311s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
311s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
311s Selecting previously unselected package gcc-14-aarch64-linux-gnu.
311s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
311s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
312s Selecting previously unselected package gcc-14.
312s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ...
312s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
312s Selecting previously unselected package gcc-aarch64-linux-gnu.
312s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
312s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
312s Selecting previously unselected package gcc.
312s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ...
312s Unpacking gcc (4:14.2.0-1ubuntu1) ...
312s Selecting previously unselected package libstdc++-14-dev:arm64.
312s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
312s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
312s Selecting previously unselected package g++-14-aarch64-linux-gnu.
312s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
312s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
312s Selecting previously unselected package g++-14.
312s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ...
312s Unpacking g++-14 (14.2.0-17ubuntu3) ...
312s Selecting previously unselected package g++-aarch64-linux-gnu.
312s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
312s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
312s Selecting previously unselected package g++.
312s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ...
312s Unpacking g++ (4:14.2.0-1ubuntu1) ...
312s Selecting previously unselected package build-essential.
312s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ...
312s Unpacking build-essential (12.10ubuntu1) ...
312s Selecting previously unselected package dctrl-tools.
312s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ...
312s Unpacking dctrl-tools (2.24-3build3) ...
312s Selecting previously unselected package fonts-dejavu-mono.
313s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ...
313s Unpacking fonts-dejavu-mono (2.37-8) ...
313s Selecting previously unselected package fonts-dejavu-core.
313s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ...
313s Unpacking fonts-dejavu-core (2.37-8) ...
313s Selecting previously unselected package fontconfig-config.
313s Preparing to unpack .../028-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
313s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
313s Selecting previously unselected package libfontconfig1:arm64.
313s Preparing to unpack .../029-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
313s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
313s Selecting previously unselected package fontconfig.
313s Preparing to unpack .../030-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
313s Unpacking fontconfig (2.15.0-2ubuntu1) ...
313s Selecting previously unselected package libgfortran5:arm64.
313s Preparing to unpack .../031-libgfortran5_15-20250222-0ubuntu1_arm64.deb ...
313s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ...
313s Selecting previously unselected package libgfortran-14-dev:arm64.
313s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ...
313s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
313s Selecting previously unselected package gfortran-14-aarch64-linux-gnu.
313s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
313s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
313s Selecting previously unselected package gfortran-14.
313s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_arm64.deb ...
313s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
313s Selecting previously unselected package gfortran-aarch64-linux-gnu.
313s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
313s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
313s Selecting previously unselected package gfortran.
313s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ...
313s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
313s Selecting previously unselected package icu-devtools.
314s Preparing to unpack .../037-icu-devtools_76.1-1ubuntu2_arm64.deb ...
314s Unpacking icu-devtools (76.1-1ubuntu2) ...
314s Selecting previously unselected package libblas3:arm64.
314s Preparing to unpack .../038-libblas3_3.12.1-2_arm64.deb ...
314s Unpacking libblas3:arm64 (3.12.1-2) ...
314s Selecting previously unselected package libblas-dev:arm64.
314s Preparing to unpack .../039-libblas-dev_3.12.1-2_arm64.deb ...
314s Unpacking libblas-dev:arm64 (3.12.1-2) ...
314s Selecting previously unselected package libbz2-dev:arm64.
314s Preparing to unpack .../040-libbz2-dev_1.0.8-6_arm64.deb ...
314s Unpacking libbz2-dev:arm64 (1.0.8-6) ...
314s Selecting previously unselected package libpixman-1-0:arm64.
314s Preparing to unpack .../041-libpixman-1-0_0.44.0-3_arm64.deb ...
314s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
314s Selecting previously unselected package libxcb-render0:arm64.
314s Preparing to unpack .../042-libxcb-render0_1.17.0-2_arm64.deb ...
314s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
314s Selecting previously unselected package libxcb-shm0:arm64.
314s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_arm64.deb ...
314s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
314s Selecting previously unselected package libxrender1:arm64.
314s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
314s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
314s Selecting previously unselected package libcairo2:arm64.
314s Preparing to unpack .../045-libcairo2_1.18.2-2_arm64.deb ...
314s Unpacking libcairo2:arm64 (1.18.2-2) ...
314s Selecting previously unselected package libdatrie1:arm64.
314s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_arm64.deb ...
314s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
314s Selecting previously unselected package libdeflate0:arm64.
314s Preparing to unpack .../047-libdeflate0_1.23-1_arm64.deb ...
314s Unpacking libdeflate0:arm64 (1.23-1) ...
314s Selecting previously unselected package libdeflate-dev:arm64.
314s Preparing to unpack .../048-libdeflate-dev_1.23-1_arm64.deb ...
314s Unpacking libdeflate-dev:arm64 (1.23-1) ...
314s Selecting previously unselected package libgraphite2-3:arm64.
314s Preparing to unpack .../049-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ...
314s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
314s Selecting previously unselected package libharfbuzz0b:arm64.
314s Preparing to unpack .../050-libharfbuzz0b_10.2.0-1_arm64.deb ...
314s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ...
314s Selecting previously unselected package x11-common.
314s Preparing to unpack .../051-x11-common_1%3a7.7+23ubuntu3_all.deb ...
314s Unpacking x11-common (1:7.7+23ubuntu3) ...
314s Selecting previously unselected package libice6:arm64.
314s Preparing to unpack .../052-libice6_2%3a1.1.1-1_arm64.deb ...
314s Unpacking libice6:arm64 (2:1.1.1-1) ...
314s Selecting previously unselected package libicu-dev:arm64.
314s Preparing to unpack .../053-libicu-dev_76.1-1ubuntu2_arm64.deb ...
314s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ...
314s Selecting previously unselected package libjpeg-turbo8:arm64.
314s Preparing to unpack .../054-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ...
314s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
315s Selecting previously unselected package libjpeg-turbo8-dev:arm64.
315s Preparing to unpack .../055-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ...
315s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ...
315s Selecting previously unselected package libjpeg8:arm64.
315s Preparing to unpack .../056-libjpeg8_8c-2ubuntu11_arm64.deb ...
315s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ...
315s Selecting previously unselected package libjpeg8-dev:arm64.
315s Preparing to unpack .../057-libjpeg8-dev_8c-2ubuntu11_arm64.deb ...
315s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ...
315s Selecting previously unselected package libjpeg-dev:arm64.
315s Preparing to unpack .../058-libjpeg-dev_8c-2ubuntu11_arm64.deb ...
315s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ...
315s Selecting previously unselected package liblapack3:arm64.
315s Preparing to unpack .../059-liblapack3_3.12.1-2_arm64.deb ...
315s Unpacking liblapack3:arm64 (3.12.1-2) ...
315s Selecting previously unselected package liblapack-dev:arm64.
315s Preparing to unpack .../060-liblapack-dev_3.12.1-2_arm64.deb ...
315s Unpacking liblapack-dev:arm64 (3.12.1-2) ...
315s Selecting previously unselected package liblerc4:arm64.
315s Preparing to unpack .../061-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ...
315s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
315s Selecting previously unselected package libncurses-dev:arm64.
315s Preparing to unpack .../062-libncurses-dev_6.5+20250216-2_arm64.deb ...
315s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ...
315s Selecting previously unselected package libthai-data.
315s Preparing to unpack .../063-libthai-data_0.1.29-2build1_all.deb ...
315s Unpacking libthai-data (0.1.29-2build1) ...
315s Selecting previously unselected package libthai0:arm64.
315s Preparing to unpack .../064-libthai0_0.1.29-2build1_arm64.deb ...
315s Unpacking libthai0:arm64 (0.1.29-2build1) ...
315s Selecting previously unselected package libpango-1.0-0:arm64.
315s Preparing to unpack .../065-libpango-1.0-0_1.56.2-1_arm64.deb ...
315s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ...
315s Selecting previously unselected package libpangoft2-1.0-0:arm64.
315s Preparing to unpack .../066-libpangoft2-1.0-0_1.56.2-1_arm64.deb ...
315s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ...
315s Selecting previously unselected package libpangocairo-1.0-0:arm64.
315s Preparing to unpack .../067-libpangocairo-1.0-0_1.56.2-1_arm64.deb ...
315s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ...
315s Selecting previously unselected package libpaper2:arm64.
315s Preparing to unpack .../068-libpaper2_2.2.5-0.3_arm64.deb ...
315s Unpacking libpaper2:arm64 (2.2.5-0.3) ...
315s Selecting previously unselected package libpaper-utils.
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315s Selecting previously unselected package libpcre2-16-0:arm64.
315s Preparing to unpack .../070-libpcre2-16-0_10.45-1_arm64.deb ...
315s Unpacking libpcre2-16-0:arm64 (10.45-1) ...
315s Selecting previously unselected package libpcre2-32-0:arm64.
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315s Unpacking libpcre2-32-0:arm64 (10.45-1) ...
315s Selecting previously unselected package libpcre2-posix3:arm64.
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316s Selecting previously unselected package libpcre2-dev:arm64.
316s Preparing to unpack .../073-libpcre2-dev_10.45-1_arm64.deb ...
316s Unpacking libpcre2-dev:arm64 (10.45-1) ...
316s Selecting previously unselected package libpkgconf3:arm64.
316s Preparing to unpack .../074-libpkgconf3_1.8.1-4_arm64.deb ...
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316s Selecting previously unselected package zlib1g-dev:arm64.
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316s Selecting previously unselected package libpng-dev:arm64.
316s Preparing to unpack .../076-libpng-dev_1.6.47-1_arm64.deb ...
316s Unpacking libpng-dev:arm64 (1.6.47-1) ...
316s Selecting previously unselected package libreadline-dev:arm64.
316s Preparing to unpack .../077-libreadline-dev_8.2-6_arm64.deb ...
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316s Selecting previously unselected package libsharpyuv0:arm64.
316s Preparing to unpack .../078-libsharpyuv0_1.5.0-0.1_arm64.deb ...
316s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ...
316s Selecting previously unselected package libsm6:arm64.
316s Preparing to unpack .../079-libsm6_2%3a1.2.4-1_arm64.deb ...
316s Unpacking libsm6:arm64 (2:1.2.4-1) ...
316s Selecting previously unselected package libtcl8.6:arm64.
316s Preparing to unpack .../080-libtcl8.6_8.6.16+dfsg-1_arm64.deb ...
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316s Selecting previously unselected package libjbig0:arm64.
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316s Selecting previously unselected package libwebp7:arm64.
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316s Selecting previously unselected package libtiff6:arm64.
316s Preparing to unpack .../083-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ...
316s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
316s Selecting previously unselected package libxft2:arm64.
316s Preparing to unpack .../084-libxft2_2.3.6-1build1_arm64.deb ...
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316s Selecting previously unselected package libxss1:arm64.
316s Preparing to unpack .../085-libxss1_1%3a1.2.3-1build3_arm64.deb ...
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316s Selecting previously unselected package libtk8.6:arm64.
316s Preparing to unpack .../086-libtk8.6_8.6.16-1_arm64.deb ...
316s Unpacking libtk8.6:arm64 (8.6.16-1) ...
316s Selecting previously unselected package libxt6t64:arm64.
316s Preparing to unpack .../087-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ...
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316s Preparing to unpack .../088-zip_3.0-14ubuntu2_arm64.deb ...
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317s Selecting previously unselected package liblzma-dev:arm64.
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317s Selecting previously unselected package pkgconf:arm64.
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317s Unpacking pkgconf:arm64 (1.8.1-4) ...
317s Selecting previously unselected package libtirpc-dev:arm64.
317s Preparing to unpack .../095-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ...
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317s Selecting previously unselected package r-bioc-biocgenerics.
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317s Unpacking r-bioc-biocgenerics (0.52.0-2) ...
317s Selecting previously unselected package r-bioc-s4vectors.
317s Preparing to unpack .../099-r-bioc-s4vectors_0.44.0+dfsg-2_arm64.deb ...
317s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ...
317s Selecting previously unselected package r-bioc-iranges.
317s Preparing to unpack .../100-r-bioc-iranges_2.40.1-2_arm64.deb ...
317s Unpacking r-bioc-iranges (2.40.1-2) ...
317s Selecting previously unselected package r-bioc-zlibbioc.
317s Preparing to unpack .../101-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ...
317s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ...
317s Selecting previously unselected package r-bioc-xvector.
317s Preparing to unpack .../102-r-bioc-xvector_0.46.0-2_arm64.deb ...
317s Unpacking r-bioc-xvector (0.46.0-2) ...
317s Selecting previously unselected package r-cran-curl.
317s Preparing to unpack .../103-r-cran-curl_6.2.1+dfsg-1ubuntu1_arm64.deb ...
317s Unpacking r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
318s Selecting previously unselected package r-cran-jsonlite.
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318s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ...
318s Selecting previously unselected package r-cran-mime.
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318s Unpacking r-cran-mime (0.12-2) ...
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318s Unpacking r-cran-sys (3.4.3-1) ...
318s Selecting previously unselected package r-cran-askpass.
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318s Unpacking r-cran-askpass (1.2.1-1) ...
318s Selecting previously unselected package r-cran-openssl.
318s Preparing to unpack .../108-r-cran-openssl_2.3.2+dfsg-1_arm64.deb ...
318s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
318s Selecting previously unselected package r-cran-r6.
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318s Selecting previously unselected package r-bioc-ucsc.utils.
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318s Selecting previously unselected package r-bioc-genomeinfodbdata.
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318s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
318s Selecting previously unselected package r-cran-crayon.
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318s Unpacking r-cran-crayon (1.5.3-1) ...
318s Selecting previously unselected package r-bioc-biostrings.
318s Preparing to unpack .../115-r-bioc-biostrings_2.74.1+dfsg-2_arm64.deb ...
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318s Selecting previously unselected package r-cran-runit.
318s Preparing to unpack .../116-r-cran-runit_0.4.33-1_all.deb ...
318s Unpacking r-cran-runit (0.4.33-1) ...
318s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
318s Setting up libpixman-1-0:arm64 (0.44.0-3) ...
318s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
318s Setting up libncurses-dev:arm64 (6.5+20250216-2) ...
318s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
318s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ...
318s Setting up libdatrie1:arm64 (0.2.13-3build1) ...
318s Setting up libxcb-render0:arm64 (1.17.0-2) ...
318s Setting up unzip (6.0-28ubuntu6) ...
318s Setting up x11-common (1:7.7+23ubuntu3) ...
319s Setting up libdeflate0:arm64 (1.23-1) ...
319s Setting up libxcb-shm0:arm64 (1.17.0-2) ...
319s Setting up libreadline-dev:arm64 (8.2-6) ...
319s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ...
319s Setting up libpcre2-16-0:arm64 (10.45-1) ...
319s Setting up zip (3.0-14ubuntu2) ...
319s Setting up libpcre2-32-0:arm64 (10.45-1) ...
319s Setting up libblas3:arm64 (3.12.1-2) ...
319s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
319s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ...
319s Setting up libpkgconf3:arm64 (1.8.1-4) ...
319s Setting up fonts-dejavu-mono (2.37-8) ...
319s Setting up libmpc3:arm64 (1.3.1-1build2) ...
319s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ...
319s Setting up icu-devtools (76.1-1ubuntu2) ...
319s Setting up fonts-dejavu-core (2.37-8) ...
319s Setting up pkgconf-bin (1.8.1-4) ...
319s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ...
319s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libwebp7:arm64 (1.5.0-0.1) ...
319s Setting up liblzma-dev:arm64 (5.6.4-1) ...
319s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ...
319s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
319s Setting up libpcre2-posix3:arm64 (10.45-1) ...
319s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libharfbuzz0b:arm64 (10.2.0-1) ...
319s Setting up libthai-data (0.1.29-2build1) ...
319s Setting up libxss1:arm64 (1:1.2.3-1build3) ...
319s Setting up libpaper2:arm64 (2.2.5-0.3) ...
319s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libisl23:arm64 (0.27-1) ...
319s Setting up libdeflate-dev:arm64 (1.23-1) ...
319s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ...
319s Setting up xdg-utils (1.2.1-2ubuntu1) ...
319s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
319s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ...
319s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libblas-dev:arm64 (3.12.1-2) ...
319s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode
319s Setting up dctrl-tools (2.24-3build3) ...
319s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ...
319s Setting up libbz2-dev:arm64 (1.0.8-6) ...
319s Setting up libjpeg8:arm64 (8c-2ubuntu11) ...
319s Setting up libice6:arm64 (2:1.1.1-1) ...
319s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ...
319s Setting up liblapack3:arm64 (3.12.1-2) ...
319s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
319s Setting up libpcre2-dev:arm64 (10.45-1) ...
319s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
319s Setting up libpng-dev:arm64 (1.6.47-1) ...
319s Setting up libpaper-utils (2.2.5-0.3) ...
319s Setting up pkgconf:arm64 (1.8.1-4) ...
319s Setting up libthai0:arm64 (0.1.29-2build1) ...
319s Setting up liblapack-dev:arm64 (3.12.1-2) ...
319s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode
319s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
319s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
319s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
319s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
319s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ...
319s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
319s Setting up libsm6:arm64 (2:1.2.4-1) ...
319s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
319s Setting up fontconfig (2.15.0-2ubuntu1) ...
321s Regenerating fonts cache... done.
321s Setting up libxft2:arm64 (2.3.6-1build1) ...
321s Setting up libtk8.6:arm64 (8.6.16-1) ...
321s Setting up libpango-1.0-0:arm64 (1.56.2-1) ...
321s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
321s Setting up libcairo2:arm64 (1.18.2-2) ...
321s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
321s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ...
321s Setting up cpp-14 (14.2.0-17ubuntu3) ...
321s Setting up cpp (4:14.2.0-1ubuntu1) ...
321s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
321s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ...
321s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ...
321s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
321s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
321s Setting up gcc-14 (14.2.0-17ubuntu3) ...
321s Setting up r-base-core (4.4.3-1) ...
321s Creating config file /etc/R/Renviron with new version
321s Setting up r-cran-crayon (1.5.3-1) ...
321s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
321s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
321s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
321s Setting up g++-14 (14.2.0-17ubuntu3) ...
321s Setting up r-cran-r6 (2.6.1-1) ...
321s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
321s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
321s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
321s Setting up r-bioc-biocgenerics (0.52.0-2) ...
321s Setting up r-cran-sys (3.4.3-1) ...
321s Setting up r-cran-mime (0.12-2) ...
321s Setting up gcc (4:14.2.0-1ubuntu1) ...
321s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
321s Setting up r-cran-askpass (1.2.1-1) ...
321s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
321s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
321s Setting up r-cran-runit (0.4.33-1) ...
321s Setting up g++ (4:14.2.0-1ubuntu1) ...
321s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
321s Setting up build-essential (12.10ubuntu1) ...
321s Setting up r-bioc-iranges (2.40.1-2) ...
321s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
321s Setting up gfortran (4:14.2.0-1ubuntu1) ...
321s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
321s 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
321s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
321s 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
321s Setting up r-cran-httr (1.4.7+dfsg-1) ...
321s Setting up r-bioc-xvector (0.46.0-2) ...
321s Setting up r-base-dev (4.4.3-1) ...
321s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
321s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
321s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
321s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
321s Processing triggers for install-info (7.1.1-1) ...
322s Processing triggers for libc-bin (2.41-1ubuntu2) ...
322s Processing triggers for man-db (2.13.0-1) ...
325s autopkgtest [15:18:51]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
325s autopkgtest [15:18:51]: test pkg-r-autopkgtest: [-----------------------
325s Test: Try to load the R library XVector
325s 
325s R version 4.4.3 (2025-02-28) -- "Trophy Case"
325s Copyright (C) 2025 The R Foundation for Statistical Computing
325s Platform: aarch64-unknown-linux-gnu
325s 
325s R is free software and comes with ABSOLUTELY NO WARRANTY.
325s You are welcome to redistribute it under certain conditions.
325s Type 'license()' or 'licence()' for distribution details.
325s 
325s R is a collaborative project with many contributors.
325s Type 'contributors()' for more information and
325s 'citation()' on how to cite R or R packages in publications.
325s 
325s Type 'demo()' for some demos, 'help()' for on-line help, or
325s 'help.start()' for an HTML browser interface to help.
325s Type 'q()' to quit R.
325s 
326s Loading required package: BiocGenerics
326s > library('XVector')
326s 
326s Attaching package: ‘BiocGenerics’
326s 
326s The following objects are masked from ‘package:stats’:
326s 
326s     IQR, mad, sd, var, xtabs
326s 
326s The following objects are masked from ‘package:base’:
326s 
326s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
326s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
326s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
326s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
326s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
326s     table, tapply, union, unique, unsplit, which.max, which.min
326s 
326s Loading required package: S4Vectors
326s Loading required package: stats4
326s 
326s Attaching package: ‘S4Vectors’
326s 
326s The following object is masked from ‘package:utils’:
326s 
326s     findMatches
326s 
326s The following objects are masked from ‘package:base’:
326s 
326s     expand.grid, I, unname
326s 
326s Loading required package: IRanges
327s > 
327s > 
327s Other tests are currently unsupported!
327s They will be progressively added.
328s autopkgtest [15:18:54]: test pkg-r-autopkgtest: -----------------------]
328s pkg-r-autopkgtest    PASS
328s autopkgtest [15:18:54]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
329s autopkgtest [15:18:55]: @@@@@@@@@@@@@@@@@@@@ summary
329s pkg-r-autopkgtest    PASS
350s nova [W] Using flock in prodstack6-arm64
350s Creating nova instance adt-plucky-arm64-r-bioc-xvector-20250315-151326-juju-7f2275-prod-proposed-migration-environment-2-152e67d0-704d-45e6-91ba-726f89d34925 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
350s nova [W] Timed out waiting for 5339b420-0058-451c-8cf9-ff412b05d25a to get deleted.