0s autopkgtest [15:30:11]: starting date and time: 2025-03-15 15:30:11+0000
  0s autopkgtest [15:30:11]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [15:30:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.24n8ylkk/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-pcamethods --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-20@bos03-arm64-18.secgroup --name adt-plucky-arm64-r-bioc-pcamethods-20250315-150852-juju-7f2275-prod-proposed-migration-environment-20-7f8b886d-bafc-4a01-b5f2-cbdc5dfdeb99 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/
172s autopkgtest [15:33:03]: testbed dpkg architecture: arm64
172s autopkgtest [15:33:03]: testbed apt version: 2.9.33
173s autopkgtest [15:33:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup
173s autopkgtest [15:33:04]: testbed release detected to be: None
174s autopkgtest [15:33:05]: updating testbed package index (apt update)
175s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
175s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
175s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
175s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
175s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
176s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
176s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
176s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
176s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
176s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
176s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
177s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
177s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
177s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
177s Fetched 1094 kB in 2s (522 kB/s)
178s Reading package lists...
179s Reading package lists...
179s Building dependency tree...
179s Reading state information...
179s Calculating upgrade...
180s Calculating upgrade...
180s The following packages will be upgraded:
180s   python3-jinja2 strace
180s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
180s Need to get 608 kB of archives.
180s After this operation, 11.3 kB of additional disk space will be used.
180s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
181s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
182s Fetched 608 kB in 1s (567 kB/s)
182s (Reading database ... 
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(Reading database ... 117701 files and directories currently installed.)
182s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
182s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
182s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
182s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
182s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
182s Setting up strace (6.13+ds-1ubuntu1) ...
182s Processing triggers for man-db (2.13.0-1) ...
183s Reading package lists...
184s Building dependency tree...
184s Reading state information...
184s Solving dependencies...
184s The following packages will be REMOVED:
184s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
184s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
184s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
184s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
185s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
185s After this operation, 267 MB disk space will be freed.
185s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
185s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
185s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
185s Removing libpython3.12t64:arm64 (3.12.9-1) ...
185s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
185s Removing libnsl2:arm64 (1.3.0-3build3) ...
185s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
185s Removing libunwind8:arm64 (1.6.2-3.1) ...
185s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
186s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
187s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
188s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
188s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
188s /etc/kernel/postrm.d/initramfs-tools:
188s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
188s /etc/kernel/postrm.d/zz-flash-kernel:
188s flash-kernel: Kernel 6.11.0-8-generic has been removed.
188s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
188s /etc/kernel/postrm.d/zz-update-grub:
188s Sourcing file `/etc/default/grub'
188s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
188s Generating grub configuration file ...
188s Found linux image: /boot/vmlinuz-6.14.0-10-generic
188s Found initrd image: /boot/initrd.img-6.14.0-10-generic
189s Warning: os-prober will not be executed to detect other bootable partitions.
189s Systems on them will not be added to the GRUB boot configuration.
189s Check GRUB_DISABLE_OS_PROBER documentation entry.
189s Adding boot menu entry for UEFI Firmware Settings ...
189s done
189s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
189s Processing triggers for libc-bin (2.41-1ubuntu1) ...
189s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81650 files and directories currently installed.)
189s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
189s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
189s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
189s autopkgtest [15:33:20]: upgrading testbed (apt dist-upgrade and autopurge)
190s Reading package lists...
190s Building dependency tree...
190s Reading state information...
190s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
190s Starting 2 pkgProblemResolver with broken count: 0
190s Done
191s Entering ResolveByKeep
191s 
192s Calculating upgrade...
192s The following packages will be upgraded:
192s   libc-bin libc-dev-bin libc6 libc6-dev locales
192s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
192s Need to get 9530 kB of archives.
192s After this operation, 0 B of additional disk space will be used.
192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
194s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
194s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
198s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
198s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
204s Preconfiguring packages ...
204s Fetched 9530 kB in 11s (849 kB/s)
204s (Reading database ... 
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(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
204s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
204s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
204s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
204s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
204s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
204s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
205s Setting up libc6:arm64 (2.41-1ubuntu2) ...
205s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
205s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
205s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
205s Setting up libc-bin (2.41-1ubuntu2) ...
205s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
205s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
205s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
205s Setting up locales (2.41-1ubuntu2) ...
206s Generating locales (this might take a while)...
208s   en_US.UTF-8... done
208s Generation complete.
208s Setting up libc-dev-bin (2.41-1ubuntu2) ...
208s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
208s Processing triggers for man-db (2.13.0-1) ...
209s Processing triggers for systemd (257.3-1ubuntu3) ...
210s Reading package lists...
210s Building dependency tree...
210s Reading state information...
211s Starting pkgProblemResolver with broken count: 0
211s Starting 2 pkgProblemResolver with broken count: 0
211s Done
211s Solving dependencies...
212s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
212s autopkgtest [15:33:43]: rebooting testbed after setup commands that affected boot
246s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
254s autopkgtest [15:34:25]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
257s autopkgtest [15:34:28]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-pcamethods
260s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pcamethods 1.98.0-2 (dsc) [2185 B]
260s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pcamethods 1.98.0-2 (tar) [1047 kB]
260s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-pcamethods 1.98.0-2 (diff) [3304 B]
260s gpgv: Signature made Sun Jan 12 02:50:35 2025 UTC
260s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
260s gpgv:                issuer "crusoe@debian.org"
260s gpgv: Can't check signature: No public key
260s dpkg-source: warning: cannot verify inline signature for ./r-bioc-pcamethods_1.98.0-2.dsc: no acceptable signature found
260s autopkgtest [15:34:31]: testing package r-bioc-pcamethods version 1.98.0-2
261s autopkgtest [15:34:32]: build not needed
264s autopkgtest [15:34:35]: test pkg-r-autopkgtest: preparing testbed
264s Reading package lists...
265s Building dependency tree...
265s Reading state information...
265s Starting pkgProblemResolver with broken count: 0
265s Starting 2 pkgProblemResolver with broken count: 0
265s Done
266s The following NEW packages will be installed:
266s   build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
266s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
266s   g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
266s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14
266s   gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools
266s   libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1
266s   libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev
266s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
266s   libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
266s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4
266s   liblsan0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0
266s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0
266s   libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3
266s   libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6
266s   libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1
266s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
266s   littler pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
266s   r-bioc-biobase r-bioc-biocgenerics r-bioc-pcamethods r-cran-cli
266s   r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue
266s   r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle
266s   r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-matrixstats
266s   r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
266s   r-cran-pkgkitten r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang
266s   r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite
266s   r-cran-withr unzip x11-common xdg-utils zip zlib1g-dev
266s 0 upgraded, 134 newly installed, 0 to remove and 0 not upgraded.
266s Need to get 167 MB of archives.
266s After this operation, 479 MB of additional disk space will be used.
266s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
267s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
267s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB]
279s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B]
279s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B]
279s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB]
279s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB]
279s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
279s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
279s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
283s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
284s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
287s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
288s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
290s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
293s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB]
316s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB]
317s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B]
317s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B]
317s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
320s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB]
343s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB]
343s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B]
343s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B]
343s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
344s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
344s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
345s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
346s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
346s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
347s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
347s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
348s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB]
349s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB]
373s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB]
373s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B]
373s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B]
373s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB]
373s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
374s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB]
374s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB]
374s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
374s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
374s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
374s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
374s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
375s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
375s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
376s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB]
376s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
376s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
377s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
377s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
377s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB]
401s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
402s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB]
402s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
402s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
402s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
402s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
407s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB]
416s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
417s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB]
417s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
418s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
418s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB]
418s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB]
418s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB]
418s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB]
418s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB]
418s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
419s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
419s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B]
419s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB]
421s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB]
421s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
423s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB]
423s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB]
424s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
424s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
424s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
425s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
426s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
426s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
426s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
426s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
426s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
428s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
428s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB]
429s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
429s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
429s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB]
477s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB]
478s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B]
478s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB]
478s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB]
478s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB]
478s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB]
478s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B]
478s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
478s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
480s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biobase arm64 2.66.0-2 [2331 kB]
484s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
484s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB]
488s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB]
489s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-pcamethods arm64 1.98.0-2 [1387 kB]
492s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB]
494s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-colorspace arm64 2.1-1+dfsg-1 [1563 kB]
496s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fansi arm64 1.0.5-1 [616 kB]
497s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-farver arm64 2.1.2-1 [1344 kB]
500s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB]
500s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB]
503s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
503s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
503s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-isoband arm64 0.2.7-1 [1481 kB]
506s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB]
508s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB]
511s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB]
518s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB]
523s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-labeling all 0.4.3-1 [62.1 kB]
524s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-munsell all 0.5.1-1 [213 kB]
524s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB]
524s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB]
524s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-viridislite all 0.4.2-2 [1088 kB]
526s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-scales all 1.3.0-1 [603 kB]
527s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
527s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-utf8 arm64 1.2.4-1 [140 kB]
527s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
529s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pillar all 1.10.1+dfsg-1 [453 kB]
530s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
530s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tibble arm64 3.2.1+dfsg-3 [420 kB]
531s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
531s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ggplot2 all 3.5.1+dfsg-1 [3940 kB]
538s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrixstats arm64 1.5.0-1 [496 kB]
539s Preconfiguring packages ...
539s Fetched 167 MB in 4min 33s (614 kB/s)
539s Selecting previously unselected package libisl23:arm64.
539s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
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(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 ... 81647 files and directories currently installed.)
539s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ...
539s Unpacking libisl23:arm64 (0.27-1) ...
540s Selecting previously unselected package libmpc3:arm64.
540s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ...
540s Unpacking libmpc3:arm64 (1.3.1-1build2) ...
540s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
540s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
540s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
540s Selecting previously unselected package cpp-14.
540s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ...
540s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
540s Selecting previously unselected package cpp-aarch64-linux-gnu.
540s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
540s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
540s Selecting previously unselected package cpp.
540s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ...
540s Unpacking cpp (4:14.2.0-1ubuntu1) ...
540s Selecting previously unselected package libcc1-0:arm64.
540s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libgomp1:arm64.
540s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libitm1:arm64.
540s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libasan8:arm64.
540s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package liblsan0:arm64.
540s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libtsan2:arm64.
540s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libubsan1:arm64.
540s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libhwasan0:arm64.
540s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
540s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ...
540s Selecting previously unselected package libgcc-14-dev:arm64.
540s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
540s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
540s Selecting previously unselected package gcc-14-aarch64-linux-gnu.
541s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
541s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
541s Selecting previously unselected package gcc-14.
541s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ...
541s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
541s Selecting previously unselected package gcc-aarch64-linux-gnu.
541s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
541s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
541s Selecting previously unselected package gcc.
541s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ...
541s Unpacking gcc (4:14.2.0-1ubuntu1) ...
541s Selecting previously unselected package libstdc++-14-dev:arm64.
541s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
541s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
541s Selecting previously unselected package g++-14-aarch64-linux-gnu.
541s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
541s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
542s Selecting previously unselected package g++-14.
542s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ...
542s Unpacking g++-14 (14.2.0-17ubuntu3) ...
542s Selecting previously unselected package g++-aarch64-linux-gnu.
542s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
542s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
542s Selecting previously unselected package g++.
542s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ...
542s Unpacking g++ (4:14.2.0-1ubuntu1) ...
542s Selecting previously unselected package build-essential.
542s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ...
542s Unpacking build-essential (12.10ubuntu1) ...
542s Selecting previously unselected package dctrl-tools.
542s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ...
542s Unpacking dctrl-tools (2.24-3build3) ...
542s Selecting previously unselected package fonts-dejavu-mono.
542s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ...
542s Unpacking fonts-dejavu-mono (2.37-8) ...
542s Selecting previously unselected package fonts-dejavu-core.
542s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ...
542s Unpacking fonts-dejavu-core (2.37-8) ...
542s Selecting previously unselected package fontconfig-config.
542s Preparing to unpack .../028-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
542s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
542s Selecting previously unselected package libfontconfig1:arm64.
542s Preparing to unpack .../029-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
542s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
542s Selecting previously unselected package fontconfig.
542s Preparing to unpack .../030-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
542s Unpacking fontconfig (2.15.0-2ubuntu1) ...
542s Selecting previously unselected package libgfortran5:arm64.
542s Preparing to unpack .../031-libgfortran5_15-20250222-0ubuntu1_arm64.deb ...
542s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ...
542s Selecting previously unselected package libgfortran-14-dev:arm64.
542s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ...
542s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
542s Selecting previously unselected package gfortran-14-aarch64-linux-gnu.
542s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ...
542s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
543s Selecting previously unselected package gfortran-14.
543s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_arm64.deb ...
543s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
543s Selecting previously unselected package gfortran-aarch64-linux-gnu.
543s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ...
543s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
543s Selecting previously unselected package gfortran.
543s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ...
543s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
543s Selecting previously unselected package icu-devtools.
543s Preparing to unpack .../037-icu-devtools_76.1-1ubuntu2_arm64.deb ...
543s Unpacking icu-devtools (76.1-1ubuntu2) ...
543s Selecting previously unselected package libblas3:arm64.
543s Preparing to unpack .../038-libblas3_3.12.1-2_arm64.deb ...
543s Unpacking libblas3:arm64 (3.12.1-2) ...
543s Selecting previously unselected package libblas-dev:arm64.
543s Preparing to unpack .../039-libblas-dev_3.12.1-2_arm64.deb ...
543s Unpacking libblas-dev:arm64 (3.12.1-2) ...
543s Selecting previously unselected package libbz2-dev:arm64.
543s Preparing to unpack .../040-libbz2-dev_1.0.8-6_arm64.deb ...
543s Unpacking libbz2-dev:arm64 (1.0.8-6) ...
543s Selecting previously unselected package libpixman-1-0:arm64.
543s Preparing to unpack .../041-libpixman-1-0_0.44.0-3_arm64.deb ...
543s Unpacking libpixman-1-0:arm64 (0.44.0-3) ...
543s Selecting previously unselected package libxcb-render0:arm64.
543s Preparing to unpack .../042-libxcb-render0_1.17.0-2_arm64.deb ...
543s Unpacking libxcb-render0:arm64 (1.17.0-2) ...
543s Selecting previously unselected package libxcb-shm0:arm64.
543s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_arm64.deb ...
543s Unpacking libxcb-shm0:arm64 (1.17.0-2) ...
543s Selecting previously unselected package libxrender1:arm64.
543s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ...
543s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ...
543s Selecting previously unselected package libcairo2:arm64.
543s Preparing to unpack .../045-libcairo2_1.18.2-2_arm64.deb ...
543s Unpacking libcairo2:arm64 (1.18.2-2) ...
543s Selecting previously unselected package libdatrie1:arm64.
543s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_arm64.deb ...
543s Unpacking libdatrie1:arm64 (0.2.13-3build1) ...
543s Selecting previously unselected package libdeflate0:arm64.
543s Preparing to unpack .../047-libdeflate0_1.23-1_arm64.deb ...
543s Unpacking libdeflate0:arm64 (1.23-1) ...
543s Selecting previously unselected package libdeflate-dev:arm64.
543s Preparing to unpack .../048-libdeflate-dev_1.23-1_arm64.deb ...
543s Unpacking libdeflate-dev:arm64 (1.23-1) ...
543s Selecting previously unselected package libgraphite2-3:arm64.
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548s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ...
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548s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ...
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548s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ...
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549s Setting up libpcre2-posix3:arm64 (10.45-1) ...
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549s Setting up libthai-data (0.1.29-2build1) ...
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549s Setting up dctrl-tools (2.24-3build3) ...
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549s Setting up liblapack3:arm64 (3.12.1-2) ...
549s 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
549s Setting up libpcre2-dev:arm64 (10.45-1) ...
549s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
549s Setting up libpng-dev:arm64 (1.6.47-1) ...
549s Setting up libpaper-utils (2.2.5-0.3) ...
549s Setting up pkgconf:arm64 (1.8.1-4) ...
549s Setting up libthai0:arm64 (0.1.29-2build1) ...
549s Setting up liblapack-dev:arm64 (3.12.1-2) ...
549s 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
549s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
549s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ...
549s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
549s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
549s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ...
549s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ...
549s Setting up libsm6:arm64 (2:1.2.4-1) ...
549s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ...
549s Setting up fontconfig (2.15.0-2ubuntu1) ...
551s Regenerating fonts cache... done.
551s Setting up libxft2:arm64 (2.3.6-1build1) ...
551s Setting up libtk8.6:arm64 (8.6.16-1) ...
551s Setting up libpango-1.0-0:arm64 (1.56.2-1) ...
551s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ...
551s Setting up libcairo2:arm64 (1.18.2-2) ...
551s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
551s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ...
551s Setting up cpp-14 (14.2.0-17ubuntu3) ...
551s Setting up cpp (4:14.2.0-1ubuntu1) ...
551s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
551s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ...
551s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ...
551s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
551s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
551s Setting up gcc-14 (14.2.0-17ubuntu3) ...
551s Setting up r-base-core (4.4.3-1) ...
551s Creating config file /etc/R/Renviron with new version
551s Setting up r-cran-labeling (0.4.3-1) ...
551s Setting up r-cran-lattice (0.22-6-1) ...
551s Setting up r-cran-nlme (3.1.167-1) ...
551s Setting up r-cran-farver (2.1.2-1) ...
551s Setting up r-cran-viridislite (0.4.2-2) ...
551s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
551s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
551s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
551s Setting up g++-14 (14.2.0-17ubuntu3) ...
551s Setting up r-cran-r6 (2.6.1-1) ...
551s Setting up r-cran-pkgkitten (0.2.4-1) ...
551s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
551s Setting up r-cran-magrittr (2.0.3-1) ...
551s Setting up r-cran-littler (0.3.20-2) ...
551s Setting up r-cran-rcpp (1.0.14-1) ...
551s Setting up r-bioc-biocgenerics (0.52.0-2) ...
551s Setting up r-cran-rlang (1.1.5-1) ...
551s Setting up r-cran-matrixstats (1.5.0-1) ...
551s Setting up littler (0.3.20-2) ...
551s Setting up r-cran-withr (3.0.2+dfsg-1) ...
551s Setting up r-cran-fansi (1.0.5-1) ...
551s Setting up r-cran-mass (7.3-64-1) ...
551s Setting up r-cran-glue (1.8.0-1) ...
551s Setting up r-cran-cli (3.6.4-1) ...
551s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
551s Setting up gcc (4:14.2.0-1ubuntu1) ...
551s Setting up r-bioc-biobase (2.66.0-2) ...
551s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
551s Setting up r-cran-utf8 (1.2.4-1) ...
551s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
551s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ...
551s Setting up r-cran-isoband (0.2.7-1) ...
551s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
551s Setting up r-cran-matrix (1.7-3-1) ...
551s Setting up r-cran-mgcv (1.9-1-1) ...
551s Setting up g++ (4:14.2.0-1ubuntu1) ...
551s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
551s Setting up build-essential (12.10ubuntu1) ...
551s Setting up r-cran-vctrs (0.6.5-1) ...
551s Setting up r-cran-pillar (1.10.1+dfsg-1) ...
551s Setting up r-cran-munsell (0.5.1-1) ...
551s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
551s Setting up r-bioc-pcamethods (1.98.0-2) ...
551s Setting up gfortran (4:14.2.0-1ubuntu1) ...
551s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
551s 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
551s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
551s 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
551s Setting up r-cran-scales (1.3.0-1) ...
551s Setting up r-base-dev (4.4.3-1) ...
551s Setting up r-cran-ggplot2 (3.5.1+dfsg-1) ...
551s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
551s Processing triggers for libc-bin (2.41-1ubuntu2) ...
551s Processing triggers for man-db (2.13.0-1) ...
553s Processing triggers for install-info (7.1.1-1) ...
555s autopkgtest [15:39:26]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
555s autopkgtest [15:39:26]: test pkg-r-autopkgtest: [-----------------------
555s Test: Try to load the R library pcaMethods
555s 
555s R version 4.4.3 (2025-02-28) -- "Trophy Case"
555s Copyright (C) 2025 The R Foundation for Statistical Computing
555s Platform: aarch64-unknown-linux-gnu
555s 
555s R is free software and comes with ABSOLUTELY NO WARRANTY.
555s You are welcome to redistribute it under certain conditions.
555s Type 'license()' or 'licence()' for distribution details.
555s 
555s R is a collaborative project with many contributors.
555s Type 'contributors()' for more information and
555s 'citation()' on how to cite R or R packages in publications.
555s 
555s Type 'demo()' for some demos, 'help()' for on-line help, or
555s 'help.start()' for an HTML browser interface to help.
555s Type 'q()' to quit R.
555s 
555s > library('pcaMethods')
555s Loading required package: Biobase
555s Loading required package: BiocGenerics
555s 
555s Attaching package: ‘BiocGenerics’
555s 
555s The following objects are masked from ‘package:stats’:
555s 
555s     IQR, mad, sd, var, xtabs
555s 
555s The following objects are masked from ‘package:base’:
555s 
555s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
555s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
555s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
555s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
555s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
555s     table, tapply, union, unique, unsplit, which.max, which.min
555s 
556s Welcome to Bioconductor
556s 
556s     Vignettes contain introductory material; view with
556s     'browseVignettes()'. To cite Bioconductor, see
556s     'citation("Biobase")', and for packages 'citation("pkgname")'.
556s 
556s > 
556s > 
556s 
556s Attaching package: ‘pcaMethods’
556s 
556s The following object is masked from ‘package:stats’:
556s 
556s     loadings
556s 
556s Other tests are currently unsupported!
556s They will be progressively added.
556s autopkgtest [15:39:27]: test pkg-r-autopkgtest: -----------------------]
557s pkg-r-autopkgtest    PASS
557s autopkgtest [15:39:28]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
557s autopkgtest [15:39:28]: @@@@@@@@@@@@@@@@@@@@ summary
557s pkg-r-autopkgtest    PASS
576s nova [W] Using flock in prodstack6-arm64
576s flock: timeout while waiting to get lock
576s Creating nova instance adt-plucky-arm64-r-bioc-pcamethods-20250315-150852-juju-7f2275-prod-proposed-migration-environment-20-7f8b886d-bafc-4a01-b5f2-cbdc5dfdeb99 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
576s nova [W] Timed out waiting for a4a72487-22b1-457c-976d-aad3e6ad100b to get deleted.