0s autopkgtest [15:19:46]: starting date and time: 2025-03-15 15:19:46+0000
  0s autopkgtest [15:19:46]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [15:19:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dl633o6y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-bio3d --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-arm64-20.secgroup --name adt-plucky-arm64-r-cran-bio3d-20250315-151946-juju-7f2275-prod-proposed-migration-environment-2-680173fd-3a08-42ec-b907-af72aee0fbfa --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/
134s autopkgtest [15:22:00]: testbed dpkg architecture: arm64
134s autopkgtest [15:22:00]: testbed apt version: 2.9.33
135s autopkgtest [15:22:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup
135s autopkgtest [15:22:01]: testbed release detected to be: None
136s autopkgtest [15:22:02]: updating testbed package index (apt update)
137s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
137s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
137s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
137s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
137s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
137s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
137s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
137s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
138s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
138s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
138s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
138s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
138s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
138s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
138s Fetched 1094 kB in 1s (895 kB/s)
139s Reading package lists...
140s Reading package lists...
141s Building dependency tree...
141s Reading state information...
142s Calculating upgrade...
142s Calculating upgrade...
143s The following packages will be upgraded:
143s   python3-jinja2 strace
143s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
143s Need to get 608 kB of archives.
143s After this operation, 11.3 kB of additional disk space will be used.
143s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
144s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
145s Fetched 608 kB in 1s (797 kB/s)
145s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
145s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
145s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
145s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
145s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
145s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
146s Setting up strace (6.13+ds-1ubuntu1) ...
146s Processing triggers for man-db (2.13.0-1) ...
147s Reading package lists...
147s Building dependency tree...
147s Reading state information...
148s Solving dependencies...
149s The following packages will be REMOVED:
149s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
149s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
149s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
149s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
149s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
149s After this operation, 267 MB disk space will be freed.
149s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
149s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
149s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
149s Removing libpython3.12t64:arm64 (3.12.9-1) ...
149s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
149s Removing libnsl2:arm64 (1.3.0-3build3) ...
149s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
150s Removing libunwind8:arm64 (1.6.2-3.1) ...
150s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
150s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
152s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
152s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
152s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
152s /etc/kernel/postrm.d/initramfs-tools:
152s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
152s /etc/kernel/postrm.d/zz-flash-kernel:
152s flash-kernel: Kernel 6.11.0-8-generic has been removed.
152s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
153s /etc/kernel/postrm.d/zz-update-grub:
153s Sourcing file `/etc/default/grub'
153s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
153s Generating grub configuration file ...
153s Found linux image: /boot/vmlinuz-6.14.0-10-generic
153s Found initrd image: /boot/initrd.img-6.14.0-10-generic
153s Warning: os-prober will not be executed to detect other bootable partitions.
153s Systems on them will not be added to the GRUB boot configuration.
153s Check GRUB_DISABLE_OS_PROBER documentation entry.
153s Adding boot menu entry for UEFI Firmware Settings ...
153s done
154s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
154s Processing triggers for libc-bin (2.41-1ubuntu1) ...
154s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81650 files and directories currently installed.)
154s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
154s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
154s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
154s autopkgtest [15:22:20]: upgrading testbed (apt dist-upgrade and autopurge)
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
156s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
157s Starting 2 pkgProblemResolver with broken count: 0
157s Done
158s Entering ResolveByKeep
159s 
159s Calculating upgrade...
160s The following packages will be upgraded:
160s   libc-bin libc-dev-bin libc6 libc6-dev locales
160s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
160s Need to get 9530 kB of archives.
160s After this operation, 0 B of additional disk space will be used.
160s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
161s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
161s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
162s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
163s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
164s Preconfiguring packages ...
164s Fetched 9530 kB in 3s (2836 kB/s)
164s (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.)
164s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
164s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
165s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
165s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
165s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
165s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
165s Setting up libc6:arm64 (2.41-1ubuntu2) ...
166s (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.)
166s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
166s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
166s Setting up libc-bin (2.41-1ubuntu2) ...
166s (Reading database ... 
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(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.)
166s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
166s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
166s Setting up locales (2.41-1ubuntu2) ...
167s Generating locales (this might take a while)...
170s   en_US.UTF-8... done
170s Generation complete.
170s Setting up libc-dev-bin (2.41-1ubuntu2) ...
170s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
170s Processing triggers for man-db (2.13.0-1) ...
171s Processing triggers for systemd (257.3-1ubuntu3) ...
173s Reading package lists...
173s Building dependency tree...
173s Reading state information...
174s Starting pkgProblemResolver with broken count: 0
174s Starting 2 pkgProblemResolver with broken count: 0
174s Done
175s Solving dependencies...
176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
176s autopkgtest [15:22:42]: rebooting testbed after setup commands that affected boot
200s autopkgtest [15:23:06]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025
203s autopkgtest [15:23:09]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bio3d
206s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bio3d 2.4-5-1 (dsc) [2285 B]
206s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bio3d 2.4-5-1 (tar) [1544 kB]
206s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-bio3d 2.4-5-1 (diff) [5468 B]
207s gpgv: Signature made Wed Jan 29 00:14:06 2025 UTC
207s gpgv:                using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
207s gpgv:                issuer "plessy@debian.org"
207s gpgv: Can't check signature: No public key
207s dpkg-source: warning: cannot verify inline signature for ./r-cran-bio3d_2.4-5-1.dsc: no acceptable signature found
207s autopkgtest [15:23:13]: testing package r-cran-bio3d version 2.4-5-1
208s autopkgtest [15:23:14]: build not needed
212s autopkgtest [15:23:18]: test run-unit-test: preparing testbed
212s Reading package lists...
213s Building dependency tree...
213s Reading state information...
213s Starting pkgProblemResolver with broken count: 0
213s Starting 2 pkgProblemResolver with broken count: 0
213s Done
214s The following NEW packages will be installed:
214s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
214s   fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax
214s   javascript-common libaec0 libamd3 libasan8 libblas3 libboost-dev
214s   libboost1.83-dev libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1
214s   libgcc-14-dev libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b
214s   libhdf5-310 libhdf5-hl-310 libhwasan0 libice6 libitm1 libjbig0
214s   libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4 libjs-d3
214s   libjs-es5-shim libjs-highlight.js libjs-jquery libjs-jquery-datatables
214s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-mathjax
214s   libjs-microplugin.js libjs-modernizr libjs-popper.js libjs-prettify
214s   libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3 liblerc4
214s   liblsan0 libltdl7 liblua5.4-0 libnetcdf22 libpango-1.0-0 libpangocairo-1.0-0
214s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6
214s   libstdc++-14-dev libsuitesparseconfig7 libsz2 libtcl8.6 libthai-data
214s   libthai0 libtiff6 libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0
214s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler
214s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
214s   r-base-core r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
214s   r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-s4vectors r-bioc-ucsc.utils
214s   r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-base64enc r-cran-bh
214s   r-cran-bigmemory r-cran-bigmemory.sri r-cran-bio3d r-cran-bitops r-cran-brio
214s   r-cran-bslib r-cran-cachem r-cran-callr r-cran-cli r-cran-commonmark
214s   r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-desc r-cran-diffobj
214s   r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs
214s   r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr
214s   r-cran-igraph r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-later
214s   r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix
214s   r-cran-memoise r-cran-mime r-cran-ncdf4 r-cran-openssl r-cran-pkgbuild
214s   r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise
214s   r-cran-processx r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs
214s   r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rmarkdown r-cran-rprojroot
214s   r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-sys r-cran-testthat
214s   r-cran-tinytex r-cran-uuid r-cran-vctrs r-cran-waldo r-cran-withr
214s   r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml unzip x11-common xdg-utils
214s   zip zlib1g-dev
214s 0 upgraded, 173 newly installed, 0 to remove and 0 not upgraded.
214s Need to get 190 MB of archives.
214s After this operation, 743 MB of additional disk space will be used.
214s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
215s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
215s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
215s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
215s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
215s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
215s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
215s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
215s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 javascript-common all 12 [5216 B]
215s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
215s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
216s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB]
216s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB]
216s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
216s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
216s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
216s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
216s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
216s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
217s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
217s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
217s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
217s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu2 [10.7 MB]
218s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-dev arm64 1.83.0.2ubuntu1 [4468 B]
218s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
218s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
218s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
218s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
218s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
218s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB]
218s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
218s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
218s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
218s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB]
218s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB]
218s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
218s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
218s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
218s Get:39 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB]
219s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB]
219s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
219s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
219s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
219s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
219s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
219s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
219s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
219s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-d3 all 3.5.17-4 [132 kB]
219s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
219s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
219s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
219s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
219s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
219s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
219s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
219s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
219s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
219s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
219s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
219s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
219s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 liblua5.4-0 arm64 5.4.7-1 [158 kB]
219s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB]
220s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
220s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
220s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB]
220s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB]
220s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB]
220s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB]
220s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB]
220s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
220s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
220s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
220s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
220s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
220s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
220s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
220s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
220s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
220s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
220s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB]
220s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
220s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
220s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB]
222s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB]
222s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B]
222s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB]
222s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
222s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB]
222s Get:89 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
222s Get:90 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc arm64 3.1.11.1+ds-2 [28.1 MB]
223s Get:91 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
223s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB]
223s Get:93 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-iranges arm64 2.40.1-2 [2303 kB]
223s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
223s Get:95 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
223s Get:96 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB]
223s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB]
223s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB]
223s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB]
223s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB]
223s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB]
223s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB]
223s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB]
223s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
223s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
223s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
224s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
224s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB]
224s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB]
225s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB]
225s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bh all 1.84.0-1 [5962 B]
225s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bigmemory.sri all 0.1.8-1 [13.4 kB]
225s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
225s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB]
225s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-uuid arm64 1.2-1-1 [48.7 kB]
225s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bigmemory arm64 4.6.4-1ubuntu1 [458 kB]
225s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bio3d arm64 2.4-5-1 [3013 kB]
226s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bitops arm64 1.0-9-1 [30.2 kB]
226s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-brio arm64 1.1.5-1 [39.1 kB]
226s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB]
226s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB]
226s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB]
226s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB]
226s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-htmltools arm64 0.5.8.1-1 [373 kB]
226s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
226s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB]
226s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB]
226s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
226s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB]
226s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fs arm64 1.6.5+dfsg-1 [244 kB]
226s Get:131 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB]
226s Get:132 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sass arm64 0.4.9+dfsg-1 [957 kB]
226s Get:133 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bslib all 0.8.0+dfsg-1 [4294 kB]
226s Get:134 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ps arm64 1.9.0-1 [407 kB]
226s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-processx arm64 3.8.6-1 [363 kB]
226s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-callr all 3.7.6-1 [458 kB]
226s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.2-2 [129 kB]
226s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB]
226s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-desc all 1.4.3-1 [359 kB]
226s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB]
226s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB]
226s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
226s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB]
226s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
226s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-later arm64 1.4.1+dfsg-1 [141 kB]
226s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
226s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-promises arm64 1.3.2+dfsg-1 [290 kB]
226s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httpuv arm64 1.6.15+dfsg-1 [489 kB]
226s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB]
226s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB]
227s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
227s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
227s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-igraph arm64 2.1.4-1 [5150 kB]
228s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB]
228s Get:155 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
228s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB]
228s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ncdf4 arm64 1.23-1build1 [277 kB]
228s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgbuild all 1.4.6-1 [213 kB]
228s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rprojroot all 2.0.4-2 [125 kB]
229s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
229s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgload all 1.4.0-1 [247 kB]
229s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB]
229s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcurl arm64 1.98-1.16+dfsg-1 [806 kB]
229s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tinytex all 0.56-1 [148 kB]
229s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-modernizr all 3.13.0-0.1 [101 kB]
229s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB]
229s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB]
229s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
229s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
229s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rmarkdown all 2.29+dfsg-1 [1501 kB]
229s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-waldo all 0.6.1-2 [150 kB]
229s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-testthat arm64 3.2.3-1 [1644 kB]
229s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xml arm64 3.99-0.18-1 [1745 kB]
230s Preconfiguring packages ...
230s Fetched 190 MB in 15s (12.5 MB/s)
230s Selecting previously unselected package fonts-dejavu-mono.
231s (Reading database ... 
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(Reading database ... 81647 files and directories currently installed.)
231s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8_all.deb ...
231s Unpacking fonts-dejavu-mono (2.37-8) ...
231s Selecting previously unselected package fonts-dejavu-core.
231s Preparing to unpack .../001-fonts-dejavu-core_2.37-8_all.deb ...
231s Unpacking fonts-dejavu-core (2.37-8) ...
231s Selecting previously unselected package fontconfig-config.
231s Preparing to unpack .../002-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ...
231s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
231s Selecting previously unselected package libfontconfig1:arm64.
231s Preparing to unpack .../003-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ...
231s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ...
231s Selecting previously unselected package fontconfig.
231s Preparing to unpack .../004-fontconfig_2.15.0-2ubuntu1_arm64.deb ...
231s Unpacking fontconfig (2.15.0-2ubuntu1) ...
231s Selecting previously unselected package fonts-font-awesome.
231s Preparing to unpack .../005-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
231s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
231s Selecting previously unselected package fonts-glyphicons-halflings.
231s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ...
231s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
231s Selecting previously unselected package fonts-mathjax.
232s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
232s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
232s Selecting previously unselected package javascript-common.
232s Preparing to unpack .../008-javascript-common_12_all.deb ...
232s Unpacking javascript-common (12) ...
232s Selecting previously unselected package libaec0:arm64.
232s Preparing to unpack .../009-libaec0_1.1.3-1_arm64.deb ...
232s Unpacking libaec0:arm64 (1.1.3-1) ...
232s Selecting previously unselected package libgomp1:arm64.
232s Preparing to unpack .../010-libgomp1_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package libsuitesparseconfig7:arm64.
232s Preparing to unpack .../011-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_arm64.deb ...
232s Unpacking libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ...
232s Selecting previously unselected package libamd3:arm64.
232s Preparing to unpack .../012-libamd3_1%3a7.8.3+dfsg-3_arm64.deb ...
232s Unpacking libamd3:arm64 (1:7.8.3+dfsg-3) ...
232s Selecting previously unselected package libasan8:arm64.
232s Preparing to unpack .../013-libasan8_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package libblas3:arm64.
232s Preparing to unpack .../014-libblas3_3.12.1-2_arm64.deb ...
232s Unpacking libblas3:arm64 (3.12.1-2) ...
232s Selecting previously unselected package libitm1:arm64.
232s Preparing to unpack .../015-libitm1_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package liblsan0:arm64.
232s Preparing to unpack .../016-liblsan0_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package libtsan2:arm64.
232s Preparing to unpack .../017-libtsan2_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package libubsan1:arm64.
232s Preparing to unpack .../018-libubsan1_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ...
232s Selecting previously unselected package libhwasan0:arm64.
232s Preparing to unpack .../019-libhwasan0_15-20250222-0ubuntu1_arm64.deb ...
232s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ...
233s Selecting previously unselected package libgcc-14-dev:arm64.
233s Preparing to unpack .../020-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ...
233s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ...
233s Selecting previously unselected package libstdc++-14-dev:arm64.
233s Preparing to unpack .../021-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ...
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240s Selecting previously unselected package pandoc-data.
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242s Selecting previously unselected package r-cran-curl.
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243s Selecting previously unselected package r-cran-crayon.
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244s Selecting previously unselected package r-cran-uuid.
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244s Selecting previously unselected package r-cran-bigmemory.
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244s Selecting previously unselected package r-cran-bio3d.
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244s Selecting previously unselected package r-cran-bitops.
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244s Selecting previously unselected package r-cran-brio.
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244s Selecting previously unselected package r-cran-cachem.
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244s Selecting previously unselected package r-cran-digest.
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244s Selecting previously unselected package r-cran-htmltools.
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244s Selecting previously unselected package r-cran-jquerylib.
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253s Setting up r-cran-testthat (3.2.3-1) ...
253s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
253s Setting up r-cran-bslib (0.8.0+dfsg-1) ...
253s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
253s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
253s Setting up r-cran-rmarkdown (2.29+dfsg-1) ...
253s Processing triggers for libc-bin (2.41-1ubuntu2) ...
253s Processing triggers for man-db (2.13.0-1) ...
255s Processing triggers for install-info (7.1.1-1) ...
256s autopkgtest [15:24:02]: test run-unit-test: [-----------------------
257s BEGIN TEST testthat.R
257s 
257s R version 4.4.3 (2025-02-28) -- "Trophy Case"
257s Copyright (C) 2025 The R Foundation for Statistical Computing
257s Platform: aarch64-unknown-linux-gnu
257s 
257s R is free software and comes with ABSOLUTELY NO WARRANTY.
257s You are welcome to redistribute it under certain conditions.
257s Type 'license()' or 'licence()' for distribution details.
257s 
257s R is a collaborative project with many contributors.
257s Type 'contributors()' for more information and
257s 'citation()' on how to cite R or R packages in publications.
257s 
257s Type 'demo()' for some demos, 'help()' for on-line help, or
257s 'help.start()' for an HTML browser interface to help.
257s Type 'q()' to quit R.
257s 
257s > library(testthat)
257s > test_check("bio3d")
257s Loading required package: bio3d
267s [ FAIL 0 | WARN 0 | SKIP 29 | PASS 174 ]
267s 
267s == Skipped tests (29) ==========================================================
268s * On CRAN (29): 'test-aanma.R:5:3', 'test-aanma.pdbs.R:10:3',
268s   'test-clean.pdb.R:24:3', 'test-cmap.R:20:3', 'test-cna.R:5:3',
268s   'test-core.find.R:5:3', 'test-dccm.R:27:3', 'test-dccm.R:47:3',
268s   'test-dssp.R:4:3', 'test-fitting.R:64:3', 'test-fitting.R:91:4',
268s   'test-fitting.R:116:4', 'test-get.pdb.R:4:3', 'test-get.pdb.R:24:3',
268s   'test-get.seq.R:4:3', 'test-mol2.R:34:3', 'test-mol2.R:49:3',
268s   'test-mol2.R:82:3', 'test-nma.pdbs.R:5:3', 'test-pdb.annotate.R:5:3',
268s   'test-pdbsplit.R:5:3', 'test-read.all.R:6:3', 'test-read.cif.R:5:3',
268s   'test-read.cif.R:49:3', 'test-read.ncdf.R:4:4', 'test-read.pdb.R:43:3',
268s   'test-read.pdb.R:121:3', 'test-read.pdb.R:141:3', 'test-seqaln.R:5:3'
268s 
268s [ FAIL 0 | WARN 0 | SKIP 29 | PASS 174 ]
268s > 
268s autopkgtest [15:24:14]: test run-unit-test: -----------------------]
269s run-unit-test        PASS
269s autopkgtest [15:24:15]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
269s autopkgtest [15:24:15]: test pkg-r-autopkgtest: preparing testbed
425s autopkgtest [15:26:51]: testbed dpkg architecture: arm64
426s autopkgtest [15:26:52]: testbed apt version: 2.9.33
426s autopkgtest [15:26:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup
426s autopkgtest [15:26:52]: testbed release detected to be: plucky
428s autopkgtest [15:26:54]: updating testbed package index (apt update)
428s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
428s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
428s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
429s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
429s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
429s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB]
429s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
429s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB]
429s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B]
429s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B]
429s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB]
429s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB]
429s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B]
429s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B]
429s Fetched 1094 kB in 1s (1085 kB/s)
430s Reading package lists...
431s Reading package lists...
431s Building dependency tree...
431s Reading state information...
431s Calculating upgrade...
432s Calculating upgrade...
432s The following packages will be upgraded:
432s   python3-jinja2 strace
432s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
432s Need to get 608 kB of archives.
432s After this operation, 11.3 kB of additional disk space will be used.
432s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB]
433s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
433s Fetched 608 kB in 1s (936 kB/s)
433s (Reading database ... 
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(Reading database ... 117701 files and directories currently installed.)
433s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ...
433s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
434s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
434s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
434s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
434s Setting up strace (6.13+ds-1ubuntu1) ...
434s Processing triggers for man-db (2.13.0-1) ...
435s Reading package lists...
435s Building dependency tree...
435s Reading state information...
435s Solving dependencies...
436s The following packages will be REMOVED:
436s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
436s   libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
436s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
436s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic*
436s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded.
436s After this operation, 267 MB disk space will be freed.
436s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117701 files and directories currently installed.)
436s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
436s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
436s Removing libpython3.12t64:arm64 (3.12.9-1) ...
436s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ...
436s Removing libnsl2:arm64 (1.3.0-3build3) ...
436s Removing libpython3.12-minimal:arm64 (3.12.9-1) ...
436s Removing libunwind8:arm64 (1.6.2-3.1) ...
436s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
437s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
438s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
439s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
439s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
439s /etc/kernel/postrm.d/initramfs-tools:
439s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
439s /etc/kernel/postrm.d/zz-flash-kernel:
439s flash-kernel: Kernel 6.11.0-8-generic has been removed.
439s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required.
439s /etc/kernel/postrm.d/zz-update-grub:
439s Sourcing file `/etc/default/grub'
439s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
439s Generating grub configuration file ...
439s Found linux image: /boot/vmlinuz-6.14.0-10-generic
439s Found initrd image: /boot/initrd.img-6.14.0-10-generic
440s Warning: os-prober will not be executed to detect other bootable partitions.
440s Systems on them will not be added to the GRUB boot configuration.
440s Check GRUB_DISABLE_OS_PROBER documentation entry.
440s Adding boot menu entry for UEFI Firmware Settings ...
440s done
440s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
440s Processing triggers for libc-bin (2.41-1ubuntu1) ...
440s (Reading database ... 
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81650 files and directories currently installed.)
440s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
440s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ...
440s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
440s autopkgtest [15:27:06]: upgrading testbed (apt dist-upgrade and autopurge)
440s Reading package lists...
441s Building dependency tree...
441s Reading state information...
442s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
442s Starting 2 pkgProblemResolver with broken count: 0
442s Done
442s Entering ResolveByKeep
443s 
443s Calculating upgrade...
443s The following packages will be upgraded:
443s   libc-bin libc-dev-bin libc6 libc6-dev locales
443s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
443s Need to get 9530 kB of archives.
443s After this operation, 0 B of additional disk space will be used.
443s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB]
444s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB]
444s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB]
444s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB]
444s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB]
445s Preconfiguring packages ...
445s Fetched 9530 kB in 1s (6943 kB/s)
445s (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.)
445s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ...
445s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
445s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ...
445s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
445s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ...
446s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
446s Setting up libc6:arm64 (2.41-1ubuntu2) ...
446s (Reading database ... 
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(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.)
446s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ...
446s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
446s Setting up libc-bin (2.41-1ubuntu2) ...
446s (Reading database ... 
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(Reading database ... 75%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81647 files and directories currently installed.)
446s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
446s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
446s Setting up locales (2.41-1ubuntu2) ...
447s Generating locales (this might take a while)...
449s   en_US.UTF-8... done
449s Generation complete.
449s Setting up libc-dev-bin (2.41-1ubuntu2) ...
449s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ...
449s Processing triggers for man-db (2.13.0-1) ...
450s Processing triggers for systemd (257.3-1ubuntu3) ...
451s Reading package lists...
451s Building dependency tree...
451s Reading state information...
451s Starting pkgProblemResolver with broken count: 0
451s Starting 2 pkgProblemResolver with broken count: 0
451s Done
452s Solving dependencies...
452s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
453s autopkgtest [15:27:19]: rebooting testbed after setup commands that affected boot
479s Reading package lists...
480s Building dependency tree...
480s Reading state information...
480s Starting pkgProblemResolver with broken count: 0
480s Starting 2 pkgProblemResolver with broken count: 0
480s Done
481s The following NEW packages will be installed:
481s   build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
481s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
481s   fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax g++ g++-14
481s   g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
481s   gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14
481s   gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools
481s   javascript-common libaec0 libamd3 libasan8 libblas-dev libblas3 libboost-dev
481s   libboost1.83-dev libbz2-dev libcairo2 libcc1-0 libcolamd3 libdatrie1
481s   libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev
481s   libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-310
481s   libhdf5-hl-310 libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0
481s   libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev
481s   libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js
481s   libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js
481s   libjs-jquery-ui libjs-json libjs-mathjax libjs-microplugin.js
481s   libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js
481s   libjs-twitter-bootstrap-datepicker liblapack-dev liblapack3 liblerc4
481s   liblsan0 libltdl7 liblua5.4-0 liblzma-dev libmpc3 libncurses-dev libnetcdf22
481s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
481s   libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
481s   libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6
481s   libstdc++-14-dev libsuitesparseconfig7 libsz2 libtcl8.6 libthai-data
481s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
481s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 littler
481s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
481s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
481s   r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
481s   r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-s4vectors r-bioc-ucsc.utils
481s   r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-base64enc r-cran-bh
481s   r-cran-bigmemory r-cran-bigmemory.sri r-cran-bio3d r-cran-bitops r-cran-brio
481s   r-cran-bslib r-cran-cachem r-cran-callr r-cran-cli r-cran-commonmark
481s   r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-desc r-cran-diffobj
481s   r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs
481s   r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr
481s   r-cran-igraph r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-later
481s   r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix
481s   r-cran-memoise r-cran-mime r-cran-ncdf4 r-cran-openssl r-cran-pkgbuild
481s   r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise
481s   r-cran-processx r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs
481s   r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rmarkdown r-cran-rprojroot
481s   r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-sys r-cran-testthat
481s   r-cran-tinytex r-cran-uuid r-cran-vctrs r-cran-waldo r-cran-withr
481s   r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml unzip x11-common xdg-utils
481s   zip zlib1g-dev
481s 0 upgraded, 218 newly installed, 0 to remove and 0 not upgraded.
481s Need to get 267 MB of archives.
481s After this operation, 1003 MB of additional disk space will be used.
481s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB]
482s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB]
482s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB]
482s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B]
482s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B]
482s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB]
482s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB]
482s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB]
482s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB]
482s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB]
483s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB]
483s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB]
483s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB]
483s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB]
484s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB]
484s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB]
486s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB]
486s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B]
486s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B]
486s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB]
486s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB]
486s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB]
486s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B]
486s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B]
486s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B]
486s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB]
486s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB]
486s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB]
487s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB]
487s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB]
487s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB]
487s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
487s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
487s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
487s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB]
487s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB]
487s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB]
488s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB]
488s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B]
488s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B]
488s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB]
488s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 javascript-common all 12 [5216 B]
488s Get:43 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
488s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB]
488s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB]
488s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB]
488s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB]
488s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost1.83-dev arm64 1.83.0-4.1ubuntu2 [10.7 MB]
489s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libboost-dev arm64 1.83.0.2ubuntu1 [4468 B]
489s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB]
489s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB]
489s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB]
489s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B]
489s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB]
489s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB]
489s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB]
489s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB]
489s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB]
489s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB]
489s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB]
489s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB]
489s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB]
489s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB]
489s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
489s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-310 arm64 1.14.5+repack-3 [1331 kB]
489s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [59.8 kB]
489s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
489s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB]
489s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB]
490s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB]
490s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB]
490s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B]
490s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B]
490s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B]
490s Get:75 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
490s Get:76 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-popper.js all 1.16.1+ds-6 [54.1 kB]
490s Get:77 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap4 all 4.6.1+dfsg1-4 [537 kB]
490s Get:78 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-d3 all 3.5.17-4 [132 kB]
490s Get:79 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
490s Get:80 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
490s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
490s Get:82 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
490s Get:83 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
490s Get:84 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-microplugin.js all 0.0.3+dfsg-1.1 [3712 B]
490s Get:85 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
490s Get:86 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
490s Get:87 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-json all 0~20221030+~1.0.8-1 [20.6 kB]
490s Get:88 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-prettify all 2015.12.04+dfsg-1.1 [39.3 kB]
490s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB]
490s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB]
490s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB]
490s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 liblua5.4-0 arm64 5.4.7-1 [158 kB]
490s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB]
490s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnetcdf22 arm64 1:4.9.3-1 [504 kB]
490s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB]
491s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB]
491s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB]
491s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB]
491s Get:99 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB]
491s Get:100 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB]
491s Get:101 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB]
491s Get:102 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB]
491s Get:103 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB]
491s Get:104 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B]
491s Get:105 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB]
491s Get:106 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB]
491s Get:107 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB]
491s Get:108 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB]
491s Get:109 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB]
492s Get:110 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB]
492s Get:111 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB]
492s Get:112 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB]
492s Get:113 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB]
492s Get:114 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB]
492s Get:115 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB]
492s Get:116 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB]
492s Get:117 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B]
492s Get:118 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB]
492s Get:119 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB]
492s Get:120 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB]
492s Get:121 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB]
492s Get:122 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
492s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB]
494s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB]
494s Get:125 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B]
494s Get:126 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-bootstrap-sass all 3.4.3-2 [187 kB]
494s Get:127 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
494s Get:128 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB]
494s Get:129 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
494s Get:130 http://ftpmaster.internal/ubuntu plucky/universe arm64 pandoc arm64 3.1.11.1+ds-2 [28.1 MB]
496s Get:131 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB]
496s Get:132 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB]
496s Get:133 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB]
496s Get:134 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB]
496s Get:135 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B]
496s Get:136 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
496s Get:137 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
496s Get:138 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-s4vectors arm64 0.44.0+dfsg-2 [2054 kB]
496s Get:139 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-iranges arm64 2.40.1-2 [2303 kB]
496s Get:140 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
496s Get:141 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-xvector arm64 0.46.0-2 [618 kB]
496s Get:142 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-curl arm64 6.2.1+dfsg-1ubuntu1 [196 kB]
496s Get:143 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jsonlite arm64 1.9.1+dfsg-1 [445 kB]
496s Get:144 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mime arm64 0.12-2 [35.8 kB]
496s Get:145 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sys arm64 3.4.3-1 [45.2 kB]
496s Get:146 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-askpass arm64 1.2.1-1 [24.8 kB]
496s Get:147 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-openssl arm64 2.3.2+dfsg-1 [406 kB]
496s Get:148 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-r6 all 2.6.1-1 [101 kB]
496s Get:149 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
496s Get:150 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
496s Get:151 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
497s Get:152 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
497s Get:153 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-crayon all 1.5.3-1 [165 kB]
497s Get:154 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-bioc-biostrings arm64 2.74.1+dfsg-2 [13.3 MB]
498s Get:155 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-base64enc arm64 0.1-3-3 [27.4 kB]
498s Get:156 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bh all 1.84.0-1 [5962 B]
498s Get:157 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bigmemory.sri all 0.1.8-1 [13.4 kB]
498s Get:158 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
498s Get:159 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB]
499s Get:160 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-uuid arm64 1.2-1-1 [48.7 kB]
499s Get:161 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bigmemory arm64 4.6.4-1ubuntu1 [458 kB]
499s Get:162 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bio3d arm64 2.4-5-1 [3013 kB]
499s Get:163 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bitops arm64 1.0-9-1 [30.2 kB]
499s Get:164 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-brio arm64 1.1.5-1 [39.1 kB]
499s Get:165 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB]
499s Get:166 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmap arm64 1.2.0-1 [70.6 kB]
499s Get:167 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cachem arm64 1.1.0-1 [74.1 kB]
499s Get:168 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB]
499s Get:169 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-htmltools arm64 0.5.8.1-1 [373 kB]
499s Get:170 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-jquerylib all 0.1.4+dfsg-4 [13.5 kB]
499s Get:171 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB]
499s Get:172 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB]
499s Get:173 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
499s Get:174 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-memoise all 2.0.1-1 [53.9 kB]
499s Get:175 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fs arm64 1.6.5+dfsg-1 [244 kB]
499s Get:176 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rappdirs arm64 0.3.3-1 [47.5 kB]
499s Get:177 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sass arm64 0.4.9+dfsg-1 [957 kB]
499s Get:178 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-bslib all 0.8.0+dfsg-1 [4294 kB]
500s Get:179 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ps arm64 1.9.0-1 [407 kB]
500s Get:180 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-processx arm64 3.8.6-1 [363 kB]
500s Get:181 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-callr all 3.7.6-1 [458 kB]
500s Get:182 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.2-2 [129 kB]
500s Get:183 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB]
500s Get:184 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-desc all 1.4.3-1 [359 kB]
500s Get:185 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-diffobj arm64 0.3.5-1 [1116 kB]
500s Get:186 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB]
500s Get:187 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
500s Get:188 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB]
500s Get:189 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
500s Get:190 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-later arm64 1.4.1+dfsg-1 [141 kB]
500s Get:191 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB]
500s Get:192 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-promises arm64 1.3.2+dfsg-1 [290 kB]
500s Get:193 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-httpuv arm64 1.6.15+dfsg-1 [489 kB]
500s Get:194 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB]
500s Get:195 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB]
501s Get:196 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
501s Get:197 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB]
501s Get:198 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-igraph arm64 2.1.4-1 [5150 kB]
501s Get:199 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB]
501s Get:200 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
502s Get:201 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB]
502s Get:202 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ncdf4 arm64 1.23-1build1 [277 kB]
502s Get:203 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgbuild all 1.4.6-1 [213 kB]
502s Get:204 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rprojroot all 2.0.4-2 [125 kB]
502s Get:205 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
502s Get:206 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgload all 1.4.0-1 [247 kB]
502s Get:207 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-praise all 1.0.0-4build1 [20.3 kB]
502s Get:208 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcurl arm64 1.98-1.16+dfsg-1 [806 kB]
503s Get:209 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tinytex all 0.56-1 [148 kB]
503s Get:210 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-modernizr all 3.13.0-0.1 [101 kB]
503s Get:211 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xtable all 1:1.8-4-2 [689 kB]
503s Get:212 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sourcetools arm64 0.1.7-1-1 [47.2 kB]
503s Get:213 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
503s Get:214 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
503s Get:215 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rmarkdown all 2.29+dfsg-1 [1501 kB]
504s Get:216 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-waldo all 0.6.1-2 [150 kB]
504s Get:217 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-testthat arm64 3.2.3-1 [1644 kB]
504s Get:218 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xml arm64 3.99-0.18-1 [1745 kB]
505s Preconfiguring packages ...
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505s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ...
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505s Selecting previously unselected package cpp-14-aarch64-linux-gnu.
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507s Selecting previously unselected package dctrl-tools.
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508s Selecting previously unselected package fonts-dejavu-mono.
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508s Selecting previously unselected package fonts-dejavu-core.
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508s Selecting previously unselected package fontconfig-config.
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511s Selecting previously unselected package libdeflate0:arm64.
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512s Selecting previously unselected package libice6:arm64.
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513s Selecting previously unselected package liblapack3:arm64.
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513s Selecting previously unselected package liblapack-dev:arm64.
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513s Selecting previously unselected package liblerc4:arm64.
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513s Selecting previously unselected package liblua5.4-0:arm64.
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513s Selecting previously unselected package libncurses-dev:arm64.
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517s Selecting previously unselected package r-bioc-biocgenerics.
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517s Selecting previously unselected package r-cran-curl.
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520s Selecting previously unselected package r-cran-magrittr.
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520s Selecting previously unselected package r-cran-promises.
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521s Selecting previously unselected package r-cran-httpuv.
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521s Selecting previously unselected package r-cran-lattice.
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521s Selecting previously unselected package r-cran-matrix.
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521s Selecting previously unselected package r-cran-pkgconfig.
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521s Selecting previously unselected package r-cran-vctrs.
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524s Setting up libamd3:arm64 (1:7.8.3+dfsg-3) ...
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524s Setting up libhdf5-310:arm64 (1.14.5+repack-3) ...
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526s Setting up r-base-core (4.4.3-1) ...
526s Creating config file /etc/R/Renviron with new version
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526s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ...
526s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ...
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526s Setting up r-cran-magrittr (2.0.3-1) ...
526s Setting up r-cran-rappdirs (0.3.3-1) ...
526s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
526s Setting up r-cran-littler (0.3.20-2) ...
526s Setting up r-cran-bh (1.84.0-1) ...
526s Setting up r-cran-ncdf4 (1.23-1build1) ...
526s Setting up r-cran-fs (1.6.5+dfsg-1) ...
526s Setting up r-cran-rcpp (1.0.14-1) ...
526s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
526s Setting up r-cran-brio (1.1.5-1) ...
526s Setting up r-cran-diffobj (0.3.5-1) ...
526s Setting up r-cran-bigmemory.sri (0.1.8-1) ...
526s Setting up r-bioc-biocgenerics (0.52.0-2) ...
526s Setting up r-cran-rlang (1.1.5-1) ...
526s Setting up littler (0.3.20-2) ...
526s Setting up r-cran-bio3d (2.4-5-1) ...
526s Setting up r-cran-uuid (1.2-1-1) ...
526s Setting up r-cran-xfun (0.51+dfsg-1) ...
526s Setting up r-cran-sys (3.4.3-1) ...
526s Setting up r-cran-withr (3.0.2+dfsg-1) ...
526s Setting up r-cran-processx (3.8.6-1) ...
526s Setting up r-cran-mime (0.12-2) ...
526s Setting up r-cran-praise (1.0.0-4build1) ...
526s Setting up r-cran-base64enc (0.1-3-3) ...
526s Setting up r-cran-digest (0.6.37-1) ...
526s Setting up r-cran-yaml (2.3.10-1) ...
526s Setting up r-cran-evaluate (1.0.3-1) ...
526s Setting up r-cran-bigmemory (4.6.4-1ubuntu1) ...
526s Setting up r-cran-highr (0.11+dfsg-1) ...
526s Setting up r-cran-glue (1.8.0-1) ...
526s Setting up r-cran-xtable (1:1.8-4-2) ...
526s Setting up r-cran-cli (3.6.4-1) ...
526s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
526s Setting up r-cran-bitops (1.0-9-1) ...
526s Setting up r-cran-rprojroot (2.0.4-2) ...
526s Setting up gcc (4:14.2.0-1ubuntu1) ...
526s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
526s Setting up r-cran-askpass (1.2.1-1) ...
526s Setting up r-cran-fastmap (1.2.0-1) ...
526s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
526s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
526s Setting up r-cran-cpp11 (0.5.2-1) ...
526s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
526s Setting up r-cran-waldo (0.6.1-2) ...
526s Setting up r-cran-later (1.4.1+dfsg-1) ...
526s Setting up r-cran-matrix (1.7-3-1) ...
526s Setting up r-cran-htmltools (0.5.8.1-1) ...
526s Setting up r-cran-tinytex (0.56-1) ...
526s Setting up r-cran-knitr (1.49+dfsg-1) ...
526s Setting up g++ (4:14.2.0-1ubuntu1) ...
526s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
526s Setting up r-cran-cachem (1.1.0-1) ...
526s Setting up r-cran-sass (0.4.9+dfsg-1) ...
526s Setting up build-essential (12.10ubuntu1) ...
526s Setting up r-bioc-iranges (2.40.1-2) ...
526s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
526s Setting up r-cran-vctrs (0.6.5-1) ...
526s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
526s Setting up r-cran-callr (3.7.6-1) ...
526s Setting up r-cran-desc (1.4.3-1) ...
526s Setting up r-cran-fontawesome (0.5.3-1) ...
526s Setting up r-cran-igraph (2.1.4-1) ...
526s Setting up gfortran (4:14.2.0-1ubuntu1) ...
526s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
526s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
526s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
526s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
526s Setting up r-cran-jquerylib (0.1.4+dfsg-4) ...
526s Setting up r-cran-httr (1.4.7+dfsg-1) ...
526s Setting up r-cran-memoise (2.0.1-1) ...
526s Setting up r-cran-promises (1.3.2+dfsg-1) ...
526s Setting up r-bioc-xvector (0.46.0-2) ...
526s Setting up r-cran-pkgbuild (1.4.6-1) ...
526s Setting up r-cran-pkgload (1.4.0-1) ...
526s Setting up r-base-dev (4.4.3-1) ...
526s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
526s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
526s Setting up r-cran-testthat (3.2.3-1) ...
526s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
526s Setting up r-cran-bslib (0.8.0+dfsg-1) ...
526s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
526s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
526s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
526s Setting up r-cran-rmarkdown (2.29+dfsg-1) ...
526s Processing triggers for libc-bin (2.41-1ubuntu2) ...
526s Processing triggers for man-db (2.13.0-1) ...
528s Processing triggers for install-info (7.1.1-1) ...
534s autopkgtest [15:28:40]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
534s autopkgtest [15:28:40]: test pkg-r-autopkgtest: [-----------------------
534s Test: Try to load the R library bio3d
534s 
534s R version 4.4.3 (2025-02-28) -- "Trophy Case"
534s Copyright (C) 2025 The R Foundation for Statistical Computing
534s Platform: aarch64-unknown-linux-gnu
534s 
534s R is free software and comes with ABSOLUTELY NO WARRANTY.
534s You are welcome to redistribute it under certain conditions.
534s Type 'license()' or 'licence()' for distribution details.
534s 
534s R is a collaborative project with many contributors.
534s Type 'contributors()' for more information and
534s 'citation()' on how to cite R or R packages in publications.
534s 
534s Type 'demo()' for some demos, 'help()' for on-line help, or
534s 'help.start()' for an HTML browser interface to help.
534s Type 'q()' to quit R.
534s 
535s > library('bio3d')
535s > 
535s > 
535s Other tests are currently unsupported!
535s They will be progressively added.
535s autopkgtest [15:28:41]: test pkg-r-autopkgtest: -----------------------]
536s autopkgtest [15:28:42]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
536s pkg-r-autopkgtest    PASS
536s autopkgtest [15:28:42]: @@@@@@@@@@@@@@@@@@@@ summary
536s run-unit-test        PASS
536s pkg-r-autopkgtest    PASS
554s nova [W] Using flock in prodstack6-arm64
554s flock: timeout while waiting to get lock
554s Creating nova instance adt-plucky-arm64-r-cran-bio3d-20250315-151946-juju-7f2275-prod-proposed-migration-environment-2-680173fd-3a08-42ec-b907-af72aee0fbfa from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
554s nova [W] Timed out waiting for b1901442-962c-47e9-8c85-d93a53133f84 to get deleted.
554s nova [W] Using flock in prodstack6-arm64
554s flock: timeout while waiting to get lock
554s Creating nova instance adt-plucky-arm64-r-cran-bio3d-20250315-151946-juju-7f2275-prod-proposed-migration-environment-2-680173fd-3a08-42ec-b907-af72aee0fbfa from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)...
554s nova [W] Timed out waiting for 08245635-6b4e-4e74-aa41-cd1d1e27345b to get deleted.