0s autopkgtest [15:17:49]: starting date and time: 2025-03-15 15:17:49+0000 0s autopkgtest [15:17:49]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:17:49]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w66dfkkt/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-ape --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-arm64-6.secgroup --name adt-plucky-arm64-r-cran-ape-20250315-151748-juju-7f2275-prod-proposed-migration-environment-2-952f1de7-4955-4f09-9e71-e7d99de04405 --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/ 129s autopkgtest [15:19:58]: testbed dpkg architecture: arm64 129s autopkgtest [15:19:58]: testbed apt version: 2.9.33 130s autopkgtest [15:19:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 130s autopkgtest [15:19:59]: testbed release detected to be: None 131s autopkgtest [15:20:00]: updating testbed package index (apt update) 131s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 131s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 132s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 132s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 132s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 132s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 132s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 132s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 132s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 132s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 132s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 132s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 132s Fetched 1094 kB in 1s (1286 kB/s) 133s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 135s Calculating upgrade... 135s The following packages will be upgraded: 135s python3-jinja2 strace 135s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 608 kB of archives. 135s After this operation, 11.3 kB of additional disk space will be used. 135s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 136s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 136s Fetched 608 kB in 1s (1052 kB/s) 136s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 136s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 136s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 136s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 136s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 136s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 137s Setting up strace (6.13+ds-1ubuntu1) ... 137s Processing triggers for man-db (2.13.0-1) ... 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Solving dependencies... 138s The following packages will be REMOVED: 138s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 138s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 138s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 138s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 139s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 139s After this operation, 267 MB disk space will be freed. 139s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 139s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 139s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 139s Removing libpython3.12t64:arm64 (3.12.9-1) ... 139s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 139s Removing libnsl2:arm64 (1.3.0-3build3) ... 139s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 139s Removing libunwind8:arm64 (1.6.2-3.1) ... 139s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 139s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 141s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 141s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 141s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 141s /etc/kernel/postrm.d/initramfs-tools: 141s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 141s /etc/kernel/postrm.d/zz-flash-kernel: 141s flash-kernel: Kernel 6.11.0-8-generic has been removed. 141s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 141s /etc/kernel/postrm.d/zz-update-grub: 141s Sourcing file `/etc/default/grub' 141s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 141s Generating grub configuration file ... 142s Found linux image: /boot/vmlinuz-6.14.0-10-generic 142s Found initrd image: /boot/initrd.img-6.14.0-10-generic 142s Warning: os-prober will not be executed to detect other bootable partitions. 142s Systems on them will not be added to the GRUB boot configuration. 142s Check GRUB_DISABLE_OS_PROBER documentation entry. 142s Adding boot menu entry for UEFI Firmware Settings ... 142s done 142s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 142s Processing triggers for libc-bin (2.41-1ubuntu1) ... 143s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81650 files and directories currently installed.) 143s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 143s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 143s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 143s autopkgtest [15:20:12]: upgrading testbed (apt dist-upgrade and autopurge) 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 145s Entering ResolveByKeep 145s 146s Calculating upgrade... 146s The following packages will be upgraded: 146s libc-bin libc-dev-bin libc6 libc6-dev locales 146s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 9530 kB of archives. 146s After this operation, 0 B of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 148s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 148s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 150s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 150s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 153s Preconfiguring packages ... 153s Fetched 9530 kB in 7s (1364 kB/s) 154s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 154s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 154s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 154s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 154s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 154s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 154s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 154s Setting up libc6:arm64 (2.41-1ubuntu2) ... 154s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 154s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 154s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 154s Setting up libc-bin (2.41-1ubuntu2) ... 154s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 154s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 154s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 155s Setting up locales (2.41-1ubuntu2) ... 155s Generating locales (this might take a while)... 157s en_US.UTF-8... done 157s Generation complete. 157s Setting up libc-dev-bin (2.41-1ubuntu2) ... 157s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 157s Processing triggers for man-db (2.13.0-1) ... 158s Processing triggers for systemd (257.3-1ubuntu3) ... 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s Solving dependencies... 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [15:20:30]: rebooting testbed after setup commands that affected boot 165s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 188s autopkgtest [15:20:57]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 191s autopkgtest [15:21:00]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 195s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 195s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 195s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 195s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 195s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 195s gpgv: issuer "plessy@debian.org" 195s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 195s autopkgtest [15:21:04]: testing package r-cran-ape version 5.8-1-1 197s autopkgtest [15:21:06]: build not needed 200s autopkgtest [15:21:09]: test run-unit-test: preparing testbed 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 202s The following NEW packages will be installed: 202s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 202s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 202s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 202s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 202s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 202s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 202s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 202s libxss1 libxt6t64 littler r-base-core r-cran-ape r-cran-cli r-cran-cpp11 202s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 202s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 202s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 202s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 202s xdg-utils zip 202s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 202s Need to get 63.9 MB of archives. 202s After this operation, 129 MB of additional disk space will be used. 202s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 203s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 204s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 204s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 204s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB] 204s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB] 204s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 204s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 204s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 204s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 204s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 204s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 205s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB] 205s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 205s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 205s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 205s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB] 205s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 205s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 205s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 206s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 206s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 206s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 206s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 206s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 207s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 208s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 208s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 208s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 208s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 208s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 208s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 208s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 208s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 208s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 208s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 209s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 209s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 209s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 209s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 209s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 209s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 210s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 210s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 210s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 210s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 210s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 220s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB] 220s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 littler all 0.3.20-2 [2554 B] 220s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 220s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 220s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 221s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB] 221s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB] 221s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-ape arm64 5.8-1-1 [2901 kB] 221s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 221s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 221s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-fastmatch arm64 1.1-6-1 [36.0 kB] 221s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 221s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 221s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB] 221s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 221s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 221s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 221s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 221s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 221s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-igraph arm64 2.1.4-1 [5150 kB] 222s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB] 222s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-phangorn arm64 2.12.1+dfsg-1 [1803 kB] 222s Preconfiguring packages ... 222s Fetched 63.9 MB in 20s (3192 kB/s) 222s Selecting previously unselected package fonts-dejavu-mono. 222s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 81647 files and directories currently installed.) 222s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 222s Unpacking fonts-dejavu-mono (2.37-8) ... 222s Selecting previously unselected package fonts-dejavu-core. 222s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 222s Unpacking fonts-dejavu-core (2.37-8) ... 222s Selecting previously unselected package fontconfig-config. 222s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 223s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 223s Selecting previously unselected package libfontconfig1:arm64. 223s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 223s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 223s Selecting previously unselected package fontconfig. 223s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 223s Unpacking fontconfig (2.15.0-2ubuntu1) ... 223s Selecting previously unselected package libgomp1:arm64. 223s Preparing to unpack .../05-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 223s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 223s Selecting previously unselected package libsuitesparseconfig7:arm64. 223s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_arm64.deb ... 223s Unpacking libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ... 223s Selecting previously unselected package libamd3:arm64. 223s Preparing to unpack .../07-libamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 223s Unpacking libamd3:arm64 (1:7.8.3+dfsg-3) ... 223s Selecting previously unselected package libblas3:arm64. 223s Preparing to unpack .../08-libblas3_3.12.1-2_arm64.deb ... 223s Unpacking libblas3:arm64 (3.12.1-2) ... 223s Selecting previously unselected package libpixman-1-0:arm64. 223s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_arm64.deb ... 223s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 223s Selecting previously unselected package libxcb-render0:arm64. 223s Preparing to unpack .../10-libxcb-render0_1.17.0-2_arm64.deb ... 223s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 223s Selecting previously unselected package libxcb-shm0:arm64. 223s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_arm64.deb ... 223s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 223s Selecting previously unselected package libxrender1:arm64. 223s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 223s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 223s Selecting previously unselected package libcairo2:arm64. 223s Preparing to unpack .../13-libcairo2_1.18.2-2_arm64.deb ... 223s Unpacking libcairo2:arm64 (1.18.2-2) ... 223s Selecting previously unselected package libcolamd3:arm64. 223s Preparing to unpack .../14-libcolamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 223s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 223s Selecting previously unselected package libdatrie1:arm64. 223s Preparing to unpack .../15-libdatrie1_0.2.13-3build1_arm64.deb ... 223s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 223s Selecting previously unselected package libdeflate0:arm64. 223s Preparing to unpack .../16-libdeflate0_1.23-1_arm64.deb ... 223s Unpacking libdeflate0:arm64 (1.23-1) ... 223s Selecting previously unselected package libgfortran5:arm64. 223s Preparing to unpack .../17-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 223s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 223s Selecting previously unselected package libltdl7:arm64. 223s Preparing to unpack .../18-libltdl7_2.5.4-4_arm64.deb ... 223s Unpacking libltdl7:arm64 (2.5.4-4) ... 223s Selecting previously unselected package libglpk40:arm64. 223s Preparing to unpack .../19-libglpk40_5.0-1build2_arm64.deb ... 223s Unpacking libglpk40:arm64 (5.0-1build2) ... 223s Selecting previously unselected package libgraphite2-3:arm64. 223s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 223s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 223s Selecting previously unselected package libharfbuzz0b:arm64. 223s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_arm64.deb ... 223s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 223s Selecting previously unselected package x11-common. 223s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu3_all.deb ... 223s Unpacking x11-common (1:7.7+23ubuntu3) ... 223s Selecting previously unselected package libice6:arm64. 223s Preparing to unpack .../23-libice6_2%3a1.1.1-1_arm64.deb ... 223s Unpacking libice6:arm64 (2:1.1.1-1) ... 223s Selecting previously unselected package libjpeg-turbo8:arm64. 223s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 223s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 223s Selecting previously unselected package libjpeg8:arm64. 223s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 224s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 224s Selecting previously unselected package liblapack3:arm64. 224s Preparing to unpack .../26-liblapack3_3.12.1-2_arm64.deb ... 224s Unpacking liblapack3:arm64 (3.12.1-2) ... 224s Selecting previously unselected package liblerc4:arm64. 224s Preparing to unpack .../27-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 224s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 224s Selecting previously unselected package libthai-data. 224s Preparing to unpack .../28-libthai-data_0.1.29-2build1_all.deb ... 224s Unpacking libthai-data (0.1.29-2build1) ... 224s Selecting previously unselected package libthai0:arm64. 224s Preparing to unpack .../29-libthai0_0.1.29-2build1_arm64.deb ... 224s Unpacking libthai0:arm64 (0.1.29-2build1) ... 224s Selecting previously unselected package libpango-1.0-0:arm64. 224s Preparing to unpack .../30-libpango-1.0-0_1.56.2-1_arm64.deb ... 224s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 224s Selecting previously unselected package libpangoft2-1.0-0:arm64. 224s Preparing to unpack .../31-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 224s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 224s Selecting previously unselected package libpangocairo-1.0-0:arm64. 224s Preparing to unpack .../32-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 224s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 224s Selecting previously unselected package libpaper2:arm64. 224s Preparing to unpack .../33-libpaper2_2.2.5-0.3_arm64.deb ... 224s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 224s Selecting previously unselected package libpaper-utils. 224s Preparing to unpack .../34-libpaper-utils_2.2.5-0.3_arm64.deb ... 224s Unpacking libpaper-utils (2.2.5-0.3) ... 224s Selecting previously unselected package libsharpyuv0:arm64. 224s Preparing to unpack .../35-libsharpyuv0_1.5.0-0.1_arm64.deb ... 224s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 224s Selecting previously unselected package libsm6:arm64. 224s Preparing to unpack .../36-libsm6_2%3a1.2.4-1_arm64.deb ... 224s Unpacking libsm6:arm64 (2:1.2.4-1) ... 224s Selecting previously unselected package libtcl8.6:arm64. 224s Preparing to unpack .../37-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 224s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 224s Selecting previously unselected package libjbig0:arm64. 224s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 224s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 224s Selecting previously unselected package libwebp7:arm64. 224s Preparing to unpack .../39-libwebp7_1.5.0-0.1_arm64.deb ... 224s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 224s Selecting previously unselected package libtiff6:arm64. 224s Preparing to unpack .../40-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 224s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 224s Selecting previously unselected package libxft2:arm64. 224s Preparing to unpack .../41-libxft2_2.3.6-1build1_arm64.deb ... 224s Unpacking libxft2:arm64 (2.3.6-1build1) ... 224s Selecting previously unselected package libxss1:arm64. 224s Preparing to unpack .../42-libxss1_1%3a1.2.3-1build3_arm64.deb ... 224s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 224s Selecting previously unselected package libtk8.6:arm64. 224s Preparing to unpack .../43-libtk8.6_8.6.16-1_arm64.deb ... 224s Unpacking libtk8.6:arm64 (8.6.16-1) ... 224s Selecting previously unselected package libxt6t64:arm64. 224s Preparing to unpack .../44-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 224s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 224s Selecting previously unselected package zip. 224s Preparing to unpack .../45-zip_3.0-14ubuntu2_arm64.deb ... 224s Unpacking zip (3.0-14ubuntu2) ... 224s Selecting previously unselected package unzip. 224s Preparing to unpack .../46-unzip_6.0-28ubuntu6_arm64.deb ... 224s Unpacking unzip (6.0-28ubuntu6) ... 224s Selecting previously unselected package xdg-utils. 224s Preparing to unpack .../47-xdg-utils_1.2.1-2ubuntu1_all.deb ... 224s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 224s Selecting previously unselected package r-base-core. 224s Preparing to unpack .../48-r-base-core_4.4.3-1_arm64.deb ... 224s Unpacking r-base-core (4.4.3-1) ... 225s Selecting previously unselected package r-cran-littler. 225s Preparing to unpack .../49-r-cran-littler_0.3.20-2_arm64.deb ... 225s Unpacking r-cran-littler (0.3.20-2) ... 225s Selecting previously unselected package littler. 225s Preparing to unpack .../50-littler_0.3.20-2_all.deb ... 225s Unpacking littler (0.3.20-2) ... 225s Selecting previously unselected package r-cran-lattice. 225s Preparing to unpack .../51-r-cran-lattice_0.22-6-1_arm64.deb ... 225s Unpacking r-cran-lattice (0.22-6-1) ... 225s Selecting previously unselected package r-cran-nlme. 225s Preparing to unpack .../52-r-cran-nlme_3.1.167-1_arm64.deb ... 225s Unpacking r-cran-nlme (3.1.167-1) ... 225s Selecting previously unselected package r-cran-pkgkitten. 225s Preparing to unpack .../53-r-cran-pkgkitten_0.2.4-1_all.deb ... 225s Unpacking r-cran-pkgkitten (0.2.4-1) ... 225s Selecting previously unselected package r-cran-rcpp. 225s Preparing to unpack .../54-r-cran-rcpp_1.0.14-1_arm64.deb ... 225s Unpacking r-cran-rcpp (1.0.14-1) ... 225s Selecting previously unselected package r-cran-digest. 225s Preparing to unpack .../55-r-cran-digest_0.6.37-1_arm64.deb ... 225s Unpacking r-cran-digest (0.6.37-1) ... 225s Selecting previously unselected package r-cran-ape. 225s Preparing to unpack .../56-r-cran-ape_5.8-1-1_arm64.deb ... 225s Unpacking r-cran-ape (5.8-1-1) ... 225s Selecting previously unselected package r-cran-cli. 225s Preparing to unpack .../57-r-cran-cli_3.6.4-1_arm64.deb ... 225s Unpacking r-cran-cli (3.6.4-1) ... 225s Selecting previously unselected package r-cran-cpp11. 225s Preparing to unpack .../58-r-cran-cpp11_0.5.2-1_all.deb ... 225s Unpacking r-cran-cpp11 (0.5.2-1) ... 225s Selecting previously unselected package r-cran-fastmatch. 225s Preparing to unpack .../59-r-cran-fastmatch_1.1-6-1_arm64.deb ... 225s Unpacking r-cran-fastmatch (1.1-6-1) ... 225s Selecting previously unselected package r-cran-generics. 225s Preparing to unpack .../60-r-cran-generics_0.1.3-1_all.deb ... 225s Unpacking r-cran-generics (0.1.3-1) ... 225s Selecting previously unselected package r-cran-glue. 225s Preparing to unpack .../61-r-cran-glue_1.8.0-1_arm64.deb ... 225s Unpacking r-cran-glue (1.8.0-1) ... 226s Selecting previously unselected package r-cran-rlang. 226s Preparing to unpack .../62-r-cran-rlang_1.1.5-1_arm64.deb ... 226s Unpacking r-cran-rlang (1.1.5-1) ... 226s Selecting previously unselected package r-cran-lifecycle. 226s Preparing to unpack .../63-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 226s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 226s Selecting previously unselected package r-cran-magrittr. 226s Preparing to unpack .../64-r-cran-magrittr_2.0.3-1_arm64.deb ... 226s Unpacking r-cran-magrittr (2.0.3-1) ... 226s Selecting previously unselected package r-cran-matrix. 226s Preparing to unpack .../65-r-cran-matrix_1.7-3-1_arm64.deb ... 226s Unpacking r-cran-matrix (1.7-3-1) ... 226s Selecting previously unselected package r-cran-pkgconfig. 226s Preparing to unpack .../66-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 226s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 226s Selecting previously unselected package r-cran-vctrs. 226s Preparing to unpack .../67-r-cran-vctrs_0.6.5-1_arm64.deb ... 226s Unpacking r-cran-vctrs (0.6.5-1) ... 226s Selecting previously unselected package r-cran-igraph. 226s Preparing to unpack .../68-r-cran-igraph_2.1.4-1_arm64.deb ... 226s Unpacking r-cran-igraph (2.1.4-1) ... 226s Selecting previously unselected package r-cran-quadprog. 226s Preparing to unpack .../69-r-cran-quadprog_1.5-8-1build1_arm64.deb ... 226s Unpacking r-cran-quadprog (1.5-8-1build1) ... 226s Selecting previously unselected package r-cran-phangorn. 226s Preparing to unpack .../70-r-cran-phangorn_2.12.1+dfsg-1_arm64.deb ... 226s Unpacking r-cran-phangorn (2.12.1+dfsg-1) ... 226s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 226s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 226s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 226s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 226s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 226s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 226s Setting up libxcb-render0:arm64 (1.17.0-2) ... 226s Setting up unzip (6.0-28ubuntu6) ... 226s Setting up x11-common (1:7.7+23ubuntu3) ... 226s Setting up libdeflate0:arm64 (1.23-1) ... 226s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 226s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 226s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 226s Setting up zip (3.0-14ubuntu2) ... 226s Setting up libblas3:arm64 (3.12.1-2) ... 226s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 226s Setting up fonts-dejavu-mono (2.37-8) ... 226s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 226s Setting up fonts-dejavu-core (2.37-8) ... 226s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 226s Setting up libltdl7:arm64 (2.5.4-4) ... 226s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 226s Setting up libwebp7:arm64 (1.5.0-0.1) ... 226s Setting up libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ... 226s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 226s Setting up libthai-data (0.1.29-2build1) ... 226s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 226s Setting up libpaper2:arm64 (2.2.5-0.3) ... 226s Setting up xdg-utils (1.2.1-2ubuntu1) ... 226s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 226s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 226s Setting up libice6:arm64 (2:1.1.1-1) ... 226s Setting up liblapack3:arm64 (3.12.1-2) ... 226s 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 226s Setting up libamd3:arm64 (1:7.8.3+dfsg-3) ... 226s Setting up libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 226s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 227s Setting up libpaper-utils (2.2.5-0.3) ... 227s Setting up libthai0:arm64 (0.1.29-2build1) ... 227s Setting up libglpk40:arm64 (5.0-1build2) ... 227s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 227s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 227s Setting up libsm6:arm64 (2:1.2.4-1) ... 227s Setting up fontconfig (2.15.0-2ubuntu1) ... 229s Regenerating fonts cache... done. 229s Setting up libxft2:arm64 (2.3.6-1build1) ... 229s Setting up libtk8.6:arm64 (8.6.16-1) ... 229s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 229s Setting up libcairo2:arm64 (1.18.2-2) ... 229s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 229s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 229s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 229s Setting up r-base-core (4.4.3-1) ... 229s Creating config file /etc/R/Renviron with new version 229s Setting up r-cran-fastmatch (1.1-6-1) ... 229s Setting up r-cran-lattice (0.22-6-1) ... 229s Setting up r-cran-nlme (3.1.167-1) ... 229s Setting up r-cran-pkgkitten (0.2.4-1) ... 229s Setting up r-cran-magrittr (2.0.3-1) ... 229s Setting up r-cran-quadprog (1.5-8-1build1) ... 229s Setting up r-cran-littler (0.3.20-2) ... 229s Setting up r-cran-rcpp (1.0.14-1) ... 229s Setting up r-cran-rlang (1.1.5-1) ... 229s Setting up littler (0.3.20-2) ... 229s Setting up r-cran-generics (0.1.3-1) ... 229s Setting up r-cran-digest (0.6.37-1) ... 229s Setting up r-cran-ape (5.8-1-1) ... 229s Setting up r-cran-glue (1.8.0-1) ... 229s Setting up r-cran-cli (3.6.4-1) ... 229s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 229s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 229s Setting up r-cran-cpp11 (0.5.2-1) ... 229s Setting up r-cran-matrix (1.7-3-1) ... 229s Setting up r-cran-vctrs (0.6.5-1) ... 229s Setting up r-cran-igraph (2.1.4-1) ... 229s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 229s Processing triggers for libc-bin (2.41-1ubuntu2) ... 229s Processing triggers for man-db (2.13.0-1) ... 230s Processing triggers for install-info (7.1.1-1) ... 232s autopkgtest [15:21:41]: test run-unit-test: [----------------------- 232s 232s R version 4.4.3 (2025-02-28) -- "Trophy Case" 232s Copyright (C) 2025 The R Foundation for Statistical Computing 232s Platform: aarch64-unknown-linux-gnu 232s 232s R is free software and comes with ABSOLUTELY NO WARRANTY. 232s You are welcome to redistribute it under certain conditions. 232s Type 'license()' or 'licence()' for distribution details. 232s 232s R is a collaborative project with many contributors. 232s Type 'contributors()' for more information and 232s 'citation()' on how to cite R or R packages in publications. 232s 232s Type 'demo()' for some demos, 'help()' for on-line help, or 232s 'help.start()' for an HTML browser interface to help. 232s Type 'q()' to quit R. 232s 232s > Stangle("DrawingPhylogenies.Rnw") 232s Writing to file DrawingPhylogenies.R 232s > source("DrawingPhylogenies.R", echo=TRUE) 232s 232s > options(width = 80, prompt = "> ") 232s 232s > library(ape) 232s 232s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 232s 232s > foo <- function() { 232s + col <- "green" 232s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 232s + las = 1) 232s + box(lty .... [TRUNCATED] 232s 232s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 232s 232s > plot(mytr) 232s 232s > foo() 233s 233s > plot(mytr, "c", FALSE) 233s 233s > foo() 233s 233s > plot(mytr, "u") 233s 233s > foo() 233s 233s > par(xpd = TRUE) 233s 233s > plot(mytr, "f") 233s 233s > foo() 233s 233s > box("outer") 233s 233s > tr <- compute.brlen(stree(8, "l"), 0.1) 233s 233s > tr$tip.label[] <- "" 233s 233s > foo <- function() { 233s + col <- "green" 233s + axis(1, col = col, col.ticks = col, col.axis = col) 233s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 233s 233s > layout(matrix(1:12, 6, 2)) 233s 233s > par(mar = c(2, 2, 0.3, 0)) 233s 233s > for (type in c("p", "c")) { 233s + plot(tr, type) 233s + foo() 233s + plot(tr, type, node.pos = 2) 233s + foo() 233s + plot(tr, type, FALSE) 233s + foo() 233s .... [TRUNCATED] 233s 233s > foo <- function() { 233s + col <- "green" 233s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 233s + las = 1) 233s + box(lty .... [TRUNCATED] 233s 233s > layout(matrix(1:4, 2, 2)) 233s 233s > par(las = 1) 233s 233s > plot(tr, "u") 233s 233s > foo() 233s 233s > plot(tr, "u", FALSE) 233s 233s > foo() 233s 233s > plot(tr, "f") 233s 233s > foo() 233s 233s > plot(tr, "f", FALSE) 233s 233s > foo() 233s 233s > args(node.depth.edgelength) 233s function (phy) 233s NULL 233s 233s > args(node.depth) 233s function (phy, method = 1) 233s NULL 233s 233s > args(node.height) 233s function (phy, clado.style = FALSE) 233s NULL 233s 233s > args(unrooted.xy) 233s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 233s NULL 233s 233s > args(phylogram.plot) 233s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 233s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 233s node.lty = NULL) 233s NULL 233s 233s > args(cladogram.plot) 233s function (edge, xx, yy, edge.color, edge.width, edge.lty) 233s NULL 233s 233s > args(circular.plot) 233s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 233s edge.lty) 233s NULL 233s 233s > args(plot.phylo) 233s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 233s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 233s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 233s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 233s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 233s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 233s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 233s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 233s ...) 233s NULL 233s 233s > geo <- factor(c("Africa", "World", "Africa")) 233s 233s > (mycol <- c("blue", "red")[geo]) 233s [1] "blue" "red" "blue" 233s 233s > plot(mytr, tip.color = mycol) 233s 233s > par(xpd = TRUE) 233s 233s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 233s 233s > args(def) 233s function (x, ..., default = NULL, regexp = FALSE) 233s NULL 233s 233s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 233s 233s > identical(mycol, mycol2) 233s [1] TRUE 233s 233s > (i <- which.edge(mytr, c("Homo", "Pan"))) 233s [1] 2 3 233s 233s > co <- rep("black", Nedge(mytr)) 233s 233s > co[i] <- "blue" 233s 233s > par(xpd = TRUE) 233s 233s > plot(mytr, edge.col = co) 233s 233s > edgelabels() 233s 233s > args(axisPhylo) 233s function (side = NULL, root.time = NULL, backward = TRUE, ...) 233s NULL 233s 233s > args(add.scale.bar) 233s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 233s ...) 233s NULL 233s 233s > plot(mytr) 233s 233s > add.scale.bar() 233s 233s > axisPhylo() 233s 233s > axis(3) 233s 233s > args(nodelabels) 233s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 233s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 233s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 233s ...) 233s NULL 233s 233s > args(tiplabels) 233s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 233s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 233s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 233s offset = 0, ...) 233s NULL 233s 233s > args(edgelabels) 233s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 233s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 233s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 233s date = NULL, ...) 233s NULL 233s 233s > par(xpd = TRUE) 233s 233s > plot(mytr) 233s 233s > nodelabels() 233s 233s > tiplabels() 233s 233s > edgelabels() 233s 233s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 233s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 233s 233s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 233s 233s > v <- c(0, 0.5, 1) 233s 233s > layout(matrix(1:9, 3, 3)) 233s 233s > par(mar = c(3, 3, 3, 0), las = 1) 233s 233s > for (i in v) { 233s + for (j in v) { 233s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 233s + ")")) 233s + abline(v = 0, h = .... [TRUNCATED] 233s 233s > plot(rep(0, 3), 0:2, "n", las = 1) 233s 233s > abline(v = 0, h = 0:2, lty = 3) 233s 233s > text(0, 0:2, mytr$tip.label, adj = -1) 233s 233s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 233s 233s > args(phydataplot) 233s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 233s width = NULL, legend = "below", funcol = rainbow, ...) 233s NULL 233s 233s > args(ring) 233s function (x, phy, style = "ring", offset = 1, ...) 233s NULL 233s 233s > x <- matrix(1:6, 3, 10) 233s 233s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 233s 233s > x 233s A B C D E F G H I J 233s Homo 1 4 1 4 1 4 1 4 1 4 233s Gorilla 2 5 2 5 2 5 2 5 2 5 233s Pan 3 6 3 6 3 6 3 6 3 6 233s 233s > mytr$tip.label 233s [1] "Pan" "Homo" "Gorilla" 233s 233s > par(mar = c(10, 2, 5, 5)) 233s 233s > plot(mytr, x.lim = 30) 233s 233s > phydataplot(x, mytr, "m", border = "white", offset = 2, 233s + width = 1) 233s 233s > phydataplot(x, mytr, "m", border = "white", offset = 15, 233s + width = 1, continuous = 2) 233s 233s > n <- 100 233s 233s > p <- 3 233s 233s > set.seed(3) 233s 233s > tr <- rcoal(n) 233s 233s > x <- matrix(runif(p * n), n, p) 233s 233s > rownames(x) <- tr$tip.label 233s 233s > COL <- c("red", "green", "blue") 233s 233s > par(xpd = TRUE) 233s 233s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 233s + no.margin = TRUE) 233s 233s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 233s + col = COL[j]) 233s 233s > tree <- rtree(10) 233s 233s > tree$edge.length[1] <- 1000 233s 233s > layout(matrix(1:2, 1)) 233s 233s > plot(tree) 233s 233s > axisPhylo() 233s 233s > plotBreakLongEdges(tree) 233s 233s > axisPhylo() 233s 233s > el <- tree$edge.length 233s 233s > sum(el > mean(el) + 2 * sd(el)) 233s [1] 1 233s 233s > tree$edge.length[8] <- 1000 233s 233s > el <- tree$edge.length 233s 233s > sum(el > mean(el) + 2 * sd(el)) 233s [1] 2 233s 233s > layout(matrix(1:2, 1)) 233s 233s > plotBreakLongEdges(tree) 233s 233s > plotBreakLongEdges(tree, n = 2) 233s 233s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 233s + simplify = FALSE) 233s 233s > kronoviz(TR, type = "c", show.tip.label = FALSE) 233s 233s > dates <- as.Date(.leap.seconds) 233s 233s > tr <- rcoal(length(dates)) 233s 233s > plotTreeTime(tr, dates) 233s 233s > par(oma = rep(2, 4)) 233s 233s > plot(mytr) 233s 233s > box(lty = 3) 233s 233s > box("figure", col = "blue") 233s 233s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 233s + font = 2, col = "blue") 233s 233s > box("outer") 233s 233s > layout(matrix(1:4, 2, 2)) 233s 233s > par(oma = rep(2, 4)) 233s 233s > for (i in 1:4) { 233s + par(mar = rep(i, 4)) 233s + plot(mytr) 233s + box(lty = 3) 233s + box("figure", col = "blue") 233s + } 233s 233s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 233s + font = 2, col = "blue") 233s 233s > box("outer") 233s 233s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 233s 233s > for (i in 1:3) plot(rtree(5)) 233s 233s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 233s $type 233s [1] "phylogram" 233s 233s $use.edge.length 233s [1] TRUE 233s 233s $node.pos 233s [1] 1 233s 233s $node.depth 233s [1] 1 233s 233s $show.tip.label 233s [1] TRUE 233s 233s $show.node.label 233s [1] FALSE 233s 233s $font 233s [1] 3 233s 233s $cex 233s [1] 0.83 233s 233s $adj 233s [1] 0 233s 233s $srt 233s [1] 0 233s 233s $no.margin 233s [1] FALSE 233s 233s $label.offset 233s [1] 0 233s 233s $x.lim 233s [1] 0.00000 3.13046 233s 233s $y.lim 233s [1] 1 5 233s 233s $direction 233s [1] "rightwards" 233s 233s $tip.color 233s [1] "black" 233s 233s $Ntip 233s [1] 5 233s 233s $Nnode 233s [1] 4 233s 233s $root.time 233s NULL 233s 233s $align.tip.label 233s [1] FALSE 233s 233s $edge 233s [,1] [,2] 233s [1,] 6 1 233s [2,] 6 7 233s [3,] 7 2 233s [4,] 7 8 233s [5,] 8 3 233s [6,] 8 9 233s [7,] 9 4 233s [8,] 9 5 233s 233s $xx 233s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 233s [8] 1.3631198 1.9857132 233s 233s $yy 233s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 233s 233s 233s > layout(matrix(1:2, 2)) 233s 233s > plot(rtree(4)) 233s 233s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 233s 233s > x <- pp$xx[1] 233s 233s > y <- pp$yy[1] 233s 233s > (pu <- par("usr")) 233s [1] -0.06364557 1.65478492 0.88000000 4.12000000 233s 233s > (x - pu[1])/(pu[2] - pu[1]) 233s [1] 0.9349839 233s 233s > (y - pu[3])/(pu[4] - pu[3]) 233s [1] 0.03703704 233s 233s > pi <- par("pin") 233s 233s > mi <- par("mai") 233s 233s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 233s 233s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 233s 233s > plot(rtree(4)) 233s 233s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 233s 233s > x <- pp$xx[5] 233s 233s > y <- pp$yy[5] 233s 233s > pu <- par("usr") 233s 233s > pi <- par("pin") 233s 233s > mi <- par("mai") 233s 233s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 233s 233s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 233s 233s > yi1 <- yi1 + par("fin")[2] 233s 233s > di <- par("din") 233s 233s > layout(1) 233s 233s > par(new = TRUE, mai = rep(0, 4)) 233s 233s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 233s + ylim = 0:1, xaxs = "i", yaxs = "i") 233s 233s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 233s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 233s 233s > foo <- function(phy1, phy2, from) { 233s + layout(matrix(1:2, 2)) 233s + plot(phy1, font = 1) 233s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 233s 233s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 233s 233s > par(xpd = TRUE) 233s 233s > foo(trb, mytr, "Primates") 233s 233s > plot(mytr, plot = FALSE) 233s 233s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 233s 233s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 233s + pp$yy[2] + 0.1, col = "yellow", border = NA) 233s 233s > par(new = TRUE) 233s 233s > plot(mytr) 233s > 233s 233s R version 4.4.3 (2025-02-28) -- "Trophy Case" 233s Copyright (C) 2025 The R Foundation for Statistical Computing 233s Platform: aarch64-unknown-linux-gnu 233s 233s R is free software and comes with ABSOLUTELY NO WARRANTY. 233s You are welcome to redistribute it under certain conditions. 233s Type 'license()' or 'licence()' for distribution details. 233s 233s R is a collaborative project with many contributors. 233s Type 'contributors()' for more information and 233s 'citation()' on how to cite R or R packages in publications. 233s 233s Type 'demo()' for some demos, 'help()' for on-line help, or 233s 'help.start()' for an HTML browser interface to help. 233s Type 'q()' to quit R. 233s 233s > Stangle("MoranI.Rnw") 233s Writing to file MoranI.R 233s > source("MoranI.R", echo=TRUE) 233s 233s > options(width = 80, prompt = "> ") 233s 233s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 233s 233s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 233s 233s > names(body) <- names(longevity) <- c("Homo", "Pongo", 233s + "Macaca", "Ateles", "Galago") 233s 233s > library(ape) 233s 233s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 233s 233s > trnwk[2] <- ":0.38,Galago:1.00);" 233s 233s > tr <- read.tree(text = trnwk) 233s 233s > plot(tr) 233s 233s > axisPhylo() 233s 233s > w <- 1/cophenetic(tr) 233s 233s > w 233s Homo Pongo Macaca Ateles Galago 233s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 233s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 233s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 233s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 233s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 233s 233s > diag(w) <- 0 233s 233s > Moran.I(body, w) 233s $observed 233s [1] -0.07312179 233s 233s $expected 233s [1] -0.25 233s 233s $sd 233s [1] 0.08910814 233s 233s $p.value 233s [1] 0.04714628 233s 233s 233s > Moran.I(body, w, alt = "greater") 233s $observed 233s [1] -0.07312179 233s 233s $expected 233s [1] -0.25 233s 233s $sd 233s [1] 0.08910814 233s 233s $p.value 233s [1] 0.02357314 233s 233s 233s > Moran.I(longevity, w) 233s $observed 233s [1] -0.1837739 233s 233s $expected 233s [1] -0.25 233s 233s $sd 233s [1] 0.09114549 233s 233s $p.value 233s [1] 0.4674727 233s 233s 233s > data(carnivora) 233s 233s > carnivora$log10SW <- log10(carnivora$SW) 233s 233s > carnivora$log10FW <- log10(carnivora$FW) 233s 233s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 233s 233s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 233s 233s > plot(co1) 233s 233s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 233s 233s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 233s 233s > print(plot(co2)) 234s 234s > plot(co2, FALSE) 234s > 234s 234s R version 4.4.3 (2025-02-28) -- "Trophy Case" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: aarch64-unknown-linux-gnu 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s > Stangle("RandomTopologies.Rnw") 234s Writing to file RandomTopologies.R 234s > source("RandomTopologies.R", echo=TRUE) 234s 234s > options(width = 80, prompt = "> ") 234s 234s > library(ape) 234s 234s > n <- 1:10 234s 234s > data.frame(N.topo = sapply(n, howmanytrees)) 234s N.topo 234s 1 1 234s 2 1 234s 3 3 234s 4 15 234s 5 105 234s 6 945 234s 7 10395 234s 8 135135 234s 9 2027025 234s 10 34459425 234s 234s > howmanytrees(25) 234s [1] 1.192568e+30 234s 234s > howmanytrees(25) * 0.21 234s [1] 2.504393e+29 234s 234s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 234s N.topo 234s 1 1 234s 2 1 234s 3 1 234s 4 2 234s 5 3 234s 6 6 234s 7 11 234s 8 23 234s 9 46 234s 10 98 234s 234s > n2 <- c(50, 100, 200) 234s 234s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 234s + row.names = n2) 234s N.topo 234s 50 5.150149e+16 234s 100 1.019560e+36 234s 200 1.141703e+75 234s 234s > 1/howmanytrees(50) 234s [1] 3.632505e-77 234s 234s > 1/sapply(n, howmanytrees) 234s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 234s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 234s 234s > 1/sapply(n, howmanytrees, labeled = FALSE) 234s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 234s [7] 0.09090909 0.04347826 0.02173913 0.01020408 234s 234s > library(phangorn) 235s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 235s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 235s 235s > TR <- allTrees(4, rooted = TRUE) 235s 235s > TR 235s 15 phylogenetic trees 235s 235s > layout(matrix(1:15, 3, 5)) 235s 235s > par(mar = rep(1.5, 4), xpd = TRUE) 235s 235s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 235s 235s > K <- 100 235s 235s > n <- 50 235s 235s > N <- howmanytrees(n, labeled = FALSE) 235s 235s > p <- 1/N 235s 235s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 235s [1] 0 235s 235s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 235s [1] -5.431212e-17 235s 235s > f <- function(n, K) { 235s + N <- howmanytrees(n, labeled = FALSE) 235s + p <- 1/N 235s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 235s + } 235s 235s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 235s + 10000)) 235s 235s > DF$P <- mapply(f, n = DF$n, K = DF$K) 235s 235s > library(lattice) 235s 235s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 235s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 235s 235s > subset(DF, n == 20) 235s n K P 235s 17 20 2 1.160494e-11 235s 34 20 5 1.160491e-10 235s 51 20 10 5.222149e-10 235s 68 20 100 5.743191e-08 235s 85 20 1000 5.783570e-06 235s 102 20 10000 5.671842e-04 235s 235s > f(20, 1e+05) 235s [1] 0.04638755 235s 235s > f(30, 1e+06) 235s [1] 2.525152e-07 235s 235s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 235s 235s > TR5 <- read.tree(text = txt) 235s 235s > layout(matrix(1:3, 1)) 235s 235s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 235s 235s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 235s + labeled = FALSE) 235s [1] 2 235s 235s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 235s + labeled = FALSE) 235s [1] 1 235s 235s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 235s + labeled = FALSE) 235s [1] Inf 235s 235s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 235s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 236s 236s > foo.test <- function(x, labeled = TRUE) { 236s + uTR <- unique(x, use.tip.label = labeled) 236s + f <- integer(length(uTR)) 236s + for (j in seq_along( .... [TRUNCATED] 236s 236s > lapply(TR, foo.test) 239s [1] 60 70 77 57 66 64 80 73 66 74 68 59 63 61 62 242s [1] 56 120 46 53 54 111 65 96 48 48 61 52 63 71 56 244s [1] 153 175 42 165 41 48 47 31 58 42 43 37 41 43 34 244s [[1]] 244s 244s Chi-squared test for given probabilities 244s 244s data: f 244s X-squared = 9.95, df = 14, p-value = 0.7658 244s 244s 244s [[2]] 244s 244s Chi-squared test for given probabilities 244s 244s data: f 244s X-squared = 114.77, df = 14, p-value < 2.2e-16 244s 244s 244s [[3]] 244s 244s Chi-squared test for given probabilities 244s 244s data: f 244s X-squared = 548.15, df = 14, p-value < 2.2e-16 244s 244s 244s 244s > lapply(TR, foo.test, labeled = FALSE) 245s [1] 788 212 245s [1] 673 327 246s [1] 493 507 246s [[1]] 246s 246s Chi-squared test for given probabilities 246s 246s data: f 246s X-squared = 331.78, df = 1, p-value < 2.2e-16 246s 246s 246s [[2]] 246s 246s Chi-squared test for given probabilities 246s 246s data: f 246s X-squared = 119.72, df = 1, p-value < 2.2e-16 246s 246s 246s [[3]] 246s 246s Chi-squared test for given probabilities 246s 246s data: f 246s X-squared = 0.196, df = 1, p-value = 0.658 246s 246s 246s 246s > .Machine$double.xmax 246s [1] 1.797693e+308 246s 246s > howmanytrees(151) 246s [1] 3.753274e+306 246s 246s > howmanytrees(792, labeled = FALSE) 246s [1] 1.029038e+308 246s 246s > (N <- howmanytrees(2e+06)) 246s approximately 3.692364 * 10^12335524 246s 246s > N[2] + 1 246s n 246s 12335525 246s 246s > ceiling((N[2] + 1)/3000) 246s n 246s 4112 246s 246s > n <- 1:792 246s 246s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 246s 246s > lN <- log10(N) 246s 246s > summary(lm(lN ~ n)) 246s 246s Call: 246s lm(formula = lN ~ n) 246s 246s Residuals: 246s Min 1Q Median 3Q Max 246s -0.25968 -0.21424 -0.08311 0.12406 2.82605 246s 246s Coefficients: 246s Estimate Std. Error t value Pr(>|t|) 246s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 246s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 246s --- 246s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 246s 246s Residual standard error: 0.3175 on 790 degrees of freedom 246s Multiple R-squared: 1, Adjusted R-squared: 1 246s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 246s 246s 246s > s <- n > 700 246s 246s > summary(lm(lN[s] ~ n[s])) 246s 246s Call: 246s lm(formula = lN[s] ~ n[s]) 246s 246s Residuals: 246s Min 1Q Median 3Q Max 246s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 246s 246s Coefficients: 246s Estimate Std. Error t value Pr(>|t|) 246s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 246s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 246s --- 246s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 246s 246s Residual standard error: 0.0003738 on 90 degrees of freedom 246s Multiple R-squared: 1, Adjusted R-squared: 1 246s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 246s 246s 246s > n <- 788:792 246s 246s > log10(sapply(n, howmanytrees, labeled = FALSE)) 246s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 246s 246s > 0.3941 * n - 4.153 246s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 246s 246s > xi <- 2.477993 246s 246s > lxi <- log10(xi) 246s 246s > n <- 1000 246s 246s > (n - 1) * lxi 246s [1] 393.706 246s 246s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 246s + 1))))) 246s [1] 393.8532 246s [1] 393.9009 246s [1] 393.9187 246s [1] 393.9257 246s [1] 393.9285 246s [1] 393.9296 246s [1] 393.9301 246s [1] 393.9303 246s [1] 393.9304 246s [1] 393.9304 246s > 246s autopkgtest [15:21:55]: test run-unit-test: -----------------------] 247s autopkgtest [15:21:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 247s run-unit-test PASS 247s autopkgtest [15:21:56]: test pkg-r-autopkgtest: preparing testbed 247s Reading package lists... 248s Building dependency tree... 248s Reading state information... 248s Starting pkgProblemResolver with broken count: 0 248s Starting 2 pkgProblemResolver with broken count: 0 248s Done 249s The following NEW packages will be installed: 249s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 249s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 249s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 249s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 249s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 249s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 249s libjpeg-turbo8-dev libjpeg8-dev libjs-jquery liblapack-dev liblsan0 249s liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 249s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev 249s libtirpc-dev libtsan2 libubsan1 node-html5shiv pkg-r-autopkgtest pkgconf 249s pkgconf-bin r-base-dev r-cran-expm r-cran-gee r-cran-xml2 zlib1g-dev 249s 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 249s Need to get 93.6 MB of archives. 249s After this operation, 336 MB of additional disk space will be used. 249s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 249s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 249s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 250s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 250s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 250s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 250s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 250s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 250s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 250s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 250s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 250s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 250s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 250s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 250s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 251s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 252s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 252s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 252s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 252s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 254s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 254s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 254s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 254s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 254s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 254s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 254s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 256s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 256s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 256s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 256s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 256s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 256s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 256s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 256s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 258s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 258s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 258s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 258s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 258s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 259s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 259s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 259s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 259s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 259s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 259s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 259s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 259s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 260s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 260s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 260s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 260s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 260s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 260s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 260s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 260s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 260s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-expm arm64 1.0-0-1 [225 kB] 260s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gee arm64 4.13-29-1 [72.8 kB] 260s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xml2 arm64 1.3.7-1 [327 kB] 261s Fetched 93.6 MB in 12s (7984 kB/s) 261s Selecting previously unselected package libisl23:arm64. 261s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 86712 files and directories currently installed.) 261s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 261s Unpacking libisl23:arm64 (0.27-1) ... 261s Selecting previously unselected package libmpc3:arm64. 261s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 261s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 261s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 261s Preparing to unpack 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libhwasan0:arm64 (15-20250222-0ubuntu1) ... 262s Selecting previously unselected package libgcc-14-dev:arm64. 262s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 262s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 262s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 262s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gcc-14. 262s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 262s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gcc-aarch64-linux-gnu. 262s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 262s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package gcc. 262s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 262s Unpacking gcc (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package libstdc++-14-dev:arm64. 262s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 262s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package g++-14-aarch64-linux-gnu. 262s Preparing to unpack .../19-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 262s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 263s Selecting previously unselected package g++-14. 263s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu3_arm64.deb ... 263s Unpacking g++-14 (14.2.0-17ubuntu3) ... 263s Selecting previously unselected package g++-aarch64-linux-gnu. 263s Preparing to unpack .../21-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 263s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Selecting previously unselected package g++. 263s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 263s Unpacking g++ (4:14.2.0-1ubuntu1) ... 263s Selecting previously unselected package build-essential. 263s Preparing to unpack .../23-build-essential_12.10ubuntu1_arm64.deb ... 263s Unpacking build-essential (12.10ubuntu1) ... 263s Selecting previously unselected package dctrl-tools. 263s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 263s Unpacking dctrl-tools (2.24-3build3) ... 263s Selecting previously unselected package libgfortran-14-dev:arm64. 263s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 263s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 263s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 263s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 263s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 263s Selecting previously unselected package gfortran-14. 263s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 263s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 263s Selecting previously unselected package gfortran-aarch64-linux-gnu. 263s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 263s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Selecting previously unselected package gfortran. 263s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 263s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 263s Selecting previously unselected package icu-devtools. 263s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 263s Unpacking icu-devtools (76.1-1ubuntu2) ... 263s Selecting previously unselected package libblas-dev:arm64. 263s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 263s Unpacking libblas-dev:arm64 (3.12.1-2) ... 263s Selecting previously unselected package libbz2-dev:arm64. 263s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 263s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 263s Selecting previously unselected package libdeflate-dev:arm64. 263s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 263s Unpacking libdeflate-dev:arm64 (1.23-1) ... 263s Selecting previously unselected package libicu-dev:arm64. 263s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 263s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 264s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 264s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 264s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 264s Selecting previously unselected package libjpeg8-dev:arm64. 264s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 264s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 264s Selecting previously unselected package libjpeg-dev:arm64. 264s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 264s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 264s Selecting previously unselected package libjs-jquery. 264s Preparing to unpack .../38-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 264s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 264s Selecting previously unselected package liblapack-dev:arm64. 264s Preparing to unpack .../39-liblapack-dev_3.12.1-2_arm64.deb ... 264s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 264s Selecting previously unselected package libncurses-dev:arm64. 264s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_arm64.deb ... 264s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 264s Selecting previously unselected package libpcre2-16-0:arm64. 264s Preparing to unpack .../41-libpcre2-16-0_10.45-1_arm64.deb ... 264s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 264s Selecting previously unselected package libpcre2-32-0:arm64. 264s Preparing to unpack .../42-libpcre2-32-0_10.45-1_arm64.deb ... 264s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 264s Selecting previously unselected package libpcre2-posix3:arm64. 264s Preparing to unpack .../43-libpcre2-posix3_10.45-1_arm64.deb ... 264s Unpacking libpcre2-posix3:arm64 (10.45-1) ... 264s Selecting previously unselected package libpcre2-dev:arm64. 264s Preparing to unpack .../44-libpcre2-dev_10.45-1_arm64.deb ... 264s Unpacking libpcre2-dev:arm64 (10.45-1) ... 264s Selecting previously unselected package libpkgconf3:arm64. 264s Preparing to unpack .../45-libpkgconf3_1.8.1-4_arm64.deb ... 264s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 264s Selecting previously unselected package zlib1g-dev:arm64. 264s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 264s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 264s Selecting previously unselected package libpng-dev:arm64. 264s Preparing to unpack .../47-libpng-dev_1.6.47-1_arm64.deb ... 264s Unpacking libpng-dev:arm64 (1.6.47-1) ... 264s Selecting previously unselected package libreadline-dev:arm64. 264s Preparing to unpack .../48-libreadline-dev_8.2-6_arm64.deb ... 264s Unpacking libreadline-dev:arm64 (8.2-6) ... 264s Selecting previously unselected package node-html5shiv. 264s Preparing to unpack .../49-node-html5shiv_3.7.3+dfsg-5_all.deb ... 264s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 264s Selecting previously unselected package liblzma-dev:arm64. 264s Preparing to unpack .../50-liblzma-dev_5.6.4-1_arm64.deb ... 264s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 264s Selecting previously unselected package pkgconf-bin. 264s Preparing to unpack .../51-pkgconf-bin_1.8.1-4_arm64.deb ... 264s Unpacking pkgconf-bin (1.8.1-4) ... 264s Selecting previously unselected package pkgconf:arm64. 265s Preparing to unpack .../52-pkgconf_1.8.1-4_arm64.deb ... 265s Unpacking pkgconf:arm64 (1.8.1-4) ... 265s Selecting previously unselected package libtirpc-dev:arm64. 265s Preparing to unpack .../53-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 265s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 265s Selecting previously unselected package r-base-dev. 265s Preparing to unpack .../54-r-base-dev_4.4.3-1_all.deb ... 265s Unpacking r-base-dev (4.4.3-1) ... 265s Selecting previously unselected package pkg-r-autopkgtest. 265s Preparing to unpack .../55-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 265s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 265s Selecting previously unselected package r-cran-expm. 265s Preparing to unpack .../56-r-cran-expm_1.0-0-1_arm64.deb ... 265s Unpacking r-cran-expm (1.0-0-1) ... 265s Selecting previously unselected package r-cran-gee. 265s Preparing to unpack .../57-r-cran-gee_4.13-29-1_arm64.deb ... 265s Unpacking r-cran-gee (4.13-29-1) ... 265s Selecting previously unselected package r-cran-xml2. 265s Preparing to unpack .../58-r-cran-xml2_1.3.7-1_arm64.deb ... 265s Unpacking r-cran-xml2 (1.3.7-1) ... 265s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 265s Setting up libncurses-dev:arm64 (6.5+20250216-2) ... 265s Setting up node-html5shiv (3.7.3+dfsg-5) ... 265s Setting up r-cran-expm (1.0-0-1) ... 265s Setting up libreadline-dev:arm64 (8.2-6) ... 265s Setting up libpcre2-16-0:arm64 (10.45-1) ... 265s Setting up libpcre2-32-0:arm64 (10.45-1) ... 265s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 265s Setting up libpkgconf3:arm64 (1.8.1-4) ... 265s Setting up libmpc3:arm64 (1.3.1-1build2) ... 265s Setting up icu-devtools (76.1-1ubuntu2) ... 265s Setting up pkgconf-bin (1.8.1-4) ... 265s Setting up liblzma-dev:arm64 (5.6.4-1) ... 265s Setting up libubsan1:arm64 (15-20250222-0ubuntu1) ... 265s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 265s Setting up libpcre2-posix3:arm64 (10.45-1) ... 265s Setting up libhwasan0:arm64 (15-20250222-0ubuntu1) ... 265s Setting up libasan8:arm64 (15-20250222-0ubuntu1) ... 265s Setting up libtsan2:arm64 (15-20250222-0ubuntu1) ... 265s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 265s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 265s Setting up r-cran-gee (4.13-29-1) ... 265s Setting up libisl23:arm64 (0.27-1) ... 265s Setting up libdeflate-dev:arm64 (1.23-1) ... 265s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 265s Setting up libcc1-0:arm64 (15-20250222-0ubuntu1) ... 265s Setting up liblsan0:arm64 (15-20250222-0ubuntu1) ... 265s Setting up libblas-dev:arm64 (3.12.1-2) ... 265s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 265s Setting up dctrl-tools (2.24-3build3) ... 265s Setting up libitm1:arm64 (15-20250222-0ubuntu1) ... 265s Setting up libbz2-dev:arm64 (1.0.8-6) ... 265s Setting up libpcre2-dev:arm64 (10.45-1) ... 265s Setting up r-cran-xml2 (1.3.7-1) ... 265s Setting up libpng-dev:arm64 (1.6.47-1) ... 265s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 265s Setting up pkgconf:arm64 (1.8.1-4) ... 265s Setting up liblapack-dev:arm64 (3.12.1-2) ... 265s 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 265s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 265s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 265s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 265s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 265s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 265s Setting up cpp-14 (14.2.0-17ubuntu3) ... 265s Setting up cpp (4:14.2.0-1ubuntu1) ... 265s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 265s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 265s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 265s Setting up gcc-14 (14.2.0-17ubuntu3) ... 265s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 265s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 265s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 265s Setting up g++-14 (14.2.0-17ubuntu3) ... 265s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 265s Setting up gcc (4:14.2.0-1ubuntu1) ... 265s Setting up g++ (4:14.2.0-1ubuntu1) ... 265s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 265s Setting up build-essential (12.10ubuntu1) ... 265s Setting up gfortran (4:14.2.0-1ubuntu1) ... 265s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 265s 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 265s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 265s 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 265s Setting up r-base-dev (4.4.3-1) ... 265s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 265s Processing triggers for libc-bin (2.41-1ubuntu2) ... 265s Processing triggers for man-db (2.13.0-1) ... 266s Processing triggers for install-info (7.1.1-1) ... 267s autopkgtest [15:22:16]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 267s autopkgtest [15:22:16]: test pkg-r-autopkgtest: [----------------------- 267s Test: Try to load the R library ape 267s 267s R version 4.4.3 (2025-02-28) -- "Trophy Case" 267s Copyright (C) 2025 The R Foundation for Statistical Computing 267s Platform: aarch64-unknown-linux-gnu 267s 267s R is free software and comes with ABSOLUTELY NO WARRANTY. 267s You are welcome to redistribute it under certain conditions. 267s Type 'license()' or 'licence()' for distribution details. 267s 267s R is a collaborative project with many contributors. 267s Type 'contributors()' for more information and 267s 'citation()' on how to cite R or R packages in publications. 267s 267s Type 'demo()' for some demos, 'help()' for on-line help, or 267s 'help.start()' for an HTML browser interface to help. 267s Type 'q()' to quit R. 267s 267s > library('ape') 268s > 268s > 268s Other tests are currently unsupported! 268s They will be progressively added. 268s autopkgtest [15:22:17]: test pkg-r-autopkgtest: -----------------------] 268s autopkgtest [15:22:17]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 268s pkg-r-autopkgtest PASS 269s autopkgtest [15:22:18]: @@@@@@@@@@@@@@@@@@@@ summary 269s run-unit-test PASS 269s pkg-r-autopkgtest PASS 288s nova [W] Using flock in prodstack6-arm64 288s flock: timeout while waiting to get lock 288s Creating nova instance adt-plucky-arm64-r-cran-ape-20250315-151748-juju-7f2275-prod-proposed-migration-environment-2-952f1de7-4955-4f09-9e71-e7d99de04405 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 288s nova [W] Timed out waiting for 0fa8f6ee-7c58-4578-ab51-2f8a897eb676 to get deleted.