0s autopkgtest [02:25:18]: starting date and time: 2025-05-03 02:25:18+0000 0s autopkgtest [02:25:18]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [02:25:18]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.c1p3saoi/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:nlme --apt-upgrade r-cran-ape --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=nlme/3.1.168-1 -- lxd -r lxd-armhf-10.145.243.142 lxd-armhf-10.145.243.142:autopkgtest/ubuntu/questing/armhf 20s autopkgtest [02:25:38]: testbed dpkg architecture: armhf 22s autopkgtest [02:25:40]: testbed apt version: 3.0.0 26s autopkgtest [02:25:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [02:25:46]: testbed release detected to be: None 35s autopkgtest [02:25:53]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 37s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 37s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 37s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 37s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1920 kB] 38s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.3 kB] 38s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 38s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [204 kB] 38s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1378 kB] 38s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.5 kB] 38s Get:11 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 38s Get:12 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 38s Get:13 http://ftpmaster.internal/ubuntu questing/main Sources [1395 kB] 38s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 38s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [14.9 MB] 39s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 42s Fetched 43.3 MB in 5s (7918 kB/s) 44s Reading package lists... 50s autopkgtest [02:26:08]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 52s Starting 2 pkgProblemResolver with broken count: 0 52s Done 53s Entering ResolveByKeep 54s 54s Calculating upgrade... 54s The following packages will be upgraded: 54s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 54s libftdi1-2 libfwupd3 libnpth0t64 libnvme1t64 libsensors-config libsensors5 54s liburcu8t64 motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n 54s usb.ids 54s 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 5431 kB of archives. 54s After this operation, 3722 kB disk space will be freed. 54s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 54s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 55s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 55s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 55s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 55s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 55s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 55s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 55s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 55s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 55s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 55s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 55s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 55s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 55s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 55s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 55s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 55s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 55s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 55s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libnvme1t64 armhf 1.13-2 [74.3 kB] 56s Fetched 5431 kB in 1s (6848 kB/s) 56s (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 ... 63953 files and directories currently installed.) 56s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 56s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 56s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 56s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 56s Setting up base-files (13.7ubuntu1) ... 56s Installing new version of config file /etc/issue ... 56s Installing new version of config file /etc/issue.net ... 56s Installing new version of config file /etc/lsb-release ... 57s motd-news.service is a disabled or a static unit not running, not starting it. 57s (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 ... 63953 files and directories currently installed.) 57s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 57s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 57s Setting up dpkg (1.22.18ubuntu3) ... 58s (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 ... 63953 files and directories currently installed.) 58s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 58s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 58s Setting up libnpth0t64:armhf (1.8-3) ... 58s (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 ... 63953 files and directories currently installed.) 58s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 58s Unpacking distro-info-data (0.64) over (0.63) ... 58s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 58s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 58s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 58s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 58s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 59s Unpacking ed (1.21.1-1) over (1.21-1) ... 59s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 59s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 59s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 59s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 59s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 59s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 59s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 59s Unpacking nano (8.4-1) over (8.3-1) ... 59s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 59s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 59s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 59s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 59s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 59s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 59s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 59s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 60s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 60s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 60s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 60s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 60s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 60s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 60s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 60s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 60s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 60s Setting up motd-news-config (13.7ubuntu1) ... 60s Setting up liburcu8t64:armhf (0.15.2-2) ... 60s Setting up distro-info-data (0.64) ... 60s Setting up htop (3.4.1-4) ... 60s Setting up libsensors-config (1:3.6.2-2) ... 60s Installing new version of config file /etc/sensors3.conf ... 60s Setting up libfwupd3:armhf (2.0.8-3) ... 60s Setting up libftdi1-2:armhf (1.5-10) ... 60s Setting up libnvme1t64 (1.13-2) ... 60s Setting up ed (1.21.1-1) ... 60s Setting up usb.ids (2025.04.01-1) ... 60s Setting up libsensors5:armhf (1:3.6.2-2) ... 60s Setting up libdpkg-perl (1.22.18ubuntu3) ... 60s Setting up nano (8.4-1) ... 60s Installing new version of config file /etc/nanorc ... 60s Setting up ubuntu-pro-client (35.1ubuntu0) ... 60s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 60s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 60s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 60s 62s Setting up fwupd (2.0.8-3) ... 63s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 63s fwupd.service is a disabled or a static unit not running, not starting it. 63s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 63s Setting up dpkg-dev (1.22.18ubuntu3) ... 63s Processing triggers for dbus (1.16.2-2ubuntu1) ... 63s Processing triggers for install-info (7.1.1-1) ... 63s Processing triggers for libc-bin (2.41-6ubuntu1) ... 63s Processing triggers for man-db (2.13.0-1) ... 65s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 65s Processing triggers for initramfs-tools (0.147ubuntu1) ... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Starting pkgProblemResolver with broken count: 0 68s Starting 2 pkgProblemResolver with broken count: 0 68s Done 69s Solving dependencies... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [02:26:29]: rebooting testbed after setup commands that affected boot 112s autopkgtest [02:27:10]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 136s autopkgtest [02:27:34]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 146s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 146s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 146s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 146s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 146s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 146s gpgv: issuer "plessy@debian.org" 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 147s autopkgtest [02:27:45]: testing package r-cran-ape version 5.8-1-1 149s autopkgtest [02:27:47]: build not needed 153s autopkgtest [02:27:51]: test run-unit-test: preparing testbed 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s The following NEW packages will be installed: 156s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 156s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 156s libfreetype6 libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b 156s libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 156s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 156s libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 156s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 156s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-ape 156s r-cran-cli r-cran-cpp11 r-cran-digest r-cran-fastmatch r-cran-generics 156s r-cran-glue r-cran-igraph r-cran-lattice r-cran-lifecycle r-cran-littler 156s r-cran-magrittr r-cran-matrix r-cran-nlme r-cran-phangorn r-cran-pkgconfig 156s r-cran-pkgkitten r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip 156s x11-common xdg-utils zip 156s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 63.1 MB of archives. 156s After this operation, 117 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 157s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 157s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 157s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 157s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 157s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig armhf 2.15.0-2.2ubuntu1 [190 kB] 157s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 157s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf libsuitesparseconfig7 armhf 1:7.8.3+dfsg-3 [12.7 kB] 157s Get:9 http://ftpmaster.internal/ubuntu questing/universe armhf libamd3 armhf 1:7.8.3+dfsg-3 [29.2 kB] 157s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 157s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 157s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 157s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 157s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 157s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 157s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libcolamd3 armhf 1:7.8.3+dfsg-3 [19.8 kB] 157s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 157s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 157s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 157s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libltdl7 armhf 2.5.4-4 [39.8 kB] 157s Get:21 http://ftpmaster.internal/ubuntu questing/universe armhf libglpk40 armhf 5.0-1build2 [326 kB] 157s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 157s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 157s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 157s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 157s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 157s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 157s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 157s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 157s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libthai-data all 0.1.29-2build1 [158 kB] 157s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 157s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libpango-1.0-0 armhf 1.56.3-1 [216 kB] 157s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libpangoft2-1.0-0 armhf 1.56.3-1 [44.1 kB] 157s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libpangocairo-1.0-0 armhf 1.56.3-1 [25.0 kB] 157s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 157s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 157s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 157s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 157s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 157s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 157s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 157s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 157s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 157s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 157s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 157s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 157s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 157s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 157s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 157s Get:50 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 158s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 158s Get:52 http://ftpmaster.internal/ubuntu questing/universe armhf littler all 0.3.20-2 [2554 B] 158s Get:53 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 158s Get:54 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 158s Get:55 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 158s Get:56 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 158s Get:57 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-digest armhf 0.6.37-1 [207 kB] 158s Get:58 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-ape armhf 5.8-1-1 [2891 kB] 158s Get:59 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 158s Get:60 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-cpp11 all 0.5.2-1 [233 kB] 158s Get:61 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-fastmatch armhf 1.1-6-1 [34.2 kB] 158s Get:62 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-generics all 0.1.3-1 [81.3 kB] 158s Get:63 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 158s Get:64 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rlang armhf 1.1.5-1 [1701 kB] 158s Get:65 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 158s Get:66 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 158s Get:67 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 158s Get:68 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 158s Get:69 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 158s Get:70 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-igraph armhf 2.1.4-1 [5211 kB] 159s Get:71 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-quadprog armhf 1.5-8-1build1 [28.7 kB] 159s Get:72 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-phangorn armhf 2.12.1+dfsg-1 [1797 kB] 159s Preconfiguring packages ... 159s Fetched 63.1 MB in 2s (25.4 MB/s) 159s Selecting previously unselected package libfreetype6:armhf. 159s (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 ... 63951 files and directories currently installed.) 159s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 159s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 159s Selecting previously unselected package fonts-dejavu-mono. 159s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-mono (2.37-8) ... 159s Selecting previously unselected package fonts-dejavu-core. 159s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-core (2.37-8) ... 159s Selecting previously unselected package fontconfig-config. 159s Preparing to unpack .../03-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 160s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 160s Selecting previously unselected package libfontconfig1:armhf. 160s Preparing to unpack .../04-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 160s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 160s Selecting previously unselected package fontconfig. 160s Preparing to unpack .../05-fontconfig_2.15.0-2.2ubuntu1_armhf.deb ... 160s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 160s Selecting previously unselected package libgomp1:armhf. 160s Preparing to unpack .../06-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 160s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 160s Selecting previously unselected package libsuitesparseconfig7:armhf. 160s Preparing to unpack .../07-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_armhf.deb ... 160s Unpacking libsuitesparseconfig7:armhf (1:7.8.3+dfsg-3) ... 160s Selecting previously unselected package libamd3:armhf. 160s Preparing to unpack .../08-libamd3_1%3a7.8.3+dfsg-3_armhf.deb ... 160s Unpacking libamd3:armhf (1:7.8.3+dfsg-3) ... 160s Selecting previously unselected package libblas3:armhf. 160s Preparing to unpack .../09-libblas3_3.12.1-2_armhf.deb ... 160s Unpacking libblas3:armhf (3.12.1-2) ... 160s Selecting previously unselected package libpixman-1-0:armhf. 160s Preparing to unpack .../10-libpixman-1-0_0.44.0-3_armhf.deb ... 160s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 160s Selecting previously unselected package libxcb-render0:armhf. 160s Preparing to unpack .../11-libxcb-render0_1.17.0-2_armhf.deb ... 160s Unpacking libxcb-render0:armhf (1.17.0-2) ... 160s Selecting previously unselected package libxcb-shm0:armhf. 160s Preparing to unpack .../12-libxcb-shm0_1.17.0-2_armhf.deb ... 160s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 160s Selecting previously unselected package libxrender1:armhf. 160s Preparing to unpack .../13-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 160s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 160s Selecting previously unselected package libcairo2:armhf. 160s Preparing to unpack .../14-libcairo2_1.18.4-1_armhf.deb ... 160s Unpacking libcairo2:armhf (1.18.4-1) ... 160s Selecting previously unselected package libcolamd3:armhf. 160s Preparing to unpack .../15-libcolamd3_1%3a7.8.3+dfsg-3_armhf.deb ... 160s Unpacking libcolamd3:armhf (1:7.8.3+dfsg-3) ... 160s Selecting previously unselected package libdatrie1:armhf. 160s Preparing to unpack .../16-libdatrie1_0.2.13-3build1_armhf.deb ... 160s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 160s Selecting previously unselected package libdeflate0:armhf. 160s Preparing to unpack .../17-libdeflate0_1.23-1_armhf.deb ... 160s Unpacking libdeflate0:armhf (1.23-1) ... 160s Selecting previously unselected package libgfortran5:armhf. 160s Preparing to unpack .../18-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 160s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 160s Selecting previously unselected package libltdl7:armhf. 160s Preparing to unpack .../19-libltdl7_2.5.4-4_armhf.deb ... 160s Unpacking libltdl7:armhf (2.5.4-4) ... 160s Selecting previously unselected package libglpk40:armhf. 160s Preparing to unpack .../20-libglpk40_5.0-1build2_armhf.deb ... 160s Unpacking libglpk40:armhf (5.0-1build2) ... 160s Selecting previously unselected package libgraphite2-3:armhf. 160s Preparing to unpack .../21-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 160s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 160s Selecting previously unselected package libharfbuzz0b:armhf. 160s Preparing to unpack .../22-libharfbuzz0b_10.2.0-1_armhf.deb ... 160s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 160s Selecting previously unselected package x11-common. 160s Preparing to unpack .../23-x11-common_1%3a7.7+23ubuntu4_all.deb ... 160s Unpacking x11-common (1:7.7+23ubuntu4) ... 160s Selecting previously unselected package libice6:armhf. 160s Preparing to unpack .../24-libice6_2%3a1.1.1-1_armhf.deb ... 160s Unpacking libice6:armhf (2:1.1.1-1) ... 160s Selecting previously unselected package libjpeg-turbo8:armhf. 160s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 160s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 160s Selecting previously unselected package libjpeg8:armhf. 160s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_armhf.deb ... 160s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 160s Selecting previously unselected package liblapack3:armhf. 160s Preparing to unpack .../27-liblapack3_3.12.1-2_armhf.deb ... 160s Unpacking liblapack3:armhf (3.12.1-2) ... 160s Selecting previously unselected package liblerc4:armhf. 160s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 160s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 160s Selecting previously unselected package libthai-data. 161s Preparing to unpack .../29-libthai-data_0.1.29-2build1_all.deb ... 161s Unpacking libthai-data (0.1.29-2build1) ... 161s Selecting previously unselected package libthai0:armhf. 161s Preparing to unpack .../30-libthai0_0.1.29-2build1_armhf.deb ... 161s Unpacking libthai0:armhf (0.1.29-2build1) ... 161s Selecting previously unselected package libpango-1.0-0:armhf. 161s Preparing to unpack .../31-libpango-1.0-0_1.56.3-1_armhf.deb ... 161s Unpacking libpango-1.0-0:armhf (1.56.3-1) ... 161s Selecting previously unselected package libpangoft2-1.0-0:armhf. 161s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.3-1_armhf.deb ... 161s Unpacking libpangoft2-1.0-0:armhf (1.56.3-1) ... 161s Selecting previously unselected package libpangocairo-1.0-0:armhf. 161s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.3-1_armhf.deb ... 161s Unpacking libpangocairo-1.0-0:armhf (1.56.3-1) ... 161s Selecting previously unselected package libpaper2:armhf. 161s Preparing to unpack .../34-libpaper2_2.2.5-0.3_armhf.deb ... 161s Unpacking libpaper2:armhf (2.2.5-0.3) ... 161s Selecting previously unselected package libpaper-utils. 161s Preparing to unpack .../35-libpaper-utils_2.2.5-0.3_armhf.deb ... 161s Unpacking libpaper-utils (2.2.5-0.3) ... 161s Selecting previously unselected package libsharpyuv0:armhf. 161s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1_armhf.deb ... 161s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 161s Selecting previously unselected package libsm6:armhf. 161s Preparing to unpack .../37-libsm6_2%3a1.2.4-1_armhf.deb ... 161s Unpacking libsm6:armhf (2:1.2.4-1) ... 161s Selecting previously unselected package libtcl8.6:armhf. 161s Preparing to unpack .../38-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 161s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 161s Selecting previously unselected package libjbig0:armhf. 161s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 161s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 161s Selecting previously unselected package libwebp7:armhf. 161s Preparing to unpack .../40-libwebp7_1.5.0-0.1_armhf.deb ... 161s Unpacking libwebp7:armhf (1.5.0-0.1) ... 161s Selecting previously unselected package libtiff6:armhf. 161s Preparing to unpack .../41-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 161s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 161s Selecting previously unselected package libxft2:armhf. 161s Preparing to unpack .../42-libxft2_2.3.6-1build1_armhf.deb ... 161s Unpacking libxft2:armhf (2.3.6-1build1) ... 161s Selecting previously unselected package libxss1:armhf. 161s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build3_armhf.deb ... 161s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 161s Selecting previously unselected package libtk8.6:armhf. 161s Preparing to unpack .../44-libtk8.6_8.6.16-1_armhf.deb ... 161s Unpacking libtk8.6:armhf (8.6.16-1) ... 161s Selecting previously unselected package libxt6t64:armhf. 161s Preparing to unpack .../45-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 161s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 161s Selecting previously unselected package zip. 161s Preparing to unpack .../46-zip_3.0-14ubuntu2_armhf.deb ... 161s Unpacking zip (3.0-14ubuntu2) ... 161s Selecting previously unselected package unzip. 161s Preparing to unpack .../47-unzip_6.0-28ubuntu6_armhf.deb ... 161s Unpacking unzip (6.0-28ubuntu6) ... 161s Selecting previously unselected package xdg-utils. 161s Preparing to unpack .../48-xdg-utils_1.2.1-2ubuntu1_all.deb ... 161s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 161s Selecting previously unselected package r-base-core. 161s Preparing to unpack .../49-r-base-core_4.4.3-1_armhf.deb ... 161s Unpacking r-base-core (4.4.3-1) ... 162s Selecting previously unselected package r-cran-littler. 162s Preparing to unpack .../50-r-cran-littler_0.3.20-2_armhf.deb ... 162s Unpacking r-cran-littler (0.3.20-2) ... 162s Selecting previously unselected package littler. 162s Preparing to unpack .../51-littler_0.3.20-2_all.deb ... 162s Unpacking littler (0.3.20-2) ... 162s Selecting previously unselected package r-cran-lattice. 162s Preparing to unpack .../52-r-cran-lattice_0.22-6-1_armhf.deb ... 162s Unpacking r-cran-lattice (0.22-6-1) ... 162s Selecting previously unselected package r-cran-nlme. 162s Preparing to unpack .../53-r-cran-nlme_3.1.168-1_armhf.deb ... 162s Unpacking r-cran-nlme (3.1.168-1) ... 162s Selecting previously unselected package r-cran-pkgkitten. 162s Preparing to unpack .../54-r-cran-pkgkitten_0.2.4-1_all.deb ... 162s Unpacking r-cran-pkgkitten (0.2.4-1) ... 162s Selecting previously unselected package r-cran-rcpp. 162s Preparing to unpack .../55-r-cran-rcpp_1.0.14-1_armhf.deb ... 162s Unpacking r-cran-rcpp (1.0.14-1) ... 162s Selecting previously unselected package r-cran-digest. 162s Preparing to unpack .../56-r-cran-digest_0.6.37-1_armhf.deb ... 162s Unpacking r-cran-digest (0.6.37-1) ... 162s Selecting previously unselected package r-cran-ape. 162s Preparing to unpack .../57-r-cran-ape_5.8-1-1_armhf.deb ... 162s Unpacking r-cran-ape (5.8-1-1) ... 162s Selecting previously unselected package r-cran-cli. 162s Preparing to unpack .../58-r-cran-cli_3.6.4-1_armhf.deb ... 162s Unpacking r-cran-cli (3.6.4-1) ... 162s Selecting previously unselected package r-cran-cpp11. 162s Preparing to unpack .../59-r-cran-cpp11_0.5.2-1_all.deb ... 162s Unpacking r-cran-cpp11 (0.5.2-1) ... 162s Selecting previously unselected package r-cran-fastmatch. 162s Preparing to unpack .../60-r-cran-fastmatch_1.1-6-1_armhf.deb ... 162s Unpacking r-cran-fastmatch (1.1-6-1) ... 162s Selecting previously unselected package r-cran-generics. 162s Preparing to unpack .../61-r-cran-generics_0.1.3-1_all.deb ... 162s Unpacking r-cran-generics (0.1.3-1) ... 162s Selecting previously unselected package r-cran-glue. 162s Preparing to unpack .../62-r-cran-glue_1.8.0-1_armhf.deb ... 162s Unpacking r-cran-glue (1.8.0-1) ... 162s Selecting previously unselected package r-cran-rlang. 162s Preparing to unpack .../63-r-cran-rlang_1.1.5-1_armhf.deb ... 162s Unpacking r-cran-rlang (1.1.5-1) ... 162s Selecting previously unselected package r-cran-lifecycle. 162s Preparing to unpack .../64-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 162s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 162s Selecting previously unselected package r-cran-magrittr. 162s Preparing to unpack .../65-r-cran-magrittr_2.0.3-1_armhf.deb ... 162s Unpacking r-cran-magrittr (2.0.3-1) ... 162s Selecting previously unselected package r-cran-matrix. 162s Preparing to unpack .../66-r-cran-matrix_1.7-3-1_armhf.deb ... 162s Unpacking r-cran-matrix (1.7-3-1) ... 162s Selecting previously unselected package r-cran-pkgconfig. 162s Preparing to unpack .../67-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 162s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 163s Selecting previously unselected package r-cran-vctrs. 163s Preparing to unpack .../68-r-cran-vctrs_0.6.5-1_armhf.deb ... 163s Unpacking r-cran-vctrs (0.6.5-1) ... 163s Selecting previously unselected package r-cran-igraph. 163s Preparing to unpack .../69-r-cran-igraph_2.1.4-1_armhf.deb ... 163s Unpacking r-cran-igraph (2.1.4-1) ... 163s Selecting previously unselected package r-cran-quadprog. 163s Preparing to unpack .../70-r-cran-quadprog_1.5-8-1build1_armhf.deb ... 163s Unpacking r-cran-quadprog (1.5-8-1build1) ... 163s Selecting previously unselected package r-cran-phangorn. 163s Preparing to unpack .../71-r-cran-phangorn_2.12.1+dfsg-1_armhf.deb ... 163s Unpacking r-cran-phangorn (2.12.1+dfsg-1) ... 163s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 163s Setting up libpixman-1-0:armhf (0.44.0-3) ... 163s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 163s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 163s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 163s Setting up libdatrie1:armhf (0.2.13-3build1) ... 163s Setting up libxcb-render0:armhf (1.17.0-2) ... 163s Setting up unzip (6.0-28ubuntu6) ... 163s Setting up x11-common (1:7.7+23ubuntu4) ... 163s Setting up libdeflate0:armhf (1.23-1) ... 163s Setting up libxcb-shm0:armhf (1.17.0-2) ... 163s Setting up libgomp1:armhf (15-20250404-0ubuntu1) ... 163s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 163s Setting up zip (3.0-14ubuntu2) ... 163s Setting up libblas3:armhf (3.12.1-2) ... 163s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 163s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 163s Setting up fonts-dejavu-mono (2.37-8) ... 163s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 163s Setting up fonts-dejavu-core (2.37-8) ... 163s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 163s Setting up libltdl7:armhf (2.5.4-4) ... 163s Setting up libgfortran5:armhf (15-20250404-0ubuntu1) ... 163s Setting up libwebp7:armhf (1.5.0-0.1) ... 163s Setting up libsuitesparseconfig7:armhf (1:7.8.3+dfsg-3) ... 163s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 163s Setting up libthai-data (0.1.29-2build1) ... 163s Setting up libxss1:armhf (1:1.2.3-1build3) ... 163s Setting up libpaper2:armhf (2.2.5-0.3) ... 163s Setting up xdg-utils (1.2.1-2ubuntu1) ... 163s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 163s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 163s Setting up libice6:armhf (2:1.1.1-1) ... 163s Setting up liblapack3:armhf (3.12.1-2) ... 163s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 163s Setting up libamd3:armhf (1:7.8.3+dfsg-3) ... 163s Setting up libcolamd3:armhf (1:7.8.3+dfsg-3) ... 163s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 164s Setting up libpaper-utils (2.2.5-0.3) ... 164s Setting up libthai0:armhf (0.1.29-2build1) ... 164s Setting up libglpk40:armhf (5.0-1build2) ... 164s Setting up libtiff6:armhf (4.7.0-3ubuntu1) ... 164s Setting up libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 164s Setting up libsm6:armhf (2:1.2.4-1) ... 164s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 166s Regenerating fonts cache... done. 166s Setting up libxft2:armhf (2.3.6-1build1) ... 166s Setting up libtk8.6:armhf (8.6.16-1) ... 166s Setting up libpango-1.0-0:armhf (1.56.3-1) ... 166s Setting up libcairo2:armhf (1.18.4-1) ... 166s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 166s Setting up libpangoft2-1.0-0:armhf (1.56.3-1) ... 166s Setting up libpangocairo-1.0-0:armhf (1.56.3-1) ... 166s Setting up r-base-core (4.4.3-1) ... 166s Creating config file /etc/R/Renviron with new version 166s Setting up r-cran-fastmatch (1.1-6-1) ... 166s Setting up r-cran-lattice (0.22-6-1) ... 166s Setting up r-cran-nlme (3.1.168-1) ... 166s Setting up r-cran-pkgkitten (0.2.4-1) ... 166s Setting up r-cran-magrittr (2.0.3-1) ... 166s Setting up r-cran-quadprog (1.5-8-1build1) ... 166s Setting up r-cran-littler (0.3.20-2) ... 166s Setting up r-cran-rcpp (1.0.14-1) ... 166s Setting up r-cran-rlang (1.1.5-1) ... 166s Setting up littler (0.3.20-2) ... 166s Setting up r-cran-generics (0.1.3-1) ... 166s Setting up r-cran-digest (0.6.37-1) ... 166s Setting up r-cran-ape (5.8-1-1) ... 166s Setting up r-cran-glue (1.8.0-1) ... 166s Setting up r-cran-cli (3.6.4-1) ... 166s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 166s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 166s Setting up r-cran-cpp11 (0.5.2-1) ... 166s Setting up r-cran-matrix (1.7-3-1) ... 166s Setting up r-cran-vctrs (0.6.5-1) ... 166s Setting up r-cran-igraph (2.1.4-1) ... 166s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 166s Processing triggers for libc-bin (2.41-6ubuntu1) ... 166s Processing triggers for man-db (2.13.0-1) ... 167s Processing triggers for install-info (7.1.1-1) ... 174s autopkgtest [02:28:12]: test run-unit-test: [----------------------- 176s 176s R version 4.4.3 (2025-02-28) -- "Trophy Case" 176s Copyright (C) 2025 The R Foundation for Statistical Computing 176s Platform: arm-unknown-linux-gnueabihf (32-bit) 176s 176s R is free software and comes with ABSOLUTELY NO WARRANTY. 176s You are welcome to redistribute it under certain conditions. 176s Type 'license()' or 'licence()' for distribution details. 176s 176s R is a collaborative project with many contributors. 176s Type 'contributors()' for more information and 176s 'citation()' on how to cite R or R packages in publications. 176s 176s Type 'demo()' for some demos, 'help()' for on-line help, or 176s 'help.start()' for an HTML browser interface to help. 176s Type 'q()' to quit R. 176s 176s > Stangle("DrawingPhylogenies.Rnw") 177s Writing to file DrawingPhylogenies.R 177s > source("DrawingPhylogenies.R", echo=TRUE) 177s 177s > options(width = 80, prompt = "> ") 177s 177s > library(ape) 177s 177s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 177s 177s > foo <- function() { 177s + col <- "green" 177s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 177s + las = 1) 177s + box(lty .... [TRUNCATED] 177s 177s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 177s 177s > plot(mytr) 177s 177s > foo() 177s 177s > plot(mytr, "c", FALSE) 177s 177s > foo() 177s 177s > plot(mytr, "u") 177s 177s > foo() 177s 177s > par(xpd = TRUE) 177s 177s > plot(mytr, "f") 177s 177s > foo() 177s 177s > box("outer") 177s 177s > tr <- compute.brlen(stree(8, "l"), 0.1) 177s 177s > tr$tip.label[] <- "" 177s 177s > foo <- function() { 177s + col <- "green" 177s + axis(1, col = col, col.ticks = col, col.axis = col) 177s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 177s 177s > layout(matrix(1:12, 6, 2)) 177s 177s > par(mar = c(2, 2, 0.3, 0)) 177s 177s > for (type in c("p", "c")) { 177s + plot(tr, type) 177s + foo() 177s + plot(tr, type, node.pos = 2) 177s + foo() 177s + plot(tr, type, FALSE) 177s + foo() 177s .... [TRUNCATED] 177s 177s > foo <- function() { 177s + col <- "green" 177s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 177s + las = 1) 177s + box(lty .... [TRUNCATED] 177s 177s > layout(matrix(1:4, 2, 2)) 177s 177s > par(las = 1) 177s 177s > plot(tr, "u") 177s 177s > foo() 177s 177s > plot(tr, "u", FALSE) 177s 177s > foo() 177s 177s > plot(tr, "f") 177s 177s > foo() 177s 177s > plot(tr, "f", FALSE) 177s 177s > foo() 177s 177s > args(node.depth.edgelength) 177s function (phy) 177s NULL 177s 177s > args(node.depth) 177s function (phy, method = 1) 177s NULL 177s 177s > args(node.height) 177s function (phy, clado.style = FALSE) 177s NULL 177s 177s > args(unrooted.xy) 177s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 177s NULL 177s 177s > args(phylogram.plot) 177s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 177s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 177s node.lty = NULL) 177s NULL 177s 177s > args(cladogram.plot) 177s function (edge, xx, yy, edge.color, edge.width, edge.lty) 177s NULL 177s 177s > args(circular.plot) 177s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 177s edge.lty) 177s NULL 177s 177s > args(plot.phylo) 177s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 177s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 177s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 177s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 177s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 177s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 177s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 177s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 177s ...) 177s NULL 177s 177s > geo <- factor(c("Africa", "World", "Africa")) 177s 177s > (mycol <- c("blue", "red")[geo]) 177s [1] "blue" "red" "blue" 177s 177s > plot(mytr, tip.color = mycol) 177s 177s > par(xpd = TRUE) 177s 177s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 177s 177s > args(def) 177s function (x, ..., default = NULL, regexp = FALSE) 177s NULL 177s 177s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 177s 177s > identical(mycol, mycol2) 177s [1] TRUE 177s 177s > (i <- which.edge(mytr, c("Homo", "Pan"))) 177s [1] 2 3 177s 177s > co <- rep("black", Nedge(mytr)) 177s 177s > co[i] <- "blue" 177s 177s > par(xpd = TRUE) 177s 177s > plot(mytr, edge.col = co) 177s 177s > edgelabels() 177s 177s > args(axisPhylo) 177s function (side = NULL, root.time = NULL, backward = TRUE, ...) 177s NULL 177s 177s > args(add.scale.bar) 177s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 177s ...) 177s NULL 177s 177s > plot(mytr) 177s 177s > add.scale.bar() 177s 177s > axisPhylo() 177s 177s > axis(3) 177s 177s > args(nodelabels) 177s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 177s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 177s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 177s ...) 177s NULL 177s 177s > args(tiplabels) 177s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 177s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 177s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 177s offset = 0, ...) 177s NULL 177s 177s > args(edgelabels) 177s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 177s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 177s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 177s date = NULL, ...) 177s NULL 177s 177s > par(xpd = TRUE) 177s 177s > plot(mytr) 177s 177s > nodelabels() 177s 177s > tiplabels() 177s 177s > edgelabels() 177s 177s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 177s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 177s 177s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 177s 177s > v <- c(0, 0.5, 1) 177s 177s > layout(matrix(1:9, 3, 3)) 177s 177s > par(mar = c(3, 3, 3, 0), las = 1) 177s 177s > for (i in v) { 177s + for (j in v) { 177s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 177s + ")")) 177s + abline(v = 0, h = .... [TRUNCATED] 177s 177s > plot(rep(0, 3), 0:2, "n", las = 1) 177s 177s > abline(v = 0, h = 0:2, lty = 3) 177s 177s > text(0, 0:2, mytr$tip.label, adj = -1) 177s 177s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 177s 177s > args(phydataplot) 177s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 177s width = NULL, legend = "below", funcol = rainbow, ...) 177s NULL 177s 177s > args(ring) 177s function (x, phy, style = "ring", offset = 1, ...) 177s NULL 177s 177s > x <- matrix(1:6, 3, 10) 177s 177s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 177s 177s > x 177s A B C D E F G H I J 177s Homo 1 4 1 4 1 4 1 4 1 4 177s Gorilla 2 5 2 5 2 5 2 5 2 5 177s Pan 3 6 3 6 3 6 3 6 3 6 177s 177s > mytr$tip.label 177s [1] "Pan" "Homo" "Gorilla" 177s 177s > par(mar = c(10, 2, 5, 5)) 177s 177s > plot(mytr, x.lim = 30) 177s 177s > phydataplot(x, mytr, "m", border = "white", offset = 2, 177s + width = 1) 177s 177s > phydataplot(x, mytr, "m", border = "white", offset = 15, 177s + width = 1, continuous = 2) 177s 177s > n <- 100 177s 177s > p <- 3 177s 177s > set.seed(3) 177s 177s > tr <- rcoal(n) 177s 177s > x <- matrix(runif(p * n), n, p) 177s 177s > rownames(x) <- tr$tip.label 177s 177s > COL <- c("red", "green", "blue") 177s 177s > par(xpd = TRUE) 177s 177s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 177s + no.margin = TRUE) 177s 177s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 177s + col = COL[j]) 177s 177s > tree <- rtree(10) 177s 177s > tree$edge.length[1] <- 1000 177s 177s > layout(matrix(1:2, 1)) 177s 177s > plot(tree) 177s 177s > axisPhylo() 177s 177s > plotBreakLongEdges(tree) 177s 177s > axisPhylo() 177s 177s > el <- tree$edge.length 177s 177s > sum(el > mean(el) + 2 * sd(el)) 177s [1] 1 177s 177s > tree$edge.length[8] <- 1000 177s 177s > el <- tree$edge.length 177s 177s > sum(el > mean(el) + 2 * sd(el)) 177s [1] 2 177s 177s > layout(matrix(1:2, 1)) 177s 177s > plotBreakLongEdges(tree) 177s 177s > plotBreakLongEdges(tree, n = 2) 177s 177s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 177s + simplify = FALSE) 177s 177s > kronoviz(TR, type = "c", show.tip.label = FALSE) 177s 177s > dates <- as.Date(.leap.seconds) 177s 177s > tr <- rcoal(length(dates)) 177s 177s > plotTreeTime(tr, dates) 177s 177s > par(oma = rep(2, 4)) 177s 177s > plot(mytr) 177s 177s > box(lty = 3) 177s 177s > box("figure", col = "blue") 177s 177s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 177s + font = 2, col = "blue") 177s 177s > box("outer") 177s 177s > layout(matrix(1:4, 2, 2)) 177s 177s > par(oma = rep(2, 4)) 177s 177s > for (i in 1:4) { 177s + par(mar = rep(i, 4)) 177s + plot(mytr) 177s + box(lty = 3) 177s + box("figure", col = "blue") 177s + } 177s 177s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 177s + font = 2, col = "blue") 177s 177s > box("outer") 177s 177s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 177s 177s > for (i in 1:3) plot(rtree(5)) 177s 177s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 177s $type 177s [1] "phylogram" 177s 177s $use.edge.length 177s [1] TRUE 177s 177s $node.pos 177s [1] 1 177s 177s $node.depth 177s [1] 1 177s 177s $show.tip.label 177s [1] TRUE 177s 177s $show.node.label 177s [1] FALSE 177s 177s $font 177s [1] 3 177s 177s $cex 177s [1] 0.83 177s 177s $adj 177s [1] 0 177s 177s $srt 177s [1] 0 177s 177s $no.margin 177s [1] FALSE 177s 177s $label.offset 177s [1] 0 177s 177s $x.lim 177s [1] 0.00000 3.13046 177s 177s $y.lim 177s [1] 1 5 177s 177s $direction 177s [1] "rightwards" 177s 177s $tip.color 177s [1] "black" 177s 177s $Ntip 177s [1] 5 177s 177s $Nnode 177s [1] 4 177s 177s $root.time 177s NULL 177s 177s $align.tip.label 177s [1] FALSE 177s 177s $edge 177s [,1] [,2] 177s [1,] 6 1 177s [2,] 6 7 177s [3,] 7 2 177s [4,] 7 8 177s [5,] 8 3 177s [6,] 8 9 177s [7,] 9 4 177s [8,] 9 5 177s 177s $xx 177s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 177s [8] 1.3631198 1.9857132 177s 177s $yy 177s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 177s 177s 177s > layout(matrix(1:2, 2)) 177s 177s > plot(rtree(4)) 177s 177s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 177s 177s > x <- pp$xx[1] 177s 177s > y <- pp$yy[1] 177s 177s > (pu <- par("usr")) 177s [1] -0.06364557 1.65478492 0.88000000 4.12000000 177s 177s > (x - pu[1])/(pu[2] - pu[1]) 177s [1] 0.9349839 177s 177s > (y - pu[3])/(pu[4] - pu[3]) 177s [1] 0.03703704 177s 177s > pi <- par("pin") 177s 177s > mi <- par("mai") 177s 177s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 177s 177s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 177s 177s > plot(rtree(4)) 177s 177s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 177s 177s > x <- pp$xx[5] 177s 177s > y <- pp$yy[5] 177s 177s > pu <- par("usr") 177s 177s > pi <- par("pin") 177s 177s > mi <- par("mai") 177s 177s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 177s 177s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 177s 177s > yi1 <- yi1 + par("fin")[2] 177s 177s > di <- par("din") 177s 177s > layout(1) 177s 177s > par(new = TRUE, mai = rep(0, 4)) 177s 177s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 177s + ylim = 0:1, xaxs = "i", yaxs = "i") 177s 177s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 177s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 177s 177s > foo <- function(phy1, phy2, from) { 177s + layout(matrix(1:2, 2)) 177s + plot(phy1, font = 1) 177s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 177s 177s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 177s 177s > par(xpd = TRUE) 177s 177s > foo(trb, mytr, "Primates") 177s 177s > plot(mytr, plot = FALSE) 177s 177s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 177s 177s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 177s + pp$yy[2] + 0.1, col = "yellow", border = NA) 177s 177s > par(new = TRUE) 177s 177s > plot(mytr) 177s > 177s 177s R version 4.4.3 (2025-02-28) -- "Trophy Case" 177s Copyright (C) 2025 The R Foundation for Statistical Computing 177s Platform: arm-unknown-linux-gnueabihf (32-bit) 177s 177s R is free software and comes with ABSOLUTELY NO WARRANTY. 177s You are welcome to redistribute it under certain conditions. 177s Type 'license()' or 'licence()' for distribution details. 177s 177s R is a collaborative project with many contributors. 177s Type 'contributors()' for more information and 177s 'citation()' on how to cite R or R packages in publications. 177s 177s Type 'demo()' for some demos, 'help()' for on-line help, or 177s 'help.start()' for an HTML browser interface to help. 177s Type 'q()' to quit R. 177s 178s > Stangle("MoranI.Rnw") 178s Writing to file MoranI.R 178s > source("MoranI.R", echo=TRUE) 178s 178s > options(width = 80, prompt = "> ") 178s 178s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 178s 178s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 178s 178s > names(body) <- names(longevity) <- c("Homo", "Pongo", 178s + "Macaca", "Ateles", "Galago") 178s 178s > library(ape) 178s 178s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 178s 178s > trnwk[2] <- ":0.38,Galago:1.00);" 178s 178s > tr <- read.tree(text = trnwk) 178s 178s > plot(tr) 178s 178s > axisPhylo() 178s 178s > w <- 1/cophenetic(tr) 178s 178s > w 178s Homo Pongo Macaca Ateles Galago 178s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 178s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 178s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 178s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 178s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 178s 178s > diag(w) <- 0 178s 178s > Moran.I(body, w) 178s $observed 178s [1] -0.07312179 178s 178s $expected 178s [1] -0.25 178s 178s $sd 178s [1] 0.08910814 178s 178s $p.value 178s [1] 0.04714628 178s 178s 178s > Moran.I(body, w, alt = "greater") 178s $observed 178s [1] -0.07312179 178s 178s $expected 178s [1] -0.25 178s 178s $sd 178s [1] 0.08910814 178s 178s $p.value 178s [1] 0.02357314 178s 178s 178s > Moran.I(longevity, w) 178s $observed 178s [1] -0.1837739 178s 178s $expected 178s [1] -0.25 178s 178s $sd 178s [1] 0.09114549 178s 178s $p.value 178s [1] 0.4674727 178s 178s 178s > data(carnivora) 178s 178s > carnivora$log10SW <- log10(carnivora$SW) 178s 178s > carnivora$log10FW <- log10(carnivora$FW) 178s 178s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 178s 178s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 178s 178s > plot(co1) 178s 178s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 178s 178s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 178s 178s > print(plot(co2)) 178s 178s > plot(co2, FALSE) 178s > 178s 178s R version 4.4.3 (2025-02-28) -- "Trophy Case" 178s Copyright (C) 2025 The R Foundation for Statistical Computing 178s Platform: arm-unknown-linux-gnueabihf (32-bit) 178s 178s R is free software and comes with ABSOLUTELY NO WARRANTY. 178s You are welcome to redistribute it under certain conditions. 178s Type 'license()' or 'licence()' for distribution details. 178s 178s R is a collaborative project with many contributors. 178s Type 'contributors()' for more information and 178s 'citation()' on how to cite R or R packages in publications. 178s 178s Type 'demo()' for some demos, 'help()' for on-line help, or 178s 'help.start()' for an HTML browser interface to help. 178s Type 'q()' to quit R. 178s 178s > Stangle("RandomTopologies.Rnw") 178s Writing to file RandomTopologies.R 179s > source("RandomTopologies.R", echo=TRUE) 179s 179s > options(width = 80, prompt = "> ") 179s 179s > library(ape) 179s 179s > n <- 1:10 179s 179s > data.frame(N.topo = sapply(n, howmanytrees)) 179s N.topo 179s 1 1 179s 2 1 179s 3 3 179s 4 15 179s 5 105 179s 6 945 179s 7 10395 179s 8 135135 179s 9 2027025 179s 10 34459425 179s 179s > howmanytrees(25) 179s [1] 1.192568e+30 179s 179s > howmanytrees(25) * 0.21 179s [1] 2.504393e+29 179s 179s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 179s N.topo 179s 1 1 179s 2 1 179s 3 1 179s 4 2 179s 5 3 179s 6 6 179s 7 11 179s 8 23 179s 9 46 179s 10 98 179s 179s > n2 <- c(50, 100, 200) 179s 179s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 179s + row.names = n2) 179s N.topo 179s 50 5.150149e+16 179s 100 1.019560e+36 179s 200 1.141703e+75 179s 179s > 1/howmanytrees(50) 179s [1] 3.632505e-77 179s 179s > 1/sapply(n, howmanytrees) 179s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 179s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 179s 179s > 1/sapply(n, howmanytrees, labeled = FALSE) 179s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 179s [7] 0.09090909 0.04347826 0.02173913 0.01020408 179s 179s > library(phangorn) 181s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 181s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 181s 181s > TR <- allTrees(4, rooted = TRUE) 181s 181s > TR 181s 15 phylogenetic trees 181s 181s > layout(matrix(1:15, 3, 5)) 181s 181s > par(mar = rep(1.5, 4), xpd = TRUE) 181s 181s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 181s 181s > K <- 100 181s 181s > n <- 50 181s 181s > N <- howmanytrees(n, labeled = FALSE) 181s 181s > p <- 1/N 181s 181s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 181s [1] 0 181s 181s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 181s [1] -5.431212e-17 181s 181s > f <- function(n, K) { 181s + N <- howmanytrees(n, labeled = FALSE) 181s + p <- 1/N 181s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 181s + } 181s 181s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 181s + 10000)) 181s 181s > DF$P <- mapply(f, n = DF$n, K = DF$K) 181s 181s > library(lattice) 181s 181s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 181s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 182s 182s > subset(DF, n == 20) 182s n K P 182s 17 20 2 1.160494e-11 182s 34 20 5 1.160491e-10 182s 51 20 10 5.222149e-10 182s 68 20 100 5.743191e-08 182s 85 20 1000 5.783570e-06 182s 102 20 10000 5.671842e-04 182s 182s > f(20, 1e+05) 182s [1] 0.04638755 182s 182s > f(30, 1e+06) 182s [1] 2.525152e-07 182s 182s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 182s 182s > TR5 <- read.tree(text = txt) 182s 182s > layout(matrix(1:3, 1)) 182s 182s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 182s 182s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 182s + labeled = FALSE) 182s [1] 2 182s 182s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 182s + labeled = FALSE) 182s [1] 1 182s 182s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 182s + labeled = FALSE) 182s [1] Inf 182s 182s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 182s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 182s 182s > foo.test <- function(x, labeled = TRUE) { 182s + uTR <- unique(x, use.tip.label = labeled) 182s + f <- integer(length(uTR)) 182s + for (j in seq_along( .... [TRUNCATED] 182s 182s > lapply(TR, foo.test) 188s [1] 51 79 57 53 57 76 63 68 64 63 78 81 67 64 79 193s [1] 55 53 40 124 119 54 61 102 49 58 41 64 56 69 55 196s [1] 36 148 42 36 164 53 173 39 50 41 48 37 44 45 44 196s [[1]] 196s 196s Chi-squared test for given probabilities 196s 196s data: f 196s X-squared = 20.81, df = 14, p-value = 0.1066 196s 196s 196s [[2]] 196s 196s Chi-squared test for given probabilities 196s 196s data: f 196s X-squared = 147.14, df = 14, p-value < 2.2e-16 196s 196s 196s [[3]] 196s 196s Chi-squared test for given probabilities 196s 196s data: f 196s X-squared = 517.49, df = 14, p-value < 2.2e-16 196s 196s 196s 196s > lapply(TR, foo.test, labeled = FALSE) 197s [1] 805 195 198s [1] 655 345 198s [1] 515 485 198s [[1]] 198s 198s Chi-squared test for given probabilities 198s 198s data: f 198s X-squared = 372.1, df = 1, p-value < 2.2e-16 198s 198s 198s [[2]] 198s 198s Chi-squared test for given probabilities 198s 198s data: f 198s X-squared = 96.1, df = 1, p-value < 2.2e-16 198s 198s 198s [[3]] 198s 198s Chi-squared test for given probabilities 198s 198s data: f 198s X-squared = 0.9, df = 1, p-value = 0.3428 198s 198s 198s 198s > .Machine$double.xmax 198s [1] 1.797693e+308 198s 198s > howmanytrees(151) 198s [1] 3.753274e+306 198s 198s > howmanytrees(792, labeled = FALSE) 198s [1] 1.029038e+308 198s 198s > (N <- howmanytrees(2e+06)) 198s approximately 3.692364 * 10^12335524 198s 198s > N[2] + 1 198s n 198s 12335525 198s 198s > ceiling((N[2] + 1)/3000) 198s n 198s 4112 198s 198s > n <- 1:792 198s 198s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 198s 198s > lN <- log10(N) 198s 198s > summary(lm(lN ~ n)) 198s 198s Call: 198s lm(formula = lN ~ n) 198s 198s Residuals: 198s Min 1Q Median 3Q Max 198s -0.25968 -0.21424 -0.08311 0.12406 2.82605 198s 198s Coefficients: 198s Estimate Std. Error t value Pr(>|t|) 198s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 198s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 198s --- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Residual standard error: 0.3175 on 790 degrees of freedom 198s Multiple R-squared: 1, Adjusted R-squared: 1 198s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 198s 198s 198s > s <- n > 700 198s 198s > summary(lm(lN[s] ~ n[s])) 198s 198s Call: 198s lm(formula = lN[s] ~ n[s]) 198s 198s Residuals: 198s Min 1Q Median 3Q Max 198s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 198s 198s Coefficients: 198s Estimate Std. Error t value Pr(>|t|) 198s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 198s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 198s --- 198s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 198s 198s Residual standard error: 0.0003738 on 90 degrees of freedom 198s Multiple R-squared: 1, Adjusted R-squared: 1 198s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 198s 198s 198s > n <- 788:792 198s 198s > log10(sapply(n, howmanytrees, labeled = FALSE)) 198s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 198s 198s > 0.3941 * n - 4.153 198s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 198s 198s > xi <- 2.477993 198s 198s > lxi <- log10(xi) 198s 198s > n <- 1000 198s 198s > (n - 1) * lxi 198s [1] 393.706 198s 198s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 198s + 1))))) 198s [1] 393.8532 198s [1] 393.9009 198s [1] 393.9187 198s [1] 393.9257 198s [1] 393.9285 198s [1] 393.9296 198s [1] 393.9301 198s [1] 393.9303 198s [1] 393.9304 198s [1] 393.9304 198s > 199s autopkgtest [02:28:37]: test run-unit-test: -----------------------] 203s autopkgtest [02:28:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 203s run-unit-test PASS 206s autopkgtest [02:28:44]: test pkg-r-autopkgtest: preparing testbed 208s Reading package lists... 208s Building dependency tree... 208s Reading state information... 209s Starting pkgProblemResolver with broken count: 0 209s Starting 2 pkgProblemResolver with broken count: 0 209s Done 210s The following NEW packages will be installed: 210s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 210s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-14 g++-14-arm-linux-gnueabihf 210s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 210s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 210s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 210s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-14-dev 210s libgfortran-14-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 210s libjpeg8-dev libjs-jquery liblapack-dev liblzma-dev libmpc3 libncurses-dev 210s libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 210s libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev libubsan1 210s linux-libc-dev node-html5shiv pkg-r-autopkgtest pkgconf pkgconf-bin 210s r-base-dev r-cran-expm r-cran-gee r-cran-xml2 rpcsvc-proto zlib1g-dev 210s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 210s Need to get 79.1 MB of archives. 210s After this operation, 244 MB of additional disk space will be used. 210s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libc-dev-bin armhf 2.41-6ubuntu1 [21.7 kB] 210s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf linux-libc-dev armhf 6.14.0-15.15 [1687 kB] 210s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 210s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 210s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libc6-dev armhf 2.41-6ubuntu1 [1396 kB] 210s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libisl23 armhf 0.27-1 [546 kB] 210s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 210s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9221 kB] 211s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14 armhf 14.2.0-19ubuntu2 [1032 B] 211s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 211s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 211s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libcc1-0 armhf 15-20250404-0ubuntu1 [43.3 kB] 211s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libasan8 armhf 15-20250404-0ubuntu1 [2951 kB] 211s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libubsan1 armhf 15-20250404-0ubuntu1 [1188 kB] 211s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libgcc-14-dev armhf 14.2.0-19ubuntu2 [897 kB] 211s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [18.0 MB] 211s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14 armhf 14.2.0-19ubuntu2 [510 kB] 211s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 211s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 211s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libstdc++-14-dev armhf 14.2.0-19ubuntu2 [2576 kB] 211s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [10.5 MB] 212s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf g++-14 armhf 14.2.0-19ubuntu2 [23.0 kB] 212s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 212s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 212s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf build-essential armhf 12.12ubuntu1 [5088 B] 212s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 212s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran-14-dev armhf 14.2.0-19ubuntu2 [370 kB] 212s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9763 kB] 212s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14 armhf 14.2.0-19ubuntu2 [14.2 kB] 212s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 212s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 212s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 212s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 212s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 212s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 212s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 212s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 212s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 212s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 212s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 212s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 212s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 212s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 212s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 212s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 212s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 212s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 212s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 212s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf libpng-dev armhf 1.6.47-1.1 [251 kB] 212s Get:50 http://ftpmaster.internal/ubuntu questing/main armhf libreadline-dev armhf 8.2-6 [153 kB] 212s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 212s Get:52 http://ftpmaster.internal/ubuntu questing/main armhf liblzma-dev armhf 5.6.4-1ubuntu1 [166 kB] 212s Get:53 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 212s Get:54 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 212s Get:55 http://ftpmaster.internal/ubuntu questing/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 212s Get:56 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-dev all 4.4.3-1 [4176 B] 212s Get:57 http://ftpmaster.internal/ubuntu questing/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 212s Get:58 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-expm armhf 1.0-0-1 [223 kB] 212s Get:59 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-gee armhf 4.13-29-1 [71.1 kB] 212s Get:60 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-xml2 armhf 1.3.8-1 [324 kB] 213s Fetched 79.1 MB in 3s (29.7 MB/s) 213s Selecting previously unselected package libc-dev-bin. 213s (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 ... 69022 files and directories currently installed.) 213s Preparing to unpack .../00-libc-dev-bin_2.41-6ubuntu1_armhf.deb ... 213s Unpacking libc-dev-bin (2.41-6ubuntu1) ... 213s Selecting previously unselected package linux-libc-dev:armhf. 213s Preparing to unpack .../01-linux-libc-dev_6.14.0-15.15_armhf.deb ... 213s Unpacking linux-libc-dev:armhf (6.14.0-15.15) ... 213s Selecting previously unselected package libcrypt-dev:armhf. 213s Preparing to unpack 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cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 214s Selecting previously unselected package cpp-14. 214s Preparing to unpack .../08-cpp-14_14.2.0-19ubuntu2_armhf.deb ... 214s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 214s Selecting previously unselected package cpp-arm-linux-gnueabihf. 214s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 214s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 214s Selecting previously unselected package cpp. 214s Preparing to unpack .../10-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 214s Unpacking cpp (4:14.2.0-1ubuntu1) ... 214s Selecting previously unselected package libcc1-0:armhf. 214s Preparing to unpack .../11-libcc1-0_15-20250404-0ubuntu1_armhf.deb ... 214s Unpacking libcc1-0:armhf (15-20250404-0ubuntu1) ... 214s Selecting previously unselected package libasan8:armhf. 214s Preparing to unpack .../12-libasan8_15-20250404-0ubuntu1_armhf.deb ... 214s Unpacking libasan8:armhf (15-20250404-0ubuntu1) ... 214s Selecting previously unselected package libubsan1:armhf. 214s Preparing to unpack .../13-libubsan1_15-20250404-0ubuntu1_armhf.deb ... 214s Unpacking libubsan1:armhf (15-20250404-0ubuntu1) ... 214s Selecting previously unselected package libgcc-14-dev:armhf. 214s Preparing to unpack .../14-libgcc-14-dev_14.2.0-19ubuntu2_armhf.deb ... 214s Unpacking libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 215s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 215s Preparing to unpack .../15-gcc-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 215s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 215s Selecting previously unselected package gcc-14. 215s Preparing to unpack .../16-gcc-14_14.2.0-19ubuntu2_armhf.deb ... 215s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 215s Selecting previously unselected package gcc-arm-linux-gnueabihf. 215s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 215s Unpacking gcc-arm-linux-gnueabihf 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(4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package g++. 216s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 216s Unpacking g++ (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package build-essential. 216s Preparing to unpack .../24-build-essential_12.12ubuntu1_armhf.deb ... 216s Unpacking build-essential (12.12ubuntu1) ... 216s Selecting previously unselected package dctrl-tools. 216s Preparing to unpack .../25-dctrl-tools_2.24-3build3_armhf.deb ... 216s Unpacking dctrl-tools (2.24-3build3) ... 216s Selecting previously unselected package libgfortran-14-dev:armhf. 216s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-19ubuntu2_armhf.deb ... 216s Unpacking libgfortran-14-dev:armhf (14.2.0-19ubuntu2) ... 216s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 216s Preparing to unpack .../27-gfortran-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 216s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 217s Selecting previously unselected package gfortran-14. 217s Preparing to unpack .../28-gfortran-14_14.2.0-19ubuntu2_armhf.deb ... 217s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 217s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 217s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 217s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 217s Selecting previously unselected package gfortran. 217s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 217s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 217s Selecting previously unselected package icu-devtools. 217s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_armhf.deb ... 217s Unpacking icu-devtools (76.1-1ubuntu2) ... 217s Selecting previously unselected package libblas-dev:armhf. 217s Preparing to unpack .../32-libblas-dev_3.12.1-2_armhf.deb ... 217s Unpacking libblas-dev:armhf (3.12.1-2) ... 217s Selecting previously unselected package libbz2-dev:armhf. 217s Preparing to unpack .../33-libbz2-dev_1.0.8-6_armhf.deb ... 217s Unpacking libbz2-dev:armhf (1.0.8-6) ... 217s Selecting previously unselected package libdeflate-dev:armhf. 217s Preparing to unpack .../34-libdeflate-dev_1.23-1_armhf.deb ... 217s Unpacking libdeflate-dev:armhf (1.23-1) ... 217s Selecting previously unselected package libicu-dev:armhf. 217s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_armhf.deb ... 217s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 218s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 218s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 218s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 218s Selecting previously unselected package libjpeg8-dev:armhf. 218s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 218s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 218s Selecting previously unselected package libjpeg-dev:armhf. 218s 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Unpacking libpng-dev:armhf (1.6.47-1.1) ... 219s Selecting previously unselected package libreadline-dev:armhf. 219s Preparing to unpack .../49-libreadline-dev_8.2-6_armhf.deb ... 219s Unpacking libreadline-dev:armhf (8.2-6) ... 219s Selecting previously unselected package node-html5shiv. 219s Preparing to unpack .../50-node-html5shiv_3.7.3+dfsg-5_all.deb ... 219s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 219s Selecting previously unselected package liblzma-dev:armhf. 219s Preparing to unpack .../51-liblzma-dev_5.6.4-1ubuntu1_armhf.deb ... 219s Unpacking liblzma-dev:armhf (5.6.4-1ubuntu1) ... 219s Selecting previously unselected package pkgconf-bin. 219s Preparing to unpack .../52-pkgconf-bin_1.8.1-4_armhf.deb ... 219s Unpacking pkgconf-bin (1.8.1-4) ... 219s Selecting previously unselected package pkgconf:armhf. 219s Preparing to unpack .../53-pkgconf_1.8.1-4_armhf.deb ... 219s Unpacking pkgconf:armhf (1.8.1-4) ... 219s Selecting previously unselected package libtirpc-dev:armhf. 219s Preparing to unpack .../54-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 219s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 219s Selecting previously unselected package r-base-dev. 219s Preparing to unpack .../55-r-base-dev_4.4.3-1_all.deb ... 219s Unpacking r-base-dev (4.4.3-1) ... 219s Selecting previously unselected package pkg-r-autopkgtest. 219s Preparing to unpack .../56-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 219s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 219s Selecting previously unselected package r-cran-expm. 219s Preparing to unpack .../57-r-cran-expm_1.0-0-1_armhf.deb ... 219s Unpacking r-cran-expm (1.0-0-1) ... 219s Selecting previously unselected package r-cran-gee. 219s Preparing to unpack .../58-r-cran-gee_4.13-29-1_armhf.deb ... 219s Unpacking r-cran-gee (4.13-29-1) ... 219s Selecting previously unselected package r-cran-xml2. 219s Preparing to unpack .../59-r-cran-xml2_1.3.8-1_armhf.deb ... 219s Unpacking r-cran-xml2 (1.3.8-1) ... 219s Setting up node-html5shiv (3.7.3+dfsg-5) ... 219s Setting up linux-libc-dev:armhf (6.14.0-15.15) ... 219s Setting up r-cran-expm (1.0-0-1) ... 219s Setting up libpcre2-16-0:armhf (10.45-1) ... 219s Setting up libpcre2-32-0:armhf (10.45-1) ... 219s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 219s Setting up libpkgconf3:armhf (1.8.1-4) ... 219s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 219s Setting up libmpc3:armhf (1.3.1-1build2) ... 219s Setting up icu-devtools (76.1-1ubuntu2) ... 219s Setting up pkgconf-bin (1.8.1-4) ... 219s Setting up liblzma-dev:armhf (5.6.4-1ubuntu1) ... 219s Setting up libubsan1:armhf (15-20250404-0ubuntu1) ... 219s Setting up libpcre2-posix3:armhf (10.45-1) ... 219s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 219s Setting up libasan8:armhf (15-20250404-0ubuntu1) ... 219s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 220s Setting up libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 220s Setting up r-cran-gee (4.13-29-1) ... 220s Setting up libisl23:armhf (0.27-1) ... 220s Setting up libc-dev-bin (2.41-6ubuntu1) ... 220s Setting up libdeflate-dev:armhf (1.23-1) ... 220s Setting up libcc1-0:armhf (15-20250404-0ubuntu1) ... 220s Setting up libblas-dev:armhf (3.12.1-2) ... 220s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 220s Setting up dctrl-tools (2.24-3build3) ... 220s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 220s Setting up libgfortran-14-dev:armhf (14.2.0-19ubuntu2) ... 220s Setting up r-cran-xml2 (1.3.8-1) ... 220s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 220s Setting up pkgconf:armhf (1.8.1-4) ... 220s Setting up liblapack-dev:armhf (3.12.1-2) ... 220s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 220s Setting up cpp-14 (14.2.0-19ubuntu2) ... 220s Setting up libc6-dev:armhf (2.41-6ubuntu1) ... 220s Setting up libstdc++-14-dev:armhf (14.2.0-19ubuntu2) ... 220s Setting up libicu-dev:armhf (76.1-1ubuntu2) ... 220s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 220s Setting up gfortran-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 220s Setting up libbz2-dev:armhf (1.0.8-6) ... 220s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 220s Setting up g++-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 220s Setting up libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 220s Setting up libncurses-dev:armhf (6.5+20250216-2) ... 220s Setting up libpcre2-dev:armhf (10.45-1) ... 220s Setting up libreadline-dev:armhf (8.2-6) ... 220s Setting up gcc-14 (14.2.0-19ubuntu2) ... 220s Setting up gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 220s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 220s Setting up cpp (4:14.2.0-1ubuntu1) ... 220s Setting up g++-14 (14.2.0-19ubuntu2) ... 220s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 220s Setting up gfortran-14 (14.2.0-19ubuntu2) ... 220s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 220s Setting up libpng-dev:armhf (1.6.47-1.1) ... 220s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 220s Setting up gcc (4:14.2.0-1ubuntu1) ... 220s Setting up g++ (4:14.2.0-1ubuntu1) ... 220s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 220s Setting up build-essential (12.12ubuntu1) ... 220s Setting up gfortran (4:14.2.0-1ubuntu1) ... 220s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 220s 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 220s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 220s 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 220s Setting up r-base-dev (4.4.3-1) ... 220s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 220s Processing triggers for libc-bin (2.41-6ubuntu1) ... 220s Processing triggers for man-db (2.13.0-1) ... 221s Processing triggers for install-info (7.1.1-1) ... 228s autopkgtest [02:29:06]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 228s autopkgtest [02:29:06]: test pkg-r-autopkgtest: [----------------------- 230s Test: Try to load the R library ape 230s 230s R version 4.4.3 (2025-02-28) -- "Trophy Case" 230s Copyright (C) 2025 The R Foundation for Statistical Computing 230s Platform: arm-unknown-linux-gnueabihf (32-bit) 230s 230s R is free software and comes with ABSOLUTELY NO WARRANTY. 230s You are welcome to redistribute it under certain conditions. 230s Type 'license()' or 'licence()' for distribution details. 230s 230s R is a collaborative project with many contributors. 230s Type 'contributors()' for more information and 230s 'citation()' on how to cite R or R packages in publications. 230s 230s Type 'demo()' for some demos, 'help()' for on-line help, or 230s 'help.start()' for an HTML browser interface to help. 230s Type 'q()' to quit R. 230s 231s > library('ape') 231s > 231s > 231s Other tests are currently unsupported! 231s They will be progressively added. 231s autopkgtest [02:29:09]: test pkg-r-autopkgtest: -----------------------] 235s pkg-r-autopkgtest PASS 235s autopkgtest [02:29:13]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 239s autopkgtest [02:29:17]: @@@@@@@@@@@@@@@@@@@@ summary 239s run-unit-test PASS 239s pkg-r-autopkgtest PASS