0s autopkgtest [23:11:48]: starting date and time: 2026-02-09 23:11:48+0000 0s autopkgtest [23:11:48]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:11:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tqeso5rt/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:lattice --apt-upgrade r-cran-ape --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- lxd -r lxd-armhf-10.145.243.254 lxd-armhf-10.145.243.254:autopkgtest/ubuntu/resolute/armhf 22s autopkgtest [23:12:10]: testbed dpkg architecture: armhf 24s autopkgtest [23:12:12]: testbed apt version: 3.1.15 28s autopkgtest [23:12:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [23:12:18]: testbed release detected to be: None 38s autopkgtest [23:12:26]: updating testbed package index (apt update) 40s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 40s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 40s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 41s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 41s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 43s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 44s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 44s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 44s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 46s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 46s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 48s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 75s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 96s Fetched 43.5 MB in 56s (778 kB/s) 97s Reading package lists... 103s autopkgtest [23:13:31]: upgrading testbed (apt dist-upgrade and autopurge) 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 107s The following packages will be upgraded: 107s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 107s libip6tc2 libxtables12 wget 108s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 2407 kB of archives. 108s After this operation, 152 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 108s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 108s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 108s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 110s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 110s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 111s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 111s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 112s Preconfiguring packages ... 112s Fetched 2407 kB in 4s (605 kB/s) 112s (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 ... 68683 files and directories currently installed.) 112s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 112s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 112s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 112s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 112s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 112s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 112s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 112s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 112s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 113s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 113s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 113s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 113s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 113s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 113s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 113s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 113s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 113s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 113s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 113s Setting up wget (1.25.0-2ubuntu4) ... 113s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 113s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 113s Setting up dracut-install (109-11ubuntu1) ... 113s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 113s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 113s Setting up iptables (1.8.11-2ubuntu3) ... 113s Setting up iproute2 (6.18.0-1ubuntu1) ... 113s Processing triggers for man-db (2.13.1-1build1) ... 115s Processing triggers for install-info (7.2-5) ... 115s Processing triggers for libc-bin (2.42-2ubuntu4) ... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Solving dependencies... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [23:13:49]: rebooting testbed after setup commands that affected boot 164s autopkgtest [23:14:32]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 190s autopkgtest [23:14:58]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 203s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 203s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 203s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 203s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 203s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 203s gpgv: issuer "plessy@debian.org" 203s gpgv: Can't check signature: No public key 203s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 204s autopkgtest [23:15:12]: testing package r-cran-ape version 5.8-1-1 206s autopkgtest [23:15:14]: build not needed 211s autopkgtest [23:15:19]: test run-unit-test: preparing testbed 213s Reading package lists... 213s Building dependency tree... 213s Reading state information... 214s Solving dependencies... 215s The following NEW packages will be installed: 215s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 215s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 215s libfreetype6 libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b 215s libice6 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 215s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 215s libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 215s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 215s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-ape r-cran-cli 215s r-cran-cpp11 r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue 215s r-cran-igraph r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr 215s r-cran-matrix r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 215s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 215s xdg-utils zip 215s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 63.7 MB of archives. 215s After this operation, 114 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 215s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 216s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 217s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 217s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 218s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 218s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 218s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libsuitesparseconfig7 armhf 1:7.12.1+dfsg-1 [21.4 kB] 218s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libamd3 armhf 1:7.12.1+dfsg-1 [37.5 kB] 218s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 218s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 219s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 219s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 219s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 219s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 219s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libcolamd3 armhf 1:7.12.1+dfsg-1 [28.2 kB] 221s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 221s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 221s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 221s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libltdl7 armhf 2.5.4-9 [40.4 kB] 221s Get:21 http://ftpmaster.internal/ubuntu resolute/universe armhf libglpk40 armhf 5.0-2 [325 kB] 221s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 221s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 221s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 221s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 221s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 222s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 222s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 225s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 226s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 226s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 226s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 226s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 226s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 226s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 226s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 226s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 226s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 226s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 228s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 228s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 228s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 228s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 228s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 228s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 229s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 229s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 230s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 230s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 230s Get:50 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 255s Get:51 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-lattice armhf 0.22-9-1 [1399 kB] 256s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 258s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-littler armhf 0.3.22-1 [81.0 kB] 259s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 259s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rcpp armhf 1.1.0-1 [2009 kB] 262s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-digest armhf 0.6.39-1 [211 kB] 262s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-ape armhf 5.8-1-1 [2891 kB] 267s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cli armhf 3.6.4-1 [1377 kB] 268s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cpp11 all 0.5.3-1 [242 kB] 269s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-fastmatch armhf 1.1-6-1 [34.2 kB] 269s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-generics all 0.1.4-1 [84.0 kB] 269s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-glue armhf 1.8.0-1 [162 kB] 269s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-rlang armhf 1.1.5-3 [1700 kB] 271s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 271s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-magrittr armhf 2.0.3-1 [154 kB] 271s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 277s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 277s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vctrs armhf 0.6.5-1 [1310 kB] 279s Get:69 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-igraph armhf 2.1.4-1build1 [5220 kB] 287s Get:70 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-quadprog armhf 1.5-8-1build2 [29.8 kB] 287s Get:71 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-phangorn armhf 2.12.1+dfsg-1 [1797 kB] 290s Preconfiguring packages ... 290s Fetched 63.7 MB in 1min 14s (857 kB/s) 290s Selecting previously unselected package libfreetype6:armhf. 290s (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 ... 68686 files and directories currently installed.) 290s Preparing to unpack .../00-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 290s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 290s Selecting previously unselected package fonts-dejavu-mono. 290s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8build1_all.deb ... 290s Unpacking fonts-dejavu-mono (2.37-8build1) ... 290s Selecting previously unselected package fonts-dejavu-core. 290s Preparing to unpack .../02-fonts-dejavu-core_2.37-8build1_all.deb ... 290s Unpacking fonts-dejavu-core (2.37-8build1) ... 290s Selecting previously unselected package fontconfig-config. 290s Preparing to unpack .../03-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 291s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 291s Selecting previously unselected package libfontconfig1:armhf. 291s Preparing to unpack .../04-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 291s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 291s Selecting previously unselected package fontconfig. 291s Preparing to unpack .../05-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 291s Unpacking fontconfig (2.17.1-3ubuntu1) ... 291s Selecting previously unselected package libgomp1:armhf. 291s Preparing to unpack .../06-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 291s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 291s Selecting previously unselected package libsuitesparseconfig7:armhf. 291s Preparing to unpack .../07-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_armhf.deb ... 291s Unpacking libsuitesparseconfig7:armhf (1:7.12.1+dfsg-1) ... 291s Selecting previously unselected package libamd3:armhf. 291s Preparing to unpack .../08-libamd3_1%3a7.12.1+dfsg-1_armhf.deb ... 291s Unpacking libamd3:armhf (1:7.12.1+dfsg-1) ... 291s Selecting previously unselected package libblas3:armhf. 291s Preparing to unpack .../09-libblas3_3.12.1-7ubuntu1_armhf.deb ... 291s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 291s Selecting previously unselected package libpixman-1-0:armhf. 291s Preparing to unpack .../10-libpixman-1-0_0.46.4-1_armhf.deb ... 291s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 291s Selecting previously unselected package libxcb-render0:armhf. 291s Preparing to unpack .../11-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 291s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 291s Selecting previously unselected package libxcb-shm0:armhf. 291s Preparing to unpack .../12-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 291s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 291s Selecting previously unselected package libxrender1:armhf. 291s Preparing to unpack .../13-libxrender1_1%3a0.9.12-1_armhf.deb ... 291s Unpacking libxrender1:armhf (1:0.9.12-1) ... 291s Selecting previously unselected package libcairo2:armhf. 291s Preparing to unpack .../14-libcairo2_1.18.4-3_armhf.deb ... 291s Unpacking libcairo2:armhf (1.18.4-3) ... 291s Selecting previously unselected package libcolamd3:armhf. 291s Preparing to unpack .../15-libcolamd3_1%3a7.12.1+dfsg-1_armhf.deb ... 291s Unpacking libcolamd3:armhf (1:7.12.1+dfsg-1) ... 291s Selecting previously unselected package libdatrie1:armhf. 291s Preparing to unpack .../16-libdatrie1_0.2.14-1_armhf.deb ... 291s Unpacking libdatrie1:armhf (0.2.14-1) ... 291s Selecting previously unselected package libdeflate0:armhf. 291s Preparing to unpack .../17-libdeflate0_1.23-2build1_armhf.deb ... 291s Unpacking libdeflate0:armhf (1.23-2build1) ... 291s Selecting previously unselected package libgfortran5:armhf. 291s Preparing to unpack .../18-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 291s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 291s Selecting previously unselected package libltdl7:armhf. 291s Preparing to unpack .../19-libltdl7_2.5.4-9_armhf.deb ... 291s Unpacking libltdl7:armhf (2.5.4-9) ... 291s Selecting previously unselected package libglpk40:armhf. 292s Preparing to unpack .../20-libglpk40_5.0-2_armhf.deb ... 292s Unpacking libglpk40:armhf (5.0-2) ... 292s Selecting previously unselected package libgraphite2-3:armhf. 292s Preparing to unpack .../21-libgraphite2-3_1.3.14-11ubuntu1_armhf.deb ... 292s Unpacking libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 292s Selecting previously unselected package libharfbuzz0b:armhf. 292s Preparing to unpack .../22-libharfbuzz0b_12.3.2-1_armhf.deb ... 292s Unpacking libharfbuzz0b:armhf (12.3.2-1) ... 292s Selecting previously unselected package x11-common. 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.../28-liblerc4_4.0.0+ds-5ubuntu2_armhf.deb ... 292s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 292s Selecting previously unselected package libthai-data. 292s Preparing to unpack .../29-libthai-data_0.1.30-1_all.deb ... 292s Unpacking libthai-data (0.1.30-1) ... 292s Selecting previously unselected package libthai0:armhf. 292s Preparing to unpack .../30-libthai0_0.1.30-1_armhf.deb ... 292s Unpacking libthai0:armhf (0.1.30-1) ... 292s Selecting previously unselected package libpango-1.0-0:armhf. 292s Preparing to unpack .../31-libpango-1.0-0_1.57.0-1_armhf.deb ... 292s Unpacking libpango-1.0-0:armhf (1.57.0-1) ... 292s Selecting previously unselected package libpangoft2-1.0-0:armhf. 292s Preparing to unpack .../32-libpangoft2-1.0-0_1.57.0-1_armhf.deb ... 292s Unpacking libpangoft2-1.0-0:armhf (1.57.0-1) ... 292s Selecting previously unselected package libpangocairo-1.0-0:armhf. 292s Preparing to unpack .../33-libpangocairo-1.0-0_1.57.0-1_armhf.deb ... 292s Unpacking libpangocairo-1.0-0:armhf (1.57.0-1) ... 292s Selecting previously unselected package libpaper2:armhf. 292s Preparing to unpack .../34-libpaper2_2.2.5-0.3build1_armhf.deb ... 292s Unpacking libpaper2:armhf (2.2.5-0.3build1) ... 292s Selecting previously unselected package libpaper-utils. 292s Preparing to unpack .../35-libpaper-utils_2.2.5-0.3build1_armhf.deb ... 292s Unpacking libpaper-utils (2.2.5-0.3build1) ... 292s Selecting previously unselected package libsharpyuv0:armhf. 292s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1build1_armhf.deb ... 292s Unpacking libsharpyuv0:armhf (1.5.0-0.1build1) ... 293s Selecting previously unselected package libsm6:armhf. 293s Preparing to unpack .../37-libsm6_2%3a1.2.6-1build1_armhf.deb ... 293s Unpacking libsm6:armhf (2:1.2.6-1build1) ... 293s Selecting previously unselected package libtcl8.6:armhf. 293s Preparing to unpack .../38-libtcl8.6_8.6.17+dfsg-1build1_armhf.deb ... 293s Unpacking libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 293s Selecting previously unselected package libjbig0:armhf. 293s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu3_armhf.deb ... 293s Unpacking libjbig0:armhf (2.1-6.1ubuntu3) ... 293s Selecting previously unselected package libwebp7:armhf. 293s Preparing to unpack .../40-libwebp7_1.5.0-0.1build1_armhf.deb ... 293s Unpacking libwebp7:armhf (1.5.0-0.1build1) ... 293s Selecting previously unselected package libtiff6:armhf. 293s Preparing to unpack .../41-libtiff6_4.7.0-3ubuntu3_armhf.deb ... 293s Unpacking libtiff6:armhf (4.7.0-3ubuntu3) ... 293s Selecting previously unselected package libxft2:armhf. 293s Preparing to unpack .../42-libxft2_2.3.6-1build2_armhf.deb ... 293s Unpacking libxft2:armhf (2.3.6-1build2) ... 293s Selecting previously unselected package libxss1:armhf. 293s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build4_armhf.deb ... 293s Unpacking libxss1:armhf (1:1.2.3-1build4) ... 293s Selecting previously unselected package libtk8.6:armhf. 293s Preparing to unpack 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Preparing to unpack .../50-r-cran-lattice_0.22-9-1_armhf.deb ... 294s Unpacking r-cran-lattice (0.22-9-1) ... 294s Selecting previously unselected package r-cran-nlme. 294s Preparing to unpack .../51-r-cran-nlme_3.1.168-1_armhf.deb ... 294s Unpacking r-cran-nlme (3.1.168-1) ... 294s Selecting previously unselected package r-cran-littler. 294s Preparing to unpack .../52-r-cran-littler_0.3.22-1_armhf.deb ... 294s Unpacking r-cran-littler (0.3.22-1) ... 294s Selecting previously unselected package r-cran-pkgkitten. 294s Preparing to unpack .../53-r-cran-pkgkitten_0.2.4-1_all.deb ... 294s Unpacking r-cran-pkgkitten (0.2.4-1) ... 294s Selecting previously unselected package r-cran-rcpp. 294s Preparing to unpack .../54-r-cran-rcpp_1.1.0-1_armhf.deb ... 294s Unpacking r-cran-rcpp (1.1.0-1) ... 294s Selecting previously unselected package r-cran-digest. 294s Preparing to unpack .../55-r-cran-digest_0.6.39-1_armhf.deb ... 294s Unpacking r-cran-digest (0.6.39-1) ... 294s Selecting previously unselected package r-cran-ape. 294s Preparing to unpack .../56-r-cran-ape_5.8-1-1_armhf.deb ... 294s Unpacking r-cran-ape (5.8-1-1) ... 294s Selecting previously unselected package r-cran-cli. 294s Preparing to unpack .../57-r-cran-cli_3.6.4-1_armhf.deb ... 294s Unpacking r-cran-cli (3.6.4-1) ... 294s Selecting previously unselected package r-cran-cpp11. 294s Preparing to unpack .../58-r-cran-cpp11_0.5.3-1_all.deb ... 294s Unpacking r-cran-cpp11 (0.5.3-1) ... 294s Selecting previously unselected package r-cran-fastmatch. 294s Preparing to unpack .../59-r-cran-fastmatch_1.1-6-1_armhf.deb ... 294s Unpacking r-cran-fastmatch (1.1-6-1) ... 295s Selecting previously unselected package r-cran-generics. 295s Preparing to unpack .../60-r-cran-generics_0.1.4-1_all.deb ... 295s Unpacking r-cran-generics (0.1.4-1) ... 295s Selecting previously unselected package r-cran-glue. 295s Preparing to unpack .../61-r-cran-glue_1.8.0-1_armhf.deb ... 295s Unpacking r-cran-glue (1.8.0-1) ... 295s Selecting previously unselected package r-cran-rlang. 295s Preparing to unpack .../62-r-cran-rlang_1.1.5-3_armhf.deb ... 295s Unpacking r-cran-rlang (1.1.5-3) ... 295s Selecting previously unselected package r-cran-lifecycle. 295s Preparing to unpack .../63-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 295s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 295s Selecting previously unselected package r-cran-magrittr. 295s Preparing to unpack .../64-r-cran-magrittr_2.0.3-1_armhf.deb ... 295s Unpacking r-cran-magrittr (2.0.3-1) ... 295s Selecting previously unselected package r-cran-matrix. 295s Preparing to unpack .../65-r-cran-matrix_1.7-4-1_armhf.deb ... 295s Unpacking r-cran-matrix (1.7-4-1) ... 295s Selecting previously unselected package r-cran-pkgconfig. 295s Preparing to unpack .../66-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 295s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 295s Selecting previously unselected package r-cran-vctrs. 295s Preparing to unpack .../67-r-cran-vctrs_0.6.5-1_armhf.deb ... 295s Unpacking r-cran-vctrs (0.6.5-1) ... 295s Selecting previously unselected package r-cran-igraph. 295s Preparing to unpack .../68-r-cran-igraph_2.1.4-1build1_armhf.deb ... 295s Unpacking r-cran-igraph (2.1.4-1build1) ... 295s Selecting previously unselected package r-cran-quadprog. 295s Preparing to unpack .../69-r-cran-quadprog_1.5-8-1build2_armhf.deb ... 295s Unpacking r-cran-quadprog (1.5-8-1build2) ... 295s Selecting previously unselected package r-cran-phangorn. 295s Preparing to unpack .../70-r-cran-phangorn_2.12.1+dfsg-1_armhf.deb ... 295s Unpacking r-cran-phangorn (2.12.1+dfsg-1) ... 295s Setting up libgraphite2-3:armhf (1.3.14-11ubuntu1) ... 295s Setting up libpixman-1-0:armhf (0.46.4-1) ... 295s Setting up libsharpyuv0:armhf (1.5.0-0.1build1) ... 295s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu2) ... 295s Setting up libxrender1:armhf (1:0.9.12-1) ... 295s Setting up libdatrie1:armhf (0.2.14-1) ... 295s Setting up libxcb-render0:armhf (1.17.0-2ubuntu1) ... 295s Setting up unzip (6.0-29ubuntu1) ... 295s Setting up x11-common (1:7.7+24ubuntu1) ... 296s Setting up libdeflate0:armhf (1.23-2build1) ... 296s Setting up libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 296s Setting up libgomp1:armhf (15.2.0-12ubuntu1) ... 296s Setting up libjbig0:armhf (2.1-6.1ubuntu3) ... 296s Setting up zip (3.0-15ubuntu3) ... 296s Setting up libblas3:armhf (3.12.1-7ubuntu1) ... 296s 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 296s Setting up libfreetype6:armhf (2.14.1+dfsg-2) ... 296s Setting up fonts-dejavu-mono (2.37-8build1) ... 296s Setting up libtcl8.6:armhf (8.6.17+dfsg-1build1) ... 296s Setting up fonts-dejavu-core (2.37-8build1) ... 296s Setting up libjpeg-turbo8:armhf (2.1.5-4ubuntu3) ... 296s Setting up libltdl7:armhf (2.5.4-9) ... 296s Setting up libgfortran5:armhf (15.2.0-12ubuntu1) ... 296s Setting up libwebp7:armhf (1.5.0-0.1build1) ... 296s Setting up libsuitesparseconfig7:armhf (1:7.12.1+dfsg-1) ... 296s Setting up libharfbuzz0b:armhf (12.3.2-1) ... 296s Setting up libthai-data (0.1.30-1) ... 296s Setting up libxss1:armhf (1:1.2.3-1build4) ... 296s Setting up libpaper2:armhf (2.2.5-0.3build1) ... 296s Setting up xdg-utils (1.2.1-2ubuntu2) ... 296s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 296s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 296s Setting up libice6:armhf (2:1.1.1-1build1) ... 296s Setting up liblapack3:armhf (3.12.1-7ubuntu1) ... 296s 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 296s Setting up libamd3:armhf (1:7.12.1+dfsg-1) ... 296s Setting up libcolamd3:armhf (1:7.12.1+dfsg-1) ... 296s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 296s Setting up libpaper-utils (2.2.5-0.3build1) ... 296s Setting up libthai0:armhf (0.1.30-1) ... 296s Setting up libglpk40:armhf (5.0-2) ... 296s Setting up libtiff6:armhf (4.7.0-3ubuntu3) ... 296s Setting up libfontconfig1:armhf (2.17.1-3ubuntu1) ... 296s Setting up libsm6:armhf (2:1.2.6-1build1) ... 296s Setting up fontconfig (2.17.1-3ubuntu1) ... 298s Regenerating fonts cache... done. 298s Setting up libxft2:armhf (2.3.6-1build2) ... 298s Setting up libtk8.6:armhf (8.6.17-1) ... 298s Setting up libpango-1.0-0:armhf (1.57.0-1) ... 298s Setting up libcairo2:armhf (1.18.4-3) ... 298s Setting up libxt6t64:armhf (1:1.2.1-1.3) ... 298s Setting up libpangoft2-1.0-0:armhf (1.57.0-1) ... 298s Setting up libpangocairo-1.0-0:armhf (1.57.0-1) ... 298s Setting up r-base-core (4.5.2-1ubuntu2) ... 299s Creating config file /etc/R/Renviron with new version 299s Setting up r-cran-fastmatch (1.1-6-1) ... 299s Setting up r-cran-lattice (0.22-9-1) ... 299s Setting up r-cran-nlme (3.1.168-1) ... 299s Setting up r-cran-pkgkitten (0.2.4-1) ... 299s Setting up r-cran-magrittr (2.0.3-1) ... 299s Setting up r-cran-quadprog (1.5-8-1build2) ... 299s Setting up r-cran-littler (0.3.22-1) ... 299s Setting up r-cran-rcpp (1.1.0-1) ... 299s Setting up r-cran-rlang (1.1.5-3) ... 299s Setting up r-cran-generics (0.1.4-1) ... 299s Setting up r-cran-digest (0.6.39-1) ... 299s Setting up r-cran-ape (5.8-1-1) ... 299s Setting up r-cran-glue (1.8.0-1) ... 299s Setting up r-cran-cli (3.6.4-1) ... 299s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 299s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 299s Setting up r-cran-cpp11 (0.5.3-1) ... 299s Setting up r-cran-matrix (1.7-4-1) ... 299s Setting up r-cran-vctrs (0.6.5-1) ... 299s Setting up r-cran-igraph (2.1.4-1build1) ... 299s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 299s Processing triggers for libc-bin (2.42-2ubuntu4) ... 299s Processing triggers for man-db (2.13.1-1build1) ... 300s Processing triggers for install-info (7.2-5) ... 308s autopkgtest [23:16:56]: test run-unit-test: [----------------------- 310s 310s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 310s Copyright (C) 2025 The R Foundation for Statistical Computing 310s Platform: arm-unknown-linux-gnueabihf (32-bit) 310s 310s R is free software and comes with ABSOLUTELY NO WARRANTY. 310s You are welcome to redistribute it under certain conditions. 310s Type 'license()' or 'licence()' for distribution details. 310s 310s R is a collaborative project with many contributors. 310s Type 'contributors()' for more information and 310s 'citation()' on how to cite R or R packages in publications. 310s 310s Type 'demo()' for some demos, 'help()' for on-line help, or 310s 'help.start()' for an HTML browser interface to help. 310s Type 'q()' to quit R. 310s 310s > Stangle("DrawingPhylogenies.Rnw") 310s Writing to file DrawingPhylogenies.R 310s > source("DrawingPhylogenies.R", echo=TRUE) 310s 310s > options(width = 80, prompt = "> ") 310s 310s > library(ape) 311s 311s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 311s 311s > foo <- function() { 311s + col <- "green" 311s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 311s + las = 1) 311s + box(lty .... [TRUNCATED] 311s 311s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 311s 311s > plot(mytr) 311s 311s > foo() 311s 311s > plot(mytr, "c", FALSE) 311s 311s > foo() 311s 311s > plot(mytr, "u") 311s 311s > foo() 311s 311s > par(xpd = TRUE) 311s 311s > plot(mytr, "f") 311s 311s > foo() 311s 311s > box("outer") 311s 311s > tr <- compute.brlen(stree(8, "l"), 0.1) 311s 311s > tr$tip.label[] <- "" 311s 311s > foo <- function() { 311s + col <- "green" 311s + axis(1, col = col, col.ticks = col, col.axis = col) 311s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 311s 311s > layout(matrix(1:12, 6, 2)) 311s 311s > par(mar = c(2, 2, 0.3, 0)) 311s 311s > for (type in c("p", "c")) { 311s + plot(tr, type) 311s + foo() 311s + plot(tr, type, node.pos = 2) 311s + foo() 311s + plot(tr, type, FALSE) 311s + foo() 311s .... [TRUNCATED] 311s 311s > foo <- function() { 311s + col <- "green" 311s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 311s + las = 1) 311s + box(lty .... [TRUNCATED] 311s 311s > layout(matrix(1:4, 2, 2)) 311s 311s > par(las = 1) 311s 311s > plot(tr, "u") 311s 311s > foo() 311s 311s > plot(tr, "u", FALSE) 311s 311s > foo() 311s 311s > plot(tr, "f") 311s 311s > foo() 311s 311s > plot(tr, "f", FALSE) 311s 311s > foo() 311s 311s > args(node.depth.edgelength) 311s function (phy) 311s NULL 311s 311s > args(node.depth) 311s function (phy, method = 1) 311s NULL 311s 311s > args(node.height) 311s function (phy, clado.style = FALSE) 311s NULL 311s 311s > args(unrooted.xy) 311s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 311s NULL 311s 311s > args(phylogram.plot) 311s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 311s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 311s node.lty = NULL) 311s NULL 311s 311s > args(cladogram.plot) 311s function (edge, xx, yy, edge.color, edge.width, edge.lty) 311s NULL 311s 311s > args(circular.plot) 311s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 311s edge.lty) 311s NULL 311s 311s > args(plot.phylo) 311s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 311s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 311s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 311s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 311s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 311s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 311s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 311s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 311s ...) 311s NULL 311s 311s > geo <- factor(c("Africa", "World", "Africa")) 311s 311s > (mycol <- c("blue", "red")[geo]) 311s [1] "blue" "red" "blue" 311s 311s > plot(mytr, tip.color = mycol) 311s 311s > par(xpd = TRUE) 311s 311s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 311s 311s > args(def) 311s function (x, ..., default = NULL, regexp = FALSE) 311s NULL 311s 311s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 311s 311s > identical(mycol, mycol2) 311s [1] TRUE 311s 311s > (i <- which.edge(mytr, c("Homo", "Pan"))) 311s [1] 2 3 311s 311s > co <- rep("black", Nedge(mytr)) 311s 311s > co[i] <- "blue" 311s 311s > par(xpd = TRUE) 311s 311s > plot(mytr, edge.col = co) 311s 311s > edgelabels() 311s 311s > args(axisPhylo) 311s function (side = NULL, root.time = NULL, backward = TRUE, ...) 311s NULL 311s 311s > args(add.scale.bar) 311s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 311s ...) 311s NULL 311s 311s > plot(mytr) 311s 311s > add.scale.bar() 311s 311s > axisPhylo() 311s 311s > axis(3) 311s 311s > args(nodelabels) 311s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 311s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 311s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 311s ...) 311s NULL 311s 311s > args(tiplabels) 311s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 311s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 311s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 311s offset = 0, ...) 311s NULL 311s 311s > args(edgelabels) 311s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 311s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 311s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 311s date = NULL, ...) 311s NULL 311s 311s > par(xpd = TRUE) 311s 311s > plot(mytr) 311s 311s > nodelabels() 311s 311s > tiplabels() 311s 311s > edgelabels() 311s 311s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 311s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 311s 311s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 311s 311s > v <- c(0, 0.5, 1) 311s 311s > layout(matrix(1:9, 3, 3)) 311s 311s > par(mar = c(3, 3, 3, 0), las = 1) 311s 311s > for (i in v) { 311s + for (j in v) { 311s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 311s + ")")) 311s + abline(v = 0, h = .... [TRUNCATED] 311s 311s > plot(rep(0, 3), 0:2, "n", las = 1) 311s 311s > abline(v = 0, h = 0:2, lty = 3) 311s 311s > text(0, 0:2, mytr$tip.label, adj = -1) 311s 311s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 311s 311s > args(phydataplot) 311s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 311s width = NULL, legend = "below", funcol = rainbow, ...) 311s NULL 311s 311s > args(ring) 311s function (x, phy, style = "ring", offset = 1, ...) 311s NULL 311s 311s > x <- matrix(1:6, 3, 10) 311s 311s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 311s 311s > x 311s A B C D E F G H I J 311s Homo 1 4 1 4 1 4 1 4 1 4 311s Gorilla 2 5 2 5 2 5 2 5 2 5 311s Pan 3 6 3 6 3 6 3 6 3 6 311s 311s > mytr$tip.label 311s [1] "Pan" "Homo" "Gorilla" 311s 311s > par(mar = c(10, 2, 5, 5)) 311s 311s > plot(mytr, x.lim = 30) 311s 311s > phydataplot(x, mytr, "m", border = "white", offset = 2, 311s + width = 1) 311s 311s > phydataplot(x, mytr, "m", border = "white", offset = 15, 311s + width = 1, continuous = 2) 311s 311s > n <- 100 311s 311s > p <- 3 311s 311s > set.seed(3) 311s 311s > tr <- rcoal(n) 311s 311s > x <- matrix(runif(p * n), n, p) 311s 311s > rownames(x) <- tr$tip.label 311s 311s > COL <- c("red", "green", "blue") 311s 311s > par(xpd = TRUE) 311s 311s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 311s + no.margin = TRUE) 311s 311s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 311s + col = COL[j]) 311s 311s > tree <- rtree(10) 311s 311s > tree$edge.length[1] <- 1000 311s 311s > layout(matrix(1:2, 1)) 311s 311s > plot(tree) 311s 311s > axisPhylo() 311s 311s > plotBreakLongEdges(tree) 311s 311s > axisPhylo() 311s 311s > el <- tree$edge.length 311s 311s > sum(el > mean(el) + 2 * sd(el)) 311s [1] 1 311s 311s > tree$edge.length[8] <- 1000 311s 311s > el <- tree$edge.length 311s 311s > sum(el > mean(el) + 2 * sd(el)) 311s [1] 2 311s 311s > layout(matrix(1:2, 1)) 311s 311s > plotBreakLongEdges(tree) 311s 311s > plotBreakLongEdges(tree, n = 2) 311s 311s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 311s + simplify = FALSE) 311s 311s > kronoviz(TR, type = "c", show.tip.label = FALSE) 311s 311s > dates <- as.Date(.leap.seconds) 311s 311s > tr <- rcoal(length(dates)) 311s 311s > plotTreeTime(tr, dates) 311s 311s > par(oma = rep(2, 4)) 311s 311s > plot(mytr) 311s 311s > box(lty = 3) 311s 311s > box("figure", col = "blue") 311s 311s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 311s + font = 2, col = "blue") 311s 311s > box("outer") 311s 311s > layout(matrix(1:4, 2, 2)) 311s 311s > par(oma = rep(2, 4)) 311s 311s > for (i in 1:4) { 311s + par(mar = rep(i, 4)) 311s + plot(mytr) 311s + box(lty = 3) 311s + box("figure", col = "blue") 311s + } 311s 311s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 311s + font = 2, col = "blue") 311s 311s > box("outer") 311s 311s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 311s 311s > for (i in 1:3) plot(rtree(5)) 311s 311s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 311s $type 311s [1] "phylogram" 311s 311s $use.edge.length 311s [1] TRUE 311s 311s $node.pos 311s [1] 1 311s 311s $node.depth 311s [1] 1 311s 311s $show.tip.label 311s [1] TRUE 311s 311s $show.node.label 311s [1] FALSE 311s 311s $font 311s [1] 3 311s 311s $cex 311s [1] 0.83 311s 311s $adj 311s [1] 0 311s 311s $srt 311s [1] 0 311s 311s $no.margin 311s [1] FALSE 311s 311s $label.offset 311s [1] 0 311s 311s $x.lim 311s [1] 0.00000 3.13046 311s 311s $y.lim 311s [1] 1 5 311s 311s $direction 311s [1] "rightwards" 311s 311s $tip.color 311s [1] "black" 311s 311s $Ntip 311s [1] 5 311s 311s $Nnode 311s [1] 4 311s 311s $root.time 311s NULL 311s 311s $align.tip.label 311s [1] FALSE 311s 311s $edge 311s [,1] [,2] 311s [1,] 6 1 311s [2,] 6 7 311s [3,] 7 2 311s [4,] 7 8 311s [5,] 8 3 311s [6,] 8 9 311s [7,] 9 4 311s [8,] 9 5 311s 311s $xx 311s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 311s [8] 1.3631198 1.9857132 311s 311s $yy 311s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 311s 311s 311s > layout(matrix(1:2, 2)) 311s 311s > plot(rtree(4)) 311s 311s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 311s 311s > x <- pp$xx[1] 311s 311s > y <- pp$yy[1] 311s 311s > (pu <- par("usr")) 311s [1] -0.06364557 1.65478492 0.88000000 4.12000000 311s 311s > (x - pu[1])/(pu[2] - pu[1]) 311s [1] 0.9349839 311s 311s > (y - pu[3])/(pu[4] - pu[3]) 311s [1] 0.03703704 311s 311s > pi <- par("pin") 311s 311s > mi <- par("mai") 311s 311s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 311s 311s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 311s 311s > plot(rtree(4)) 311s 311s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 311s 311s > x <- pp$xx[5] 311s 311s > y <- pp$yy[5] 311s 311s > pu <- par("usr") 311s 311s > pi <- par("pin") 311s 311s > mi <- par("mai") 311s 311s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 311s 311s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 311s 311s > yi1 <- yi1 + par("fin")[2] 311s 311s > di <- par("din") 311s 311s > layout(1) 311s 311s > par(new = TRUE, mai = rep(0, 4)) 311s 311s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 311s + ylim = 0:1, xaxs = "i", yaxs = "i") 311s 311s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 311s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 311s 311s > foo <- function(phy1, phy2, from) { 311s + layout(matrix(1:2, 2)) 311s + plot(phy1, font = 1) 311s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 311s 311s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 311s 311s > par(xpd = TRUE) 311s 311s > foo(trb, mytr, "Primates") 312s 312s > plot(mytr, plot = FALSE) 312s 312s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 312s 312s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 312s + pp$yy[2] + 0.1, col = "yellow", border = NA) 312s 312s > par(new = TRUE) 312s 312s > plot(mytr) 312s > 312s 312s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 312s Copyright (C) 2025 The R Foundation for Statistical Computing 312s Platform: arm-unknown-linux-gnueabihf (32-bit) 312s 312s R is free software and comes with ABSOLUTELY NO WARRANTY. 312s You are welcome to redistribute it under certain conditions. 312s Type 'license()' or 'licence()' for distribution details. 312s 312s R is a collaborative project with many contributors. 312s Type 'contributors()' for more information and 312s 'citation()' on how to cite R or R packages in publications. 312s 312s Type 'demo()' for some demos, 'help()' for on-line help, or 312s 'help.start()' for an HTML browser interface to help. 312s Type 'q()' to quit R. 312s 312s > Stangle("MoranI.Rnw") 312s Writing to file MoranI.R 312s > source("MoranI.R", echo=TRUE) 312s 312s > options(width = 80, prompt = "> ") 312s 312s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 312s 312s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 312s 312s > names(body) <- names(longevity) <- c("Homo", "Pongo", 312s + "Macaca", "Ateles", "Galago") 312s 312s > library(ape) 312s 312s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 312s 312s > trnwk[2] <- ":0.38,Galago:1.00);" 312s 312s > tr <- read.tree(text = trnwk) 312s 312s > plot(tr) 312s 312s > axisPhylo() 312s 312s > w <- 1/cophenetic(tr) 312s 312s > w 312s Homo Pongo Macaca Ateles Galago 312s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 312s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 312s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 312s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 312s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 312s 312s > diag(w) <- 0 312s 312s > Moran.I(body, w) 312s $observed 312s [1] -0.07312179 312s 312s $expected 312s [1] -0.25 312s 312s $sd 312s [1] 0.08910814 312s 312s $p.value 312s [1] 0.04714628 312s 312s 312s > Moran.I(body, w, alt = "greater") 312s $observed 312s [1] -0.07312179 312s 312s $expected 312s [1] -0.25 312s 312s $sd 312s [1] 0.08910814 312s 312s $p.value 312s [1] 0.02357314 312s 312s 312s > Moran.I(longevity, w) 312s $observed 312s [1] -0.1837739 312s 312s $expected 312s [1] -0.25 312s 312s $sd 312s [1] 0.09114549 312s 312s $p.value 312s [1] 0.4674727 312s 312s 312s > data(carnivora) 312s 312s > carnivora$log10SW <- log10(carnivora$SW) 312s 312s > carnivora$log10FW <- log10(carnivora$FW) 312s 312s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 312s 312s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 312s 312s > plot(co1) 312s 312s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 312s 312s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 312s 312s > print(plot(co2)) 312s 312s > plot(co2, FALSE) 312s > 313s 313s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 313s Copyright (C) 2025 The R Foundation for Statistical Computing 313s Platform: arm-unknown-linux-gnueabihf (32-bit) 313s 313s R is free software and comes with ABSOLUTELY NO WARRANTY. 313s You are welcome to redistribute it under certain conditions. 313s Type 'license()' or 'licence()' for distribution details. 313s 313s R is a collaborative project with many contributors. 313s Type 'contributors()' for more information and 313s 'citation()' on how to cite R or R packages in publications. 313s 313s Type 'demo()' for some demos, 'help()' for on-line help, or 313s 'help.start()' for an HTML browser interface to help. 313s Type 'q()' to quit R. 313s 313s > Stangle("RandomTopologies.Rnw") 313s Writing to file RandomTopologies.R 313s > source("RandomTopologies.R", echo=TRUE) 313s 313s > options(width = 80, prompt = "> ") 313s 313s > library(ape) 313s 313s > n <- 1:10 313s 313s > data.frame(N.topo = sapply(n, howmanytrees)) 313s N.topo 313s 1 1 313s 2 1 313s 3 3 313s 4 15 313s 5 105 313s 6 945 313s 7 10395 313s 8 135135 313s 9 2027025 313s 10 34459425 313s 313s > howmanytrees(25) 313s [1] 1.192568e+30 313s 313s > howmanytrees(25) * 0.21 313s [1] 2.504393e+29 313s 313s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 313s N.topo 313s 1 1 313s 2 1 313s 3 1 313s 4 2 313s 5 3 313s 6 6 313s 7 11 313s 8 23 313s 9 46 313s 10 98 313s 313s > n2 <- c(50, 100, 200) 313s 313s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 313s + row.names = n2) 313s N.topo 313s 50 5.150149e+16 313s 100 1.019560e+36 313s 200 1.141703e+75 313s 313s > 1/howmanytrees(50) 313s [1] 3.632505e-77 313s 313s > 1/sapply(n, howmanytrees) 313s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 313s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 313s 313s > 1/sapply(n, howmanytrees, labeled = FALSE) 313s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 313s [7] 0.09090909 0.04347826 0.02173913 0.01020408 313s 313s > library(phangorn) 315s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 315s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 315s 315s > TR <- allTrees(4, rooted = TRUE) 315s 315s > TR 315s 15 phylogenetic trees 315s 315s > layout(matrix(1:15, 3, 5)) 315s 315s > par(mar = rep(1.5, 4), xpd = TRUE) 315s 315s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 315s 315s > K <- 100 315s 315s > n <- 50 315s 315s > N <- howmanytrees(n, labeled = FALSE) 315s 315s > p <- 1/N 315s 315s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 315s [1] 0 315s 315s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 315s [1] -5.431212e-17 315s 315s > f <- function(n, K) { 315s + N <- howmanytrees(n, labeled = FALSE) 315s + p <- 1/N 315s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 315s + } 315s 315s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 315s + 10000)) 315s 315s > DF$P <- mapply(f, n = DF$n, K = DF$K) 315s 315s > library(lattice) 315s 315s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 315s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 315s 315s > subset(DF, n == 20) 315s n K P 315s 17 20 2 1.160494e-11 315s 34 20 5 1.160491e-10 315s 51 20 10 5.222149e-10 315s 68 20 100 5.743191e-08 315s 85 20 1000 5.783570e-06 315s 102 20 10000 5.671842e-04 315s 315s > f(20, 1e+05) 315s [1] 0.04638755 315s 315s > f(30, 1e+06) 315s [1] 2.525152e-07 315s 315s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 315s 315s > TR5 <- read.tree(text = txt) 315s 315s > layout(matrix(1:3, 1)) 315s 315s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 315s 315s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 315s + labeled = FALSE) 315s [1] 2 315s 315s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 315s + labeled = FALSE) 315s [1] 1 315s 315s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 315s + labeled = FALSE) 315s [1] Inf 315s 315s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 315s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 316s 316s > foo.test <- function(x, labeled = TRUE) { 316s + uTR <- unique(x, use.tip.label = labeled) 316s + f <- integer(length(uTR)) 316s + for (j in seq_along( .... [TRUNCATED] 316s 316s > lapply(TR, foo.test) 320s [1] 73 58 61 71 57 73 86 62 70 67 57 70 71 72 52 324s [1] 61 51 58 96 116 105 54 63 57 53 56 66 60 54 50 327s [1] 40 180 49 174 160 38 45 35 49 34 29 38 44 47 38 327s [[1]] 327s 327s Chi-squared test for given probabilities 327s 327s data: f 327s X-squared = 16.1, df = 14, p-value = 0.3073 327s 327s 327s [[2]] 327s 327s Chi-squared test for given probabilities 327s 327s data: f 327s X-squared = 92.51, df = 14, p-value = 1.271e-13 327s 327s 327s [[3]] 327s 327s Chi-squared test for given probabilities 327s 327s data: f 327s X-squared = 626.03, df = 14, p-value < 2.2e-16 327s 327s 327s 327s > lapply(TR, foo.test, labeled = FALSE) 328s [1] 818 182 328s [1] 683 317 329s [1] 486 514 329s [[1]] 329s 329s Chi-squared test for given probabilities 329s 329s data: f 329s X-squared = 404.5, df = 1, p-value < 2.2e-16 329s 329s 329s [[2]] 329s 329s Chi-squared test for given probabilities 329s 329s data: f 329s X-squared = 133.96, df = 1, p-value < 2.2e-16 329s 329s 329s [[3]] 329s 329s Chi-squared test for given probabilities 329s 329s data: f 329s X-squared = 0.784, df = 1, p-value = 0.3759 329s 329s 329s 329s > .Machine$double.xmax 329s [1] 1.797693e+308 329s 329s > howmanytrees(151) 329s [1] 3.753274e+306 329s 329s > howmanytrees(792, labeled = FALSE) 329s [1] 1.029038e+308 329s 329s > (N <- howmanytrees(2e+06)) 329s approximately 3.692364 * 10^12335524 329s 329s > N[2] + 1 329s n 329s 12335525 329s 329s > ceiling((N[2] + 1)/3000) 329s n 329s 4112 329s 329s > n <- 1:792 329s 329s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 329s 329s > lN <- log10(N) 329s 329s > summary(lm(lN ~ n)) 329s 329s Call: 329s lm(formula = lN ~ n) 329s 329s Residuals: 329s Min 1Q Median 3Q Max 329s -0.25968 -0.21424 -0.08311 0.12406 2.82605 329s 329s Coefficients: 329s Estimate Std. Error t value Pr(>|t|) 329s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 329s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 329s --- 329s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 329s 329s Residual standard error: 0.3175 on 790 degrees of freedom 329s Multiple R-squared: 1, Adjusted R-squared: 1 329s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 329s 329s 329s > s <- n > 700 329s 329s > summary(lm(lN[s] ~ n[s])) 329s 329s Call: 329s lm(formula = lN[s] ~ n[s]) 329s 329s Residuals: 329s Min 1Q Median 3Q Max 329s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 329s 329s Coefficients: 329s Estimate Std. Error t value Pr(>|t|) 329s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 329s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 329s --- 329s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 329s 329s Residual standard error: 0.0003738 on 90 degrees of freedom 329s Multiple R-squared: 1, Adjusted R-squared: 1 329s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 329s 329s 329s > n <- 788:792 329s 329s > log10(sapply(n, howmanytrees, labeled = FALSE)) 329s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 329s 329s > 0.3941 * n - 4.153 329s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 329s 329s > xi <- 2.477993 329s 329s > lxi <- log10(xi) 329s 329s > n <- 1000 329s 329s > (n - 1) * lxi 329s [1] 393.706 329s 329s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 329s + 1))))) 329s [1] 393.8532 329s [1] 393.9009 329s [1] 393.9187 329s [1] 393.9257 329s [1] 393.9285 329s [1] 393.9296 329s [1] 393.9301 329s [1] 393.9303 329s [1] 393.9304 329s [1] 393.9304 329s > 330s autopkgtest [23:17:18]: test run-unit-test: -----------------------] 334s run-unit-test PASS 334s autopkgtest [23:17:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 338s autopkgtest [23:17:26]: test pkg-r-autopkgtest: preparing testbed 340s Reading package lists... 341s Building dependency tree... 341s Reading state information... 341s Solving dependencies... 342s The following NEW packages will be installed: 342s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 342s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-15 g++-15-arm-linux-gnueabihf 342s g++-arm-linux-gnueabihf gcc gcc-15 gcc-15-arm-linux-gnueabihf 342s gcc-arm-linux-gnueabihf gfortran gfortran-15 gfortran-15-arm-linux-gnueabihf 342s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 342s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-15-dev 342s libgfortran-15-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 342s libjpeg8-dev libjs-jquery liblapack-dev liblzma-dev libmpc3 libncurses-dev 342s libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 342s libpng-dev libreadline-dev libstdc++-15-dev libtirpc-dev libubsan1 342s libzstd-dev linux-libc-dev node-html5shiv pkg-r-autopkgtest pkgconf 342s pkgconf-bin r-base-dev r-cran-expm r-cran-gee r-cran-xml2 rpcsvc-proto 342s zlib1g-dev 342s 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded. 342s Need to get 84.1 MB of archives. 342s After this operation, 255 MB of additional disk space will be used. 342s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 342s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.19.0-3.3 [1804 kB] 345s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 345s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 345s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 348s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 348s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 348s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 366s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 366s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 366s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 366s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 366s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 370s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 372s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 373s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 407s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 407s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 407s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 407s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 411s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 431s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 431s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 431s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 431s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 431s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 431s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran-15-dev armhf 15.2.0-12ubuntu1 [380 kB] 431s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.7 MB] 450s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15 armhf 15.2.0-12ubuntu1 [18.1 kB] 450s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1020 B] 450s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 450s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 450s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 450s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 450s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 450s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 473s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 473s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 473s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 473s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 474s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 478s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 479s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 479s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 480s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 480s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 481s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 481s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 482s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 483s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 483s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 484s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 484s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 484s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 484s Get:55 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 484s Get:56 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 484s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 484s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 484s Get:59 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-expm armhf 1.0-0-1 [223 kB] 485s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-gee armhf 4.13-29-1 [71.1 kB] 485s Get:61 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xml2 armhf 1.4.1-1 [323 kB] 487s Fetched 84.1 MB in 2min 24s (584 kB/s) 487s Selecting previously unselected package libc-dev-bin. 487s (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 ... 73761 files and directories currently installed.) 487s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 487s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 487s Selecting previously unselected package linux-libc-dev:armhf. 487s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_armhf.deb ... 487s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 487s Selecting previously unselected package libcrypt-dev:armhf. 487s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 487s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 487s Selecting previously unselected package rpcsvc-proto. 487s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 487s Unpacking rpcsvc-proto (1.4.3-1build1) ... 487s Selecting previously unselected package libc6-dev:armhf. 487s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_armhf.deb ... 487s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 487s Selecting previously unselected package libisl23:armhf. 487s Preparing to unpack .../05-libisl23_0.27-1build1_armhf.deb ... 487s Unpacking libisl23:armhf (0.27-1build1) ... 487s Selecting previously unselected package libmpc3:armhf. 487s Preparing to unpack .../06-libmpc3_1.3.1-2_armhf.deb ... 487s Unpacking libmpc3:armhf (1.3.1-2) ... 487s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 487s Preparing to unpack .../07-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 487s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package cpp-15. 488s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package cpp-arm-linux-gnueabihf. 488s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 488s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 488s Selecting previously unselected package cpp. 488s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 488s Unpacking cpp (4:15.2.0-4ubuntu1) ... 488s Selecting previously unselected package libcc1-0:armhf. 488s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package libasan8:armhf. 488s Preparing to unpack .../12-libasan8_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package libubsan1:armhf. 488s Preparing to unpack .../13-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package libgcc-15-dev:armhf. 488s Preparing to unpack .../14-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 488s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 488s Preparing to unpack .../15-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 488s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 489s Selecting previously unselected package gcc-15. 489s Preparing to unpack .../16-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 489s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 489s Selecting previously unselected package gcc-arm-linux-gnueabihf. 489s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 489s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 489s Selecting previously unselected package gcc. 489s Preparing to unpack .../18-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 489s Unpacking gcc (4:15.2.0-4ubuntu1) ... 489s Selecting previously unselected package libstdc++-15-dev:armhf. 489s Preparing to unpack .../19-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 489s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 489s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 489s Preparing to unpack .../20-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 489s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 490s Selecting previously unselected package g++-15. 490s Preparing to unpack .../21-g++-15_15.2.0-12ubuntu1_armhf.deb ... 490s Unpacking g++-15 (15.2.0-12ubuntu1) ... 490s Selecting previously unselected package g++-arm-linux-gnueabihf. 490s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 490s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 490s Selecting previously unselected package g++. 490s Preparing to unpack .../23-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 490s Unpacking g++ (4:15.2.0-4ubuntu1) ... 490s Selecting previously unselected package build-essential. 490s Preparing to unpack .../24-build-essential_12.12ubuntu2_armhf.deb ... 490s Unpacking build-essential (12.12ubuntu2) ... 490s Selecting previously unselected package dctrl-tools. 490s Preparing to unpack .../25-dctrl-tools_2.24-3build4_armhf.deb ... 490s Unpacking dctrl-tools (2.24-3build4) ... 490s Selecting previously unselected package libgfortran-15-dev:armhf. 490s Preparing to unpack .../26-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 490s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 490s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 490s Preparing to unpack .../27-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 490s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 490s Selecting previously unselected package gfortran-15. 490s Preparing to unpack .../28-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 490s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 490s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 490s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 490s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 490s Selecting previously unselected package gfortran. 490s Preparing to unpack .../30-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 490s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 490s Selecting previously unselected package icu-devtools. 490s Preparing to unpack .../31-icu-devtools_78.2-1ubuntu1_armhf.deb ... 490s Unpacking icu-devtools (78.2-1ubuntu1) ... 491s Selecting previously unselected package libblas-dev:armhf. 491s Preparing to unpack .../32-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 491s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 491s Selecting previously unselected package libbz2-dev:armhf. 491s Preparing to unpack .../33-libbz2-dev_1.0.8-6build2_armhf.deb ... 491s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 491s Selecting previously unselected package libdeflate-dev:armhf. 491s Preparing to unpack .../34-libdeflate-dev_1.23-2build1_armhf.deb ... 491s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 491s Selecting previously unselected package libicu-dev:armhf. 491s Preparing to unpack .../35-libicu-dev_78.2-1ubuntu1_armhf.deb ... 491s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 491s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 491s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 491s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 491s Selecting previously unselected package libjpeg8-dev:armhf. 491s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 491s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 491s Selecting previously unselected package libjpeg-dev:armhf. 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libasan8:armhf (15.2.0-12ubuntu1) ... 493s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 493s Setting up r-cran-gee (4.13-29-1) ... 493s Setting up libisl23:armhf (0.27-1build1) ... 493s Setting up libc-dev-bin (2.42-2ubuntu4) ... 493s Setting up libdeflate-dev:armhf (1.23-2build1) ... 493s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 493s Setting up libcc1-0:armhf (15.2.0-12ubuntu1) ... 493s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 493s Setting up libblas-dev:armhf (3.12.1-7ubuntu1) ... 493s 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 493s Setting up dctrl-tools (2.24-3build4) ... 493s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 493s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 493s Setting up r-cran-xml2 (1.4.1-1) ... 493s Setting up libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 493s Setting up pkgconf:armhf (1.8.1-4build1) ... 493s Setting up liblapack-dev:armhf (3.12.1-7ubuntu1) ... 493s 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 493s Setting up cpp-15 (15.2.0-12ubuntu1) ... 493s Setting up cpp (4:15.2.0-4ubuntu1) ... 493s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 493s Setting up libicu-dev:armhf (78.2-1ubuntu1) ... 493s Setting up libbz2-dev:armhf (1.0.8-6build2) ... 493s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 493s Setting up libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 493s Setting up libncurses-dev:armhf (6.6+20251231-1) ... 493s Setting up gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 493s Setting up libpcre2-dev:armhf (10.46-1) ... 493s Setting up libreadline-dev:armhf (8.3-3) ... 493s Setting up gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 493s Setting up gcc-15 (15.2.0-12ubuntu1) ... 493s Setting up libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 493s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 493s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 493s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 493s Setting up libpng-dev:armhf (1.6.54-1) ... 493s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 493s Setting up g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 493s Setting up gcc (4:15.2.0-4ubuntu1) ... 493s Setting up g++-15 (15.2.0-12ubuntu1) ... 493s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 493s Setting up gfortran (4:15.2.0-4ubuntu1) ... 493s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 493s 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 493s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 493s 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 493s Setting up g++ (4:15.2.0-4ubuntu1) ... 493s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 493s Setting up build-essential (12.12ubuntu2) ... 493s Setting up r-base-dev (4.5.2-1ubuntu2) ... 493s Setting up pkg-r-autopkgtest (20250812) ... 493s Processing triggers for libc-bin (2.42-2ubuntu4) ... 493s Processing triggers for man-db (2.13.1-1build1) ... 494s Processing triggers for install-info (7.2-5) ... 503s autopkgtest [23:20:11]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 503s autopkgtest [23:20:11]: test pkg-r-autopkgtest: [----------------------- 505s Test: Try to load the R library ape 505s 505s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 505s Copyright (C) 2025 The R Foundation for Statistical Computing 505s Platform: arm-unknown-linux-gnueabihf (32-bit) 505s 505s R is free software and comes with ABSOLUTELY NO WARRANTY. 505s You are welcome to redistribute it under certain conditions. 505s Type 'license()' or 'licence()' for distribution details. 505s 505s R is a collaborative project with many contributors. 505s Type 'contributors()' for more information and 505s 'citation()' on how to cite R or R packages in publications. 505s 505s Type 'demo()' for some demos, 'help()' for on-line help, or 505s 'help.start()' for an HTML browser interface to help. 505s Type 'q()' to quit R. 505s 506s > library('ape') 506s > 508s autopkgtest [23:20:16]: test pkg-r-autopkgtest: -----------------------] 512s autopkgtest [23:20:20]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 512s pkg-r-autopkgtest PASS 517s autopkgtest [23:20:25]: @@@@@@@@@@@@@@@@@@@@ summary 517s run-unit-test PASS 517s pkg-r-autopkgtest PASS