0s autopkgtest [22:49:54]: starting date and time: 2026-02-09 22:49:54+0000 0s autopkgtest [22:49:54]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:49:54]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.apbvrhp5/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-5.secgroup --name adt-resolute-arm64-r-cran-ape-20260209-224954-juju-7f2275-prod-proposed-migration-environment-20-28026847-a32f-475a-bcf8-c720707adab1 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-cran-ape-20260209-224954-juju-7f2275-prod-proposed-migration-environment-20-28026847-a32f-475a-bcf8-c720707adab1 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 125s autopkgtest [22:51:59]: testbed dpkg architecture: arm64 125s autopkgtest [22:51:59]: testbed apt version: 3.1.15 126s autopkgtest [22:52:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 126s autopkgtest [22:52:00]: testbed release detected to be: None 127s autopkgtest [22:52:01]: updating testbed package index (apt update) 127s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 127s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 127s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 131s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 131s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 131s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 134s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 135s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 135s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 136s Fetched 3862 kB in 8s (509 kB/s) 137s Reading package lists... 137s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 137s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 138s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 138s Reading package lists... 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 139s The following packages will be upgraded: 139s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 139s libip6tc2 libxtables12 wget 139s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 2534 kB of archives. 139s After this operation, 18.4 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 139s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 139s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 139s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 139s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 141s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 141s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 141s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 141s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 142s dpkg-preconfigure: unable to re-open stdin: No such file or directory 142s Fetched 2534 kB in 2s (1209 kB/s) 142s (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 ... 136597 files and directories currently installed.) 142s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 142s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 142s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 142s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 142s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 142s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 142s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 143s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 143s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 143s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.deb ... 143s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 143s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_arm64.deb ... 143s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 143s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 143s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 143s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 143s Setting up wget (1.25.0-2ubuntu4) ... 143s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 143s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 143s Setting up dracut-install (109-11ubuntu1) ... 143s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 143s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 143s Setting up iptables (1.8.11-2ubuntu3) ... 143s Setting up iproute2 (6.18.0-1ubuntu1) ... 143s Processing triggers for man-db (2.13.1-1build1) ... 144s Processing triggers for install-info (7.2-5) ... 144s Processing triggers for libc-bin (2.42-2ubuntu4) ... 144s autopkgtest [22:52:18]: upgrading testbed (apt dist-upgrade and autopurge) 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Solving dependencies... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s autopkgtest [22:52:22]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 149s autopkgtest [22:52:23]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 152s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 152s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 152s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 152s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 152s gpgv: issuer "plessy@debian.org" 152s gpgv: Can't check signature: No public key 152s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 153s autopkgtest [22:52:27]: testing package r-cran-ape version 5.8-1-1 153s autopkgtest [22:52:27]: build not needed 156s autopkgtest [22:52:30]: test run-unit-test: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Solving dependencies... 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 libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 156s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 156s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 156s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 156s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 156s libxss1 libxt6t64 r-base-core r-cran-ape r-cran-cli r-cran-cpp11 156s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 156s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 156s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 156s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 156s xdg-utils zip 156s 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 64.5 MB of archives. 156s After this operation, 125 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 158s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 158s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 158s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 158s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 158s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libsuitesparseconfig7 arm64 1:7.12.1+dfsg-1 [22.0 kB] 158s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libamd3 arm64 1:7.12.1+dfsg-1 [34.6 kB] 158s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 158s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 158s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 158s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 158s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 158s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 159s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libcolamd3 arm64 1:7.12.1+dfsg-1 [27.1 kB] 159s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 159s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 159s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 159s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libltdl7 arm64 2.5.4-9 [43.3 kB] 159s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 libglpk40 arm64 5.0-2 [347 kB] 159s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 159s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 159s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 159s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 159s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 159s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 159s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 163s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 163s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 163s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 163s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 163s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 163s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 163s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 163s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 163s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 163s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 163s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 164s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 164s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 164s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 164s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 164s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 164s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 166s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 166s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 166s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 166s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 166s Get:49 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 213s Get:50 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-lattice arm64 0.22-9-1 [1399 kB] 215s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 218s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-littler arm64 0.3.22-1 [85.1 kB] 218s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 219s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rcpp arm64 1.1.0-1 [2011 kB] 222s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-digest arm64 0.6.39-1 [196 kB] 222s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-ape arm64 5.8-1-1 [2901 kB] 226s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 228s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cpp11 all 0.5.3-1 [242 kB] 228s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-fastmatch arm64 1.1-6-1 [36.0 kB] 228s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-generics all 0.1.4-1 [84.0 kB] 228s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 228s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-rlang arm64 1.1.5-3 [1706 kB] 231s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 231s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 231s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 238s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 238s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 241s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-igraph arm64 2.1.4-1build1 [5151 kB] 249s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-quadprog arm64 1.5-8-1build2 [31.9 kB] 249s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-phangorn arm64 2.12.1+dfsg-1 [1803 kB] 253s Preconfiguring packages ... 253s Fetched 64.5 MB in 1min 36s (669 kB/s) 253s Selecting previously unselected package fonts-dejavu-mono. 253s (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 ... 136600 files and directories currently installed.) 253s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 253s Unpacking fonts-dejavu-mono (2.37-8build1) ... 253s Selecting previously unselected package fonts-dejavu-core. 253s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 253s Unpacking fonts-dejavu-core (2.37-8build1) ... 253s Selecting previously unselected package fontconfig-config. 253s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 254s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 254s Selecting previously unselected package libfontconfig1:arm64. 254s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 254s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 254s Selecting previously unselected package fontconfig. 254s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 254s Unpacking fontconfig (2.17.1-3ubuntu1) ... 254s Selecting previously unselected package libgomp1:arm64. 254s Preparing to unpack .../05-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 254s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 254s Selecting previously unselected package libsuitesparseconfig7:arm64. 254s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_arm64.deb ... 254s Unpacking libsuitesparseconfig7:arm64 (1:7.12.1+dfsg-1) ... 254s Selecting previously unselected package libamd3:arm64. 254s Preparing to unpack .../07-libamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 254s Unpacking libamd3:arm64 (1:7.12.1+dfsg-1) ... 254s Selecting previously unselected package libblas3:arm64. 254s Preparing to unpack .../08-libblas3_3.12.1-7ubuntu1_arm64.deb ... 254s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 254s Selecting previously unselected package libpixman-1-0:arm64. 254s Preparing to unpack .../09-libpixman-1-0_0.46.4-1_arm64.deb ... 254s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 254s Selecting previously unselected package libxcb-render0:arm64. 254s Preparing to unpack .../10-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 254s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 254s Selecting previously unselected package libxcb-shm0:arm64. 254s Preparing to unpack .../11-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 254s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 254s Selecting previously unselected package libxrender1:arm64. 254s Preparing to unpack .../12-libxrender1_1%3a0.9.12-1_arm64.deb ... 254s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 254s Selecting previously unselected package libcairo2:arm64. 254s Preparing to unpack .../13-libcairo2_1.18.4-3_arm64.deb ... 254s Unpacking libcairo2:arm64 (1.18.4-3) ... 254s Selecting previously unselected package libcolamd3:arm64. 254s Preparing to unpack .../14-libcolamd3_1%3a7.12.1+dfsg-1_arm64.deb ... 254s Unpacking libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 254s Selecting previously unselected package libdatrie1:arm64. 254s Preparing to unpack .../15-libdatrie1_0.2.14-1_arm64.deb ... 254s Unpacking libdatrie1:arm64 (0.2.14-1) ... 254s Selecting previously unselected package libdeflate0:arm64. 254s Preparing to unpack .../16-libdeflate0_1.23-2build1_arm64.deb ... 254s Unpacking libdeflate0:arm64 (1.23-2build1) ... 254s Selecting previously unselected package libgfortran5:arm64. 254s Preparing to unpack .../17-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 254s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 254s Selecting previously unselected package libltdl7:arm64. 254s Preparing to unpack .../18-libltdl7_2.5.4-9_arm64.deb ... 254s Unpacking libltdl7:arm64 (2.5.4-9) ... 254s Selecting previously unselected package libglpk40:arm64. 254s Preparing to unpack .../19-libglpk40_5.0-2_arm64.deb ... 254s Unpacking libglpk40:arm64 (5.0-2) ... 254s Selecting previously unselected package libgraphite2-3:arm64. 254s Preparing to unpack .../20-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 254s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 254s Selecting previously unselected package libharfbuzz0b:arm64. 254s Preparing to unpack .../21-libharfbuzz0b_12.3.2-1_arm64.deb ... 254s Unpacking libharfbuzz0b:arm64 (12.3.2-1) ... 254s Selecting previously unselected package x11-common. 254s Preparing to unpack .../22-x11-common_1%3a7.7+24ubuntu1_all.deb ... 254s Unpacking x11-common (1:7.7+24ubuntu1) ... 254s Selecting previously unselected package libice6:arm64. 254s Preparing to unpack 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up xdg-utils (1.2.1-2ubuntu2) ... 257s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 257s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 257s Setting up libice6:arm64 (2:1.1.1-1build1) ... 257s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 257s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 257s Setting up libamd3:arm64 (1:7.12.1+dfsg-1) ... 257s Setting up libcolamd3:arm64 (1:7.12.1+dfsg-1) ... 257s Setting up fontconfig-config (2.17.1-3ubuntu1) ... 257s Setting up libpaper-utils (2.2.5-0.3build1) ... 257s Setting up libthai0:arm64 (0.1.30-1) ... 257s Setting up libglpk40:arm64 (5.0-2) ... 257s Setting up libtiff6:arm64 (4.7.0-3ubuntu3) ... 257s Setting up libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 257s Setting up libsm6:arm64 (2:1.2.6-1build1) ... 257s Setting up fontconfig (2.17.1-3ubuntu1) ... 259s Regenerating fonts cache... done. 259s Setting up libxft2:arm64 (2.3.6-1build2) ... 259s Setting up libtk8.6:arm64 (8.6.17-1) ... 259s Setting up libpango-1.0-0:arm64 (1.57.0-1) ... 259s Setting up libcairo2:arm64 (1.18.4-3) ... 259s Setting up libxt6t64:arm64 (1:1.2.1-1.3) ... 259s Setting up libpangoft2-1.0-0:arm64 (1.57.0-1) ... 259s Setting up libpangocairo-1.0-0:arm64 (1.57.0-1) ... 259s Setting up r-base-core (4.5.2-1ubuntu2) ... 260s Creating config file /etc/R/Renviron with new version 260s Setting up r-cran-fastmatch (1.1-6-1) ... 260s Setting up r-cran-lattice (0.22-9-1) ... 260s Setting up r-cran-nlme (3.1.168-1) ... 260s Setting up r-cran-pkgkitten (0.2.4-1) ... 260s Setting up r-cran-magrittr (2.0.3-1) ... 260s Setting up r-cran-quadprog (1.5-8-1build2) ... 260s Setting up r-cran-littler (0.3.22-1) ... 260s Setting up r-cran-rcpp (1.1.0-1) ... 260s Setting up r-cran-rlang (1.1.5-3) ... 260s Setting up r-cran-generics (0.1.4-1) ... 260s Setting up r-cran-digest (0.6.39-1) ... 260s Setting up r-cran-ape (5.8-1-1) ... 260s Setting up r-cran-glue (1.8.0-1) ... 260s Setting up r-cran-cli (3.6.4-1) ... 260s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 260s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 260s Setting up r-cran-cpp11 (0.5.3-1) ... 260s Setting up r-cran-matrix (1.7-4-1) ... 260s Setting up r-cran-vctrs (0.6.5-1) ... 260s Setting up r-cran-igraph (2.1.4-1build1) ... 260s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 260s Processing triggers for libc-bin (2.42-2ubuntu4) ... 260s Processing triggers for man-db (2.13.1-1build1) ... 260s Processing triggers for install-info (7.2-5) ... 261s autopkgtest [22:54:15]: test run-unit-test: [----------------------- 262s 262s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 262s Copyright (C) 2025 The R Foundation for Statistical Computing 262s Platform: aarch64-unknown-linux-gnu 262s 262s R is free software and comes with ABSOLUTELY NO WARRANTY. 262s You are welcome to redistribute it under certain conditions. 262s Type 'license()' or 'licence()' for distribution details. 262s 262s R is a collaborative project with many contributors. 262s Type 'contributors()' for more information and 262s 'citation()' on how to cite R or R packages in publications. 262s 262s Type 'demo()' for some demos, 'help()' for on-line help, or 262s 'help.start()' for an HTML browser interface to help. 262s Type 'q()' to quit R. 262s 262s > Stangle("DrawingPhylogenies.Rnw") 262s Writing to file DrawingPhylogenies.R 262s > source("DrawingPhylogenies.R", echo=TRUE) 262s 262s > options(width = 80, prompt = "> ") 262s 262s > library(ape) 262s 262s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 262s 262s > foo <- function() { 262s + col <- "green" 262s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 262s + las = 1) 262s + box(lty .... [TRUNCATED] 262s 262s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 262s 262s > plot(mytr) 262s 262s > foo() 262s 262s > plot(mytr, "c", FALSE) 262s 262s > foo() 262s 262s > plot(mytr, "u") 262s 262s > foo() 262s 262s > par(xpd = TRUE) 262s 262s > plot(mytr, "f") 262s 262s > foo() 262s 262s > box("outer") 262s 262s > tr <- compute.brlen(stree(8, "l"), 0.1) 262s 262s > tr$tip.label[] <- "" 262s 262s > foo <- function() { 262s + col <- "green" 262s + axis(1, col = col, col.ticks = col, col.axis = col) 262s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 262s 262s > layout(matrix(1:12, 6, 2)) 262s 262s > par(mar = c(2, 2, 0.3, 0)) 262s 262s > for (type in c("p", "c")) { 262s + plot(tr, type) 262s + foo() 262s + plot(tr, type, node.pos = 2) 262s + foo() 262s + plot(tr, type, FALSE) 262s + foo() 262s .... [TRUNCATED] 262s 262s > foo <- function() { 262s + col <- "green" 262s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 262s + las = 1) 262s + box(lty .... [TRUNCATED] 262s 262s > layout(matrix(1:4, 2, 2)) 262s 262s > par(las = 1) 262s 262s > plot(tr, "u") 262s 262s > foo() 262s 262s > plot(tr, "u", FALSE) 262s 262s > foo() 262s 262s > plot(tr, "f") 262s 262s > foo() 262s 262s > plot(tr, "f", FALSE) 262s 262s > foo() 262s 262s > args(node.depth.edgelength) 262s function (phy) 262s NULL 262s 262s > args(node.depth) 262s function (phy, method = 1) 262s NULL 262s 262s > args(node.height) 262s function (phy, clado.style = FALSE) 262s NULL 262s 262s > args(unrooted.xy) 262s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 262s NULL 262s 262s > args(phylogram.plot) 262s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 262s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 262s node.lty = NULL) 262s NULL 262s 262s > args(cladogram.plot) 262s function (edge, xx, yy, edge.color, edge.width, edge.lty) 262s NULL 262s 262s > args(circular.plot) 262s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 262s edge.lty) 262s NULL 262s 262s > args(plot.phylo) 262s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 262s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 262s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 262s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 262s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 262s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 262s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 262s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 262s ...) 262s NULL 262s 262s > geo <- factor(c("Africa", "World", "Africa")) 262s 262s > (mycol <- c("blue", "red")[geo]) 262s [1] "blue" "red" "blue" 262s 262s > plot(mytr, tip.color = mycol) 262s 262s > par(xpd = TRUE) 262s 262s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 262s 262s > args(def) 262s function (x, ..., default = NULL, regexp = FALSE) 262s NULL 262s 262s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 262s 262s > identical(mycol, mycol2) 262s [1] TRUE 262s 262s > (i <- which.edge(mytr, c("Homo", "Pan"))) 262s [1] 2 3 262s 262s > co <- rep("black", Nedge(mytr)) 262s 262s > co[i] <- "blue" 262s 262s > par(xpd = TRUE) 262s 262s > plot(mytr, edge.col = co) 262s 262s > edgelabels() 262s 262s > args(axisPhylo) 262s function (side = NULL, root.time = NULL, backward = TRUE, ...) 262s NULL 262s 262s > args(add.scale.bar) 262s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 262s ...) 262s NULL 262s 262s > plot(mytr) 262s 262s > add.scale.bar() 262s 262s > axisPhylo() 262s 262s > axis(3) 262s 262s > args(nodelabels) 262s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 262s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 262s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 262s ...) 262s NULL 262s 262s > args(tiplabels) 262s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 262s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 262s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 262s offset = 0, ...) 262s NULL 262s 262s > args(edgelabels) 262s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 262s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 262s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 262s date = NULL, ...) 262s NULL 262s 262s > par(xpd = TRUE) 262s 262s > plot(mytr) 262s 262s > nodelabels() 262s 262s > tiplabels() 262s 262s > edgelabels() 262s 262s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 262s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 262s 262s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 262s 262s > v <- c(0, 0.5, 1) 262s 262s > layout(matrix(1:9, 3, 3)) 262s 262s > par(mar = c(3, 3, 3, 0), las = 1) 262s 262s > for (i in v) { 262s + for (j in v) { 262s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 262s + ")")) 262s + abline(v = 0, h = .... [TRUNCATED] 262s 262s > plot(rep(0, 3), 0:2, "n", las = 1) 262s 262s > abline(v = 0, h = 0:2, lty = 3) 262s 262s > text(0, 0:2, mytr$tip.label, adj = -1) 262s 262s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 262s 262s > args(phydataplot) 262s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 262s width = NULL, legend = "below", funcol = rainbow, ...) 262s NULL 262s 262s > args(ring) 262s function (x, phy, style = "ring", offset = 1, ...) 262s NULL 262s 262s > x <- matrix(1:6, 3, 10) 262s 262s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 262s 262s > x 262s A B C D E F G H I J 262s Homo 1 4 1 4 1 4 1 4 1 4 262s Gorilla 2 5 2 5 2 5 2 5 2 5 262s Pan 3 6 3 6 3 6 3 6 3 6 262s 262s > mytr$tip.label 262s [1] "Pan" "Homo" "Gorilla" 262s 262s > par(mar = c(10, 2, 5, 5)) 262s 262s > plot(mytr, x.lim = 30) 262s 262s > phydataplot(x, mytr, "m", border = "white", offset = 2, 262s + width = 1) 262s 262s > phydataplot(x, mytr, "m", border = "white", offset = 15, 262s + width = 1, continuous = 2) 262s 262s > n <- 100 262s 262s > p <- 3 262s 262s > set.seed(3) 262s 262s > tr <- rcoal(n) 262s 262s > x <- matrix(runif(p * n), n, p) 262s 262s > rownames(x) <- tr$tip.label 262s 262s > COL <- c("red", "green", "blue") 262s 262s > par(xpd = TRUE) 262s 262s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 262s + no.margin = TRUE) 262s 262s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 262s + col = COL[j]) 262s 262s > tree <- rtree(10) 262s 262s > tree$edge.length[1] <- 1000 262s 262s > layout(matrix(1:2, 1)) 262s 262s > plot(tree) 262s 262s > axisPhylo() 262s 262s > plotBreakLongEdges(tree) 262s 262s > axisPhylo() 262s 262s > el <- tree$edge.length 262s 262s > sum(el > mean(el) + 2 * sd(el)) 262s [1] 1 262s 262s > tree$edge.length[8] <- 1000 262s 262s > el <- tree$edge.length 262s 262s > sum(el > mean(el) + 2 * sd(el)) 262s [1] 2 262s 262s > layout(matrix(1:2, 1)) 262s 262s > plotBreakLongEdges(tree) 262s 262s > plotBreakLongEdges(tree, n = 2) 262s 262s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 262s + simplify = FALSE) 262s 262s > kronoviz(TR, type = "c", show.tip.label = FALSE) 262s 262s > dates <- as.Date(.leap.seconds) 262s 262s > tr <- rcoal(length(dates)) 262s 262s > plotTreeTime(tr, dates) 262s 262s > par(oma = rep(2, 4)) 262s 262s > plot(mytr) 262s 262s > box(lty = 3) 262s 262s > box("figure", col = "blue") 262s 262s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 262s + font = 2, col = "blue") 262s 262s > box("outer") 262s 262s > layout(matrix(1:4, 2, 2)) 262s 262s > par(oma = rep(2, 4)) 262s 262s > for (i in 1:4) { 262s + par(mar = rep(i, 4)) 262s + plot(mytr) 262s + box(lty = 3) 262s + box("figure", col = "blue") 262s + } 262s 262s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 262s + font = 2, col = "blue") 262s 262s > box("outer") 262s 262s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 262s 262s > for (i in 1:3) plot(rtree(5)) 262s 262s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 262s $type 262s [1] "phylogram" 262s 262s $use.edge.length 262s [1] TRUE 262s 262s $node.pos 262s [1] 1 262s 262s $node.depth 262s [1] 1 262s 262s $show.tip.label 262s [1] TRUE 262s 262s $show.node.label 262s [1] FALSE 262s 262s $font 262s [1] 3 262s 262s $cex 262s [1] 0.83 262s 262s $adj 262s [1] 0 262s 262s $srt 262s [1] 0 262s 262s $no.margin 262s [1] FALSE 262s 262s $label.offset 262s [1] 0 262s 262s $x.lim 262s [1] 0.00000 3.13046 262s 262s $y.lim 262s [1] 1 5 262s 262s $direction 262s [1] "rightwards" 262s 262s $tip.color 262s [1] "black" 262s 262s $Ntip 262s [1] 5 262s 262s $Nnode 262s [1] 4 262s 262s $root.time 262s NULL 262s 262s $align.tip.label 262s [1] FALSE 262s 262s $edge 262s [,1] [,2] 262s [1,] 6 1 262s [2,] 6 7 262s [3,] 7 2 262s [4,] 7 8 262s [5,] 8 3 262s [6,] 8 9 262s [7,] 9 4 262s [8,] 9 5 262s 262s $xx 262s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 262s [8] 1.3631198 1.9857132 262s 262s $yy 262s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 262s 262s 262s > layout(matrix(1:2, 2)) 262s 262s > plot(rtree(4)) 262s 262s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 262s 262s > x <- pp$xx[1] 262s 262s > y <- pp$yy[1] 262s 262s > (pu <- par("usr")) 262s [1] -0.06364557 1.65478492 0.88000000 4.12000000 262s 262s > (x - pu[1])/(pu[2] - pu[1]) 262s [1] 0.9349839 262s 262s > (y - pu[3])/(pu[4] - pu[3]) 262s [1] 0.03703704 262s 262s > pi <- par("pin") 262s 262s > mi <- par("mai") 262s 262s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 262s 262s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 262s 262s > plot(rtree(4)) 262s 262s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 262s 262s > x <- pp$xx[5] 262s 262s > y <- pp$yy[5] 262s 262s > pu <- par("usr") 262s 262s > pi <- par("pin") 262s 262s > mi <- par("mai") 262s 262s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 262s 262s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 262s 262s > yi1 <- yi1 + par("fin")[2] 262s 262s > di <- par("din") 262s 262s > layout(1) 262s 262s > par(new = TRUE, mai = rep(0, 4)) 262s 262s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 262s + ylim = 0:1, xaxs = "i", yaxs = "i") 262s 262s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 262s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 262s 262s > foo <- function(phy1, phy2, from) { 262s + layout(matrix(1:2, 2)) 262s + plot(phy1, font = 1) 262s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 262s 262s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 262s 262s > par(xpd = TRUE) 262s 262s > foo(trb, mytr, "Primates") 263s 263s > plot(mytr, plot = FALSE) 263s 263s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 263s 263s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 263s + pp$yy[2] + 0.1, col = "yellow", border = NA) 263s 263s > par(new = TRUE) 263s 263s > plot(mytr) 263s > 263s 263s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 263s Copyright (C) 2025 The R Foundation for Statistical Computing 263s Platform: aarch64-unknown-linux-gnu 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > Stangle("MoranI.Rnw") 263s Writing to file MoranI.R 263s > source("MoranI.R", echo=TRUE) 263s 263s > options(width = 80, prompt = "> ") 263s 263s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 263s 263s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 263s 263s > names(body) <- names(longevity) <- c("Homo", "Pongo", 263s + "Macaca", "Ateles", "Galago") 263s 263s > library(ape) 263s 263s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 263s 263s > trnwk[2] <- ":0.38,Galago:1.00);" 263s 263s > tr <- read.tree(text = trnwk) 263s 263s > plot(tr) 263s 263s > axisPhylo() 263s 263s > w <- 1/cophenetic(tr) 263s 263s > w 263s Homo Pongo Macaca Ateles Galago 263s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 263s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 263s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 263s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 263s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 263s 263s > diag(w) <- 0 263s 263s > Moran.I(body, w) 263s $observed 263s [1] -0.07312179 263s 263s $expected 263s [1] -0.25 263s 263s $sd 263s [1] 0.08910814 263s 263s $p.value 263s [1] 0.04714628 263s 263s 263s > Moran.I(body, w, alt = "greater") 263s $observed 263s [1] -0.07312179 263s 263s $expected 263s [1] -0.25 263s 263s $sd 263s [1] 0.08910814 263s 263s $p.value 263s [1] 0.02357314 263s 263s 263s > Moran.I(longevity, w) 263s $observed 263s [1] -0.1837739 263s 263s $expected 263s [1] -0.25 263s 263s $sd 263s [1] 0.09114549 263s 263s $p.value 263s [1] 0.4674727 263s 263s 263s > data(carnivora) 263s 263s > carnivora$log10SW <- log10(carnivora$SW) 263s 263s > carnivora$log10FW <- log10(carnivora$FW) 263s 263s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 263s 263s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 263s 263s > plot(co1) 263s 263s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 263s 263s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 263s 263s > print(plot(co2)) 263s 263s > plot(co2, FALSE) 263s > 263s 263s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 263s Copyright (C) 2025 The R Foundation for Statistical Computing 263s Platform: aarch64-unknown-linux-gnu 263s 263s R is free software and comes with ABSOLUTELY NO WARRANTY. 263s You are welcome to redistribute it under certain conditions. 263s Type 'license()' or 'licence()' for distribution details. 263s 263s R is a collaborative project with many contributors. 263s Type 'contributors()' for more information and 263s 'citation()' on how to cite R or R packages in publications. 263s 263s Type 'demo()' for some demos, 'help()' for on-line help, or 263s 'help.start()' for an HTML browser interface to help. 263s Type 'q()' to quit R. 263s 263s > Stangle("RandomTopologies.Rnw") 263s Writing to file RandomTopologies.R 263s > source("RandomTopologies.R", echo=TRUE) 263s 263s > options(width = 80, prompt = "> ") 263s 263s > library(ape) 263s 263s > n <- 1:10 263s 263s > data.frame(N.topo = sapply(n, howmanytrees)) 263s N.topo 263s 1 1 263s 2 1 263s 3 3 263s 4 15 263s 5 105 263s 6 945 263s 7 10395 263s 8 135135 263s 9 2027025 263s 10 34459425 263s 263s > howmanytrees(25) 263s [1] 1.192568e+30 263s 263s > howmanytrees(25) * 0.21 263s [1] 2.504393e+29 263s 263s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 263s N.topo 263s 1 1 263s 2 1 263s 3 1 263s 4 2 263s 5 3 263s 6 6 263s 7 11 263s 8 23 263s 9 46 263s 10 98 263s 263s > n2 <- c(50, 100, 200) 263s 263s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 263s + row.names = n2) 263s N.topo 263s 50 5.150149e+16 263s 100 1.019560e+36 263s 200 1.141703e+75 263s 263s > 1/howmanytrees(50) 263s [1] 3.632505e-77 263s 263s > 1/sapply(n, howmanytrees) 263s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 263s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 263s 263s > 1/sapply(n, howmanytrees, labeled = FALSE) 263s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 263s [7] 0.09090909 0.04347826 0.02173913 0.01020408 263s 263s > library(phangorn) 265s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 265s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 265s 265s > TR <- allTrees(4, rooted = TRUE) 265s 265s > TR 265s 15 phylogenetic trees 265s 265s > layout(matrix(1:15, 3, 5)) 265s 265s > par(mar = rep(1.5, 4), xpd = TRUE) 265s 265s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 265s 265s > K <- 100 265s 265s > n <- 50 265s 265s > N <- howmanytrees(n, labeled = FALSE) 265s 265s > p <- 1/N 265s 265s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 265s [1] 0 265s 265s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 265s [1] -5.431212e-17 265s 265s > f <- function(n, K) { 265s + N <- howmanytrees(n, labeled = FALSE) 265s + p <- 1/N 265s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 265s + } 265s 265s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 265s + 10000)) 265s 265s > DF$P <- mapply(f, n = DF$n, K = DF$K) 265s 265s > library(lattice) 265s 265s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 265s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 265s 265s > subset(DF, n == 20) 265s n K P 265s 17 20 2 1.160494e-11 265s 34 20 5 1.160491e-10 265s 51 20 10 5.222149e-10 265s 68 20 100 5.743191e-08 265s 85 20 1000 5.783570e-06 265s 102 20 10000 5.671842e-04 265s 265s > f(20, 1e+05) 265s [1] 0.04638755 265s 265s > f(30, 1e+06) 265s [1] 2.525152e-07 265s 265s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 265s 265s > TR5 <- read.tree(text = txt) 265s 265s > layout(matrix(1:3, 1)) 265s 265s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 265s 265s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 265s + labeled = FALSE) 265s [1] 2 265s 265s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 265s + labeled = FALSE) 265s [1] 1 265s 265s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 265s + labeled = FALSE) 265s [1] Inf 265s 265s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 265s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 265s 265s > foo.test <- function(x, labeled = TRUE) { 265s + uTR <- unique(x, use.tip.label = labeled) 265s + f <- integer(length(uTR)) 265s + for (j in seq_along( .... [TRUNCATED] 265s 265s > lapply(TR, foo.test) 269s [1] 72 84 69 76 54 67 64 68 57 52 80 70 62 58 67 271s [1] 66 126 52 62 45 94 115 69 50 52 54 42 64 53 56 273s [1] 41 42 48 176 178 39 158 43 39 44 37 33 48 36 38 273s [[1]] 273s 273s Chi-squared test for given probabilities 273s 273s data: f 273s X-squared = 17.78, df = 14, p-value = 0.217 273s 273s 273s [[2]] 273s 273s Chi-squared test for given probabilities 273s 273s data: f 273s X-squared = 133.28, df = 14, p-value < 2.2e-16 273s 273s 273s [[3]] 273s 273s Chi-squared test for given probabilities 273s 273s data: f 273s X-squared = 615.53, df = 14, p-value < 2.2e-16 273s 273s 273s 273s > lapply(TR, foo.test, labeled = FALSE) 274s [1] 815 185 274s [1] 665 335 275s [1] 488 512 275s [[1]] 275s 275s Chi-squared test for given probabilities 275s 275s data: f 275s X-squared = 396.9, df = 1, p-value < 2.2e-16 275s 275s 275s [[2]] 275s 275s Chi-squared test for given probabilities 275s 275s data: f 275s X-squared = 108.9, df = 1, p-value < 2.2e-16 275s 275s 275s [[3]] 275s 275s Chi-squared test for given probabilities 275s 275s data: f 275s X-squared = 0.576, df = 1, p-value = 0.4479 275s 275s 275s 275s > .Machine$double.xmax 275s [1] 1.797693e+308 275s 275s > howmanytrees(151) 275s [1] 3.753274e+306 275s 275s > howmanytrees(792, labeled = FALSE) 275s [1] 1.029038e+308 275s 275s > (N <- howmanytrees(2e+06)) 275s approximately 3.692364 * 10^12335524 275s 275s > N[2] + 1 275s n 275s 12335525 275s 275s > ceiling((N[2] + 1)/3000) 275s n 275s 4112 275s 275s > n <- 1:792 275s 275s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 275s 275s > lN <- log10(N) 275s 275s > summary(lm(lN ~ n)) 275s 275s Call: 275s lm(formula = lN ~ n) 275s 275s Residuals: 275s Min 1Q Median 3Q Max 275s -0.25968 -0.21424 -0.08311 0.12406 2.82605 275s 275s Coefficients: 275s Estimate Std. Error t value Pr(>|t|) 275s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 275s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 275s --- 275s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 275s 275s Residual standard error: 0.3175 on 790 degrees of freedom 275s Multiple R-squared: 1, Adjusted R-squared: 1 275s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 275s 275s 275s > s <- n > 700 275s 275s > summary(lm(lN[s] ~ n[s])) 275s 275s Call: 275s lm(formula = lN[s] ~ n[s]) 275s 275s Residuals: 275s Min 1Q Median 3Q Max 275s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 275s 275s Coefficients: 275s Estimate Std. Error t value Pr(>|t|) 275s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 275s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 275s --- 275s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 275s 275s Residual standard error: 0.0003738 on 90 degrees of freedom 275s Multiple R-squared: 1, Adjusted R-squared: 1 275s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 275s 275s 275s > n <- 788:792 275s 275s > log10(sapply(n, howmanytrees, labeled = FALSE)) 275s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 275s 275s > 0.3941 * n - 4.153 275s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 275s 275s > xi <- 2.477993 275s 275s > lxi <- log10(xi) 275s 275s > n <- 1000 275s 275s > (n - 1) * lxi 275s [1] 393.706 275s 275s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 275s + 1))))) 275s [1] 393.8532 275s [1] 393.9009 275s [1] 393.9187 275s [1] 393.9257 275s [1] 393.9285 275s [1] 393.9296 275s [1] 393.9301 275s [1] 393.9303 275s [1] 393.9304 275s [1] 393.9304 275s > 275s autopkgtest [22:54:29]: test run-unit-test: -----------------------] 275s run-unit-test PASS 275s autopkgtest [22:54:29]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 276s autopkgtest [22:54:30]: test pkg-r-autopkgtest: preparing testbed 276s Reading package lists... 276s Building dependency tree... 276s Reading state information... 276s Solving dependencies... 277s The following NEW packages will be installed: 277s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 277s dctrl-tools g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 277s gcc-15 gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-15 277s gfortran-15-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 277s libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 277s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 277s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-jquery 277s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 277s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 277s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 277s linux-libc-dev node-html5shiv pkg-r-autopkgtest pkgconf pkgconf-bin 277s r-base-dev r-cran-expm r-cran-gee r-cran-xml2 rpcsvc-proto zlib1g-dev 277s 0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded. 277s Need to get 104 MB of archives. 277s After this operation, 379 MB of additional disk space will be used. 277s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 277s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 280s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 280s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 280s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 283s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 284s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 284s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 303s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 303s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 303s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 303s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 303s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 303s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 307s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 309s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 314s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 316s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 319s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 323s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 356s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 356s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 356s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 357s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 361s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 381s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 381s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 381s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 381s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 381s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 381s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 381s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 399s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 399s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 399s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 399s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 399s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 399s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 399s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 399s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 418s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 418s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 418s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 418s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 418s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 425s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 425s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 425s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 425s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 425s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 426s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 426s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 428s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 428s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 428s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 428s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 428s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 428s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 428s Get:59 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 428s Get:60 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 428s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 428s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 428s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-expm arm64 1.0-0-1 [225 kB] 428s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-gee arm64 4.13-29-1 [72.8 kB] 428s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xml2 arm64 1.4.1-1 [326 kB] 428s Fetched 104 MB in 2min 31s (687 kB/s) 428s Selecting previously unselected package libc-dev-bin. 428s (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 ... 141669 files and directories currently installed.) 428s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 428s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 428s Selecting previously unselected package linux-libc-dev:arm64. 428s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_arm64.deb ... 428s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 428s Selecting previously unselected package libcrypt-dev:arm64. 428s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 428s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 428s Selecting previously unselected package rpcsvc-proto. 428s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 428s Unpacking rpcsvc-proto (1.4.3-1build1) ... 428s Selecting previously unselected package libc6-dev:arm64. 428s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_arm64.deb ... 428s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 428s Selecting previously unselected package libisl23:arm64. 428s Preparing to unpack .../05-libisl23_0.27-1build1_arm64.deb ... 428s Unpacking libisl23:arm64 (0.27-1build1) ... 428s Selecting previously unselected package libmpc3:arm64. 428s Preparing to unpack .../06-libmpc3_1.3.1-2_arm64.deb ... 428s Unpacking libmpc3:arm64 (1.3.1-2) ... 428s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 428s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 428s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package cpp-15. 429s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package cpp-aarch64-linux-gnu. 429s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 429s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 429s Selecting previously unselected package cpp. 429s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 429s Unpacking cpp (4:15.2.0-4ubuntu1) ... 429s Selecting previously unselected package libcc1-0:arm64. 429s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libitm1:arm64. 429s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libasan8:arm64. 429s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package liblsan0:arm64. 429s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libtsan2:arm64. 429s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libubsan1:arm64. 429s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libhwasan0:arm64. 429s Preparing to unpack .../17-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package libgcc-15-dev:arm64. 429s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 429s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 429s Preparing to unpack .../19-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 429s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package gcc-15. 430s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package gcc-aarch64-linux-gnu. 430s Preparing to unpack .../21-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 430s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 430s Selecting previously unselected package gcc. 430s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 430s Unpacking gcc (4:15.2.0-4ubuntu1) ... 430s Selecting previously unselected package libstdc++-15-dev:arm64. 430s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package g++-15-aarch64-linux-gnu. 430s Preparing to unpack .../24-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package g++-15. 430s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking g++-15 (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package g++-aarch64-linux-gnu. 430s Preparing to unpack .../26-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 430s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 430s Selecting previously unselected package g++. 430s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 430s Unpacking g++ (4:15.2.0-4ubuntu1) ... 430s Selecting previously unselected package build-essential. 430s Preparing to unpack .../28-build-essential_12.12ubuntu2_arm64.deb ... 430s Unpacking build-essential (12.12ubuntu2) ... 430s Selecting previously unselected package dctrl-tools. 430s Preparing to unpack .../29-dctrl-tools_2.24-3build4_arm64.deb ... 430s Unpacking dctrl-tools (2.24-3build4) ... 430s Selecting previously unselected package libgfortran-15-dev:arm64. 430s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 430s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 430s Preparing to unpack .../31-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 430s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package gfortran-15. 431s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 431s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package gfortran-aarch64-linux-gnu. 431s Preparing to unpack .../33-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 431s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package gfortran. 431s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 431s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package icu-devtools. 431s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_arm64.deb ... 431s Unpacking icu-devtools (78.2-1ubuntu1) ... 431s Selecting previously unselected package libblas-dev:arm64. 431s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 431s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 431s Selecting previously unselected package libbz2-dev:arm64. 431s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_arm64.deb ... 431s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 431s Selecting previously unselected package libdeflate-dev:arm64. 431s Preparing to unpack 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432s Unpacking libreadline-dev:arm64 (8.3-3) ... 432s Selecting previously unselected package libzstd-dev:arm64. 432s Preparing to unpack .../54-libzstd-dev_1.5.7+dfsg-3_arm64.deb ... 432s Unpacking libzstd-dev:arm64 (1.5.7+dfsg-3) ... 432s Selecting previously unselected package node-html5shiv. 432s Preparing to unpack .../55-node-html5shiv_3.7.3+dfsg-5_all.deb ... 432s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 432s Selecting previously unselected package liblzma-dev:arm64. 432s Preparing to unpack .../56-liblzma-dev_5.8.2-2_arm64.deb ... 432s Unpacking liblzma-dev:arm64 (5.8.2-2) ... 432s Selecting previously unselected package pkgconf-bin. 432s Preparing to unpack .../57-pkgconf-bin_1.8.1-4build1_arm64.deb ... 432s Unpacking pkgconf-bin (1.8.1-4build1) ... 432s Selecting previously unselected package pkgconf:arm64. 432s Preparing to unpack .../58-pkgconf_1.8.1-4build1_arm64.deb ... 432s Unpacking pkgconf:arm64 (1.8.1-4build1) ... 432s Selecting previously unselected package 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(15.2.0-12ubuntu1) ... 432s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 432s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 432s Setting up g++-15 (15.2.0-12ubuntu1) ... 432s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 432s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Setting up libpng-dev:arm64 (1.6.54-1) ... 432s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 432s Setting up gcc (4:15.2.0-4ubuntu1) ... 432s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Setting up gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Setting up gfortran (4:15.2.0-4ubuntu1) ... 432s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 432s 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 432s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 432s 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 432s Setting up g++ (4:15.2.0-4ubuntu1) ... 432s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 432s Setting up build-essential (12.12ubuntu2) ... 432s Setting up r-base-dev (4.5.2-1ubuntu2) ... 432s Setting up pkg-r-autopkgtest (20250812) ... 432s Processing triggers for libc-bin (2.42-2ubuntu4) ... 432s Processing triggers for man-db (2.13.1-1build1) ... 436s Processing triggers for install-info (7.2-5) ... 436s autopkgtest [22:57:10]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 436s autopkgtest [22:57:10]: test pkg-r-autopkgtest: [----------------------- 437s Test: Try to load the R library ape 437s 437s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 437s Copyright (C) 2025 The R Foundation for Statistical Computing 437s Platform: aarch64-unknown-linux-gnu 437s 437s R is free software and comes with ABSOLUTELY NO WARRANTY. 437s You are welcome to redistribute it under certain conditions. 437s Type 'license()' or 'licence()' for distribution details. 437s 437s R is a collaborative project with many contributors. 437s Type 'contributors()' for more information and 437s 'citation()' on how to cite R or R packages in publications. 437s 437s Type 'demo()' for some demos, 'help()' for on-line help, or 437s 'help.start()' for an HTML browser interface to help. 437s Type 'q()' to quit R. 437s 437s > library('ape') 437s > 437s autopkgtest [22:57:11]: test pkg-r-autopkgtest: -----------------------] 438s autopkgtest [22:57:12]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 438s pkg-r-autopkgtest PASS 438s autopkgtest [22:57:12]: @@@@@@@@@@@@@@@@@@@@ summary 438s run-unit-test PASS 438s pkg-r-autopkgtest PASS