0s autopkgtest [07:10:08]: starting date and time: 2025-05-02 07:10:08+0000 0s autopkgtest [07:10:08]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [07:10:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fl_yxocz/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:nlme --apt-upgrade r-cran-ape --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=nlme/3.1.168-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-7.secgroup --name adt-questing-arm64-r-cran-ape-20250502-071008-juju-7f2275-prod-proposed-migration-environment-2-26771ad1-b902-4af5-acca-1ed115005f42 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 77s autopkgtest [07:11:25]: testbed dpkg architecture: arm64 77s autopkgtest [07:11:25]: testbed apt version: 3.0.0 77s autopkgtest [07:11:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s autopkgtest [07:11:25]: testbed release detected to be: None 78s autopkgtest [07:11:26]: updating testbed package index (apt update) 78s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 78s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 78s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [57.4 kB] 78s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2202 kB] 79s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [184 kB] 79s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [227 kB] 79s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1472 kB] 79s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [16.5 kB] 79s Fetched 4269 kB in 1s (6463 kB/s) 80s Reading package lists... 80s autopkgtest [07:11:28]: upgrading testbed (apt dist-upgrade and autopurge) 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 81s Starting 2 pkgProblemResolver with broken count: 0 81s Done 82s Entering ResolveByKeep 82s 82s Calculating upgrade... 82s The following packages will be upgraded: 82s libperl5.40 perl perl-base perl-modules-5.40 82s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 10.0 MB of archives. 82s After this operation, 0 B of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libperl5.40 arm64 5.40.1-3 [4780 kB] 83s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl arm64 5.40.1-3 [262 kB] 83s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-base arm64 5.40.1-3 [1786 kB] 83s Get:4 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 perl-modules-5.40 all 5.40.1-3 [3217 kB] 83s Fetched 10.0 MB in 1s (15.3 MB/s) 84s (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 ... 85224 files and directories currently installed.) 84s Preparing to unpack .../libperl5.40_5.40.1-3_arm64.deb ... 84s Unpacking libperl5.40:arm64 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Preparing to unpack .../perl_5.40.1-3_arm64.deb ... 84s Unpacking perl (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Preparing to unpack .../perl-base_5.40.1-3_arm64.deb ... 84s Unpacking perl-base (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Setting up perl-base (5.40.1-3) ... 84s (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 ... 85224 files and directories currently installed.) 84s Preparing to unpack .../perl-modules-5.40_5.40.1-3_all.deb ... 84s Unpacking perl-modules-5.40 (5.40.1-3) over (5.40.1-2ubuntu0.1) ... 84s Setting up perl-modules-5.40 (5.40.1-3) ... 84s Setting up libperl5.40:arm64 (5.40.1-3) ... 84s Setting up perl (5.40.1-3) ... 84s Processing triggers for man-db (2.13.0-1) ... 85s Processing triggers for libc-bin (2.41-6ubuntu1) ... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 86s Solving dependencies... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [07:11:37]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 89s autopkgtest [07:11:37]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 90s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 90s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 90s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 90s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 90s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 90s gpgv: issuer "plessy@debian.org" 90s gpgv: Can't check signature: No public key 90s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 90s autopkgtest [07:11:38]: testing package r-cran-ape version 5.8-1-1 91s autopkgtest [07:11:39]: build not needed 98s autopkgtest [07:11:46]: test run-unit-test: preparing testbed 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Starting pkgProblemResolver with broken count: 0 98s Starting 2 pkgProblemResolver with broken count: 0 98s Done 99s The following NEW packages will be installed: 99s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 99s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 99s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 99s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 99s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 99s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 99s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 99s libxss1 libxt6t64 littler r-base-core r-cran-ape r-cran-cli r-cran-cpp11 99s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 99s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 99s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 99s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 99s xdg-utils zip 99s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 63.9 MB of archives. 99s After this operation, 129 MB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 99s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 99s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 99s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 99s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig arm64 2.15.0-2.2ubuntu1 [191 kB] 99s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 99s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libsuitesparseconfig7 arm64 1:7.8.3+dfsg-3 [13.2 kB] 99s Get:8 http://ftpmaster.internal/ubuntu questing/universe arm64 libamd3 arm64 1:7.8.3+dfsg-3 [26.1 kB] 99s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 99s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 99s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 99s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 99s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 99s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 99s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libcolamd3 arm64 1:7.8.3+dfsg-3 [18.3 kB] 99s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 99s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 99s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 99s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libltdl7 arm64 2.5.4-4 [43.0 kB] 99s Get:20 http://ftpmaster.internal/ubuntu questing/universe arm64 libglpk40 arm64 5.0-1build2 [337 kB] 99s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 99s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 99s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 99s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 99s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 99s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 99s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 99s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 99s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 99s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 99s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 99s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 99s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 99s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 99s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 99s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 99s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 99s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 99s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 99s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 99s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 99s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 99s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 99s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 99s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 99s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 99s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 99s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 100s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 100s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-littler arm64 0.3.20-2 [96.1 kB] 100s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 littler all 0.3.20-2 [2554 B] 100s Get:52 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 100s Get:53 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 100s Get:54 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 100s Get:55 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-rcpp arm64 1.0.14-1 [1978 kB] 100s Get:56 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-digest arm64 0.6.37-1 [200 kB] 100s Get:57 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-ape arm64 5.8-1-1 [2901 kB] 100s Get:58 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-cli arm64 3.6.4-1 [1374 kB] 100s Get:59 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-cpp11 all 0.5.2-1 [233 kB] 100s Get:60 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-fastmatch arm64 1.1-6-1 [36.0 kB] 100s Get:61 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-generics all 0.1.3-1 [81.3 kB] 100s Get:62 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-glue arm64 1.8.0-1 [163 kB] 100s Get:63 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-rlang arm64 1.1.5-1 [1707 kB] 101s Get:64 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 101s Get:65 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-magrittr arm64 2.0.3-1 [154 kB] 101s Get:66 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 101s Get:67 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 101s Get:68 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-vctrs arm64 0.6.5-1 [1327 kB] 101s Get:69 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-igraph arm64 2.1.4-1 [5150 kB] 101s Get:70 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-quadprog arm64 1.5-8-1build1 [29.8 kB] 101s Get:71 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-phangorn arm64 2.12.1+dfsg-1 [1803 kB] 101s Preconfiguring packages ... 101s Fetched 63.9 MB in 2s (34.2 MB/s) 101s Selecting previously unselected package fonts-dejavu-mono. 101s (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 ... 85224 files and directories currently installed.) 101s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 101s Unpacking fonts-dejavu-mono (2.37-8) ... 101s Selecting previously unselected package fonts-dejavu-core. 101s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 101s Unpacking fonts-dejavu-core (2.37-8) ... 102s Selecting previously unselected package fontconfig-config. 102s Preparing to unpack .../02-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 102s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 102s Selecting previously unselected package libfontconfig1:arm64. 102s Preparing to unpack .../03-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 102s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 102s Selecting previously unselected package fontconfig. 102s Preparing to unpack .../04-fontconfig_2.15.0-2.2ubuntu1_arm64.deb ... 102s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 102s Selecting previously unselected package libgomp1:arm64. 102s Preparing to unpack .../05-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 102s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 102s Selecting previously unselected package libsuitesparseconfig7:arm64. 102s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_arm64.deb ... 102s Unpacking libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ... 102s Selecting previously unselected package libamd3:arm64. 102s Preparing to unpack .../07-libamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 102s Unpacking libamd3:arm64 (1:7.8.3+dfsg-3) ... 102s Selecting previously unselected package libblas3:arm64. 102s Preparing to unpack .../08-libblas3_3.12.1-2_arm64.deb ... 102s Unpacking libblas3:arm64 (3.12.1-2) ... 102s Selecting previously unselected package libpixman-1-0:arm64. 102s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_arm64.deb ... 102s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 102s Selecting previously unselected package libxcb-render0:arm64. 102s Preparing to unpack .../10-libxcb-render0_1.17.0-2_arm64.deb ... 102s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 102s Selecting previously unselected package libxcb-shm0:arm64. 102s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_arm64.deb ... 102s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 102s Selecting previously unselected package libxrender1:arm64. 102s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 102s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 102s Selecting previously unselected package libcairo2:arm64. 102s Preparing to unpack .../13-libcairo2_1.18.4-1_arm64.deb ... 102s Unpacking libcairo2:arm64 (1.18.4-1) ... 102s Selecting previously unselected package libcolamd3:arm64. 102s Preparing to unpack .../14-libcolamd3_1%3a7.8.3+dfsg-3_arm64.deb ... 102s Unpacking libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 102s Selecting previously unselected package libdatrie1:arm64. 102s Preparing to unpack .../15-libdatrie1_0.2.13-3build1_arm64.deb ... 102s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 102s Selecting previously unselected package libdeflate0:arm64. 102s Preparing to unpack .../16-libdeflate0_1.23-1_arm64.deb ... 102s Unpacking libdeflate0:arm64 (1.23-1) ... 102s Selecting previously unselected package libgfortran5:arm64. 102s Preparing to unpack .../17-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 102s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 102s Selecting previously unselected package libltdl7:arm64. 102s Preparing to unpack .../18-libltdl7_2.5.4-4_arm64.deb ... 102s Unpacking libltdl7:arm64 (2.5.4-4) ... 102s Selecting previously unselected package libglpk40:arm64. 102s Preparing to unpack .../19-libglpk40_5.0-1build2_arm64.deb ... 102s Unpacking libglpk40:arm64 (5.0-1build2) ... 102s Selecting previously unselected package libgraphite2-3:arm64. 102s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 102s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 102s Selecting previously unselected package libharfbuzz0b:arm64. 102s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_arm64.deb ... 102s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 102s Selecting previously unselected package x11-common. 102s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu4_all.deb ... 102s Unpacking x11-common (1:7.7+23ubuntu4) ... 102s Selecting previously unselected package libice6:arm64. 102s Preparing to unpack .../23-libice6_2%3a1.1.1-1_arm64.deb ... 102s Unpacking libice6:arm64 (2:1.1.1-1) ... 102s Selecting previously unselected package libjpeg-turbo8:arm64. 102s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 102s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 102s Selecting previously unselected package libjpeg8:arm64. 102s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 102s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 102s Selecting previously unselected package liblapack3:arm64. 102s Preparing to unpack .../26-liblapack3_3.12.1-2_arm64.deb ... 102s Unpacking liblapack3:arm64 (3.12.1-2) ... 103s Selecting previously unselected package liblerc4:arm64. 103s Preparing to unpack .../27-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 103s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 103s Selecting previously unselected package libthai-data. 103s Preparing to unpack .../28-libthai-data_0.1.29-2build1_all.deb ... 103s Unpacking libthai-data (0.1.29-2build1) ... 103s Selecting previously 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libgomp1:arm64 (15-20250404-0ubuntu1) ... 105s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 105s Setting up zip (3.0-14ubuntu2) ... 105s Setting up libblas3:arm64 (3.12.1-2) ... 105s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 105s Setting up fonts-dejavu-mono (2.37-8) ... 105s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 105s Setting up fonts-dejavu-core (2.37-8) ... 105s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 105s Setting up libltdl7:arm64 (2.5.4-4) ... 105s Setting up libgfortran5:arm64 (15-20250404-0ubuntu1) ... 105s Setting up libwebp7:arm64 (1.5.0-0.1) ... 105s Setting up libsuitesparseconfig7:arm64 (1:7.8.3+dfsg-3) ... 105s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 105s Setting up libthai-data (0.1.29-2build1) ... 105s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 105s Setting up libpaper2:arm64 (2.2.5-0.3) ... 105s Setting up xdg-utils (1.2.1-2ubuntu1) ... 105s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 105s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 105s Setting up libice6:arm64 (2:1.1.1-1) ... 105s Setting up liblapack3:arm64 (3.12.1-2) ... 105s 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 105s Setting up libamd3:arm64 (1:7.8.3+dfsg-3) ... 105s Setting up libcolamd3:arm64 (1:7.8.3+dfsg-3) ... 105s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 105s Setting up libpaper-utils (2.2.5-0.3) ... 105s Setting up libthai0:arm64 (0.1.29-2build1) ... 105s Setting up libglpk40:arm64 (5.0-1build2) ... 105s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 105s Setting up libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 105s Setting up libsm6:arm64 (2:1.2.4-1) ... 105s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 107s Regenerating fonts cache... done. 107s Setting up libxft2:arm64 (2.3.6-1build1) ... 107s Setting up libtk8.6:arm64 (8.6.16-1) ... 107s Setting up libpango-1.0-0:arm64 (1.56.3-1) ... 107s Setting up libcairo2:arm64 (1.18.4-1) ... 107s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 107s Setting up libpangoft2-1.0-0:arm64 (1.56.3-1) ... 107s Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ... 107s Setting up r-base-core (4.4.3-1) ... 108s Creating config file /etc/R/Renviron with new version 108s Setting up r-cran-fastmatch (1.1-6-1) ... 108s Setting up r-cran-lattice (0.22-6-1) ... 108s Setting up r-cran-nlme (3.1.168-1) ... 108s Setting up r-cran-pkgkitten (0.2.4-1) ... 108s Setting up r-cran-magrittr (2.0.3-1) ... 108s Setting up r-cran-quadprog (1.5-8-1build1) ... 108s Setting up r-cran-littler (0.3.20-2) ... 108s Setting up r-cran-rcpp (1.0.14-1) ... 108s Setting up r-cran-rlang (1.1.5-1) ... 108s Setting up littler (0.3.20-2) ... 108s Setting up r-cran-generics (0.1.3-1) ... 108s Setting up r-cran-digest (0.6.37-1) ... 108s Setting up r-cran-ape (5.8-1-1) ... 108s Setting up r-cran-glue (1.8.0-1) ... 108s Setting up r-cran-cli (3.6.4-1) ... 108s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 108s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 108s Setting up r-cran-cpp11 (0.5.2-1) ... 108s Setting up r-cran-matrix (1.7-3-1) ... 108s Setting up r-cran-vctrs (0.6.5-1) ... 108s Setting up r-cran-igraph (2.1.4-1) ... 108s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 108s Processing triggers for libc-bin (2.41-6ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 108s Processing triggers for install-info (7.1.1-1) ... 109s autopkgtest [07:11:57]: test run-unit-test: [----------------------- 110s 110s R version 4.4.3 (2025-02-28) -- "Trophy Case" 110s Copyright (C) 2025 The R Foundation for Statistical Computing 110s Platform: aarch64-unknown-linux-gnu 110s 110s R is free software and comes with ABSOLUTELY NO WARRANTY. 110s You are welcome to redistribute it under certain conditions. 110s Type 'license()' or 'licence()' for distribution details. 110s 110s R is a collaborative project with many contributors. 110s Type 'contributors()' for more information and 110s 'citation()' on how to cite R or R packages in publications. 110s 110s Type 'demo()' for some demos, 'help()' for on-line help, or 110s 'help.start()' for an HTML browser interface to help. 110s Type 'q()' to quit R. 110s 110s > Stangle("DrawingPhylogenies.Rnw") 110s Writing to file DrawingPhylogenies.R 110s > source("DrawingPhylogenies.R", echo=TRUE) 110s 110s > options(width = 80, prompt = "> ") 110s 110s > library(ape) 110s 110s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 110s 110s > foo <- function() { 110s + col <- "green" 110s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 110s + las = 1) 110s + box(lty .... [TRUNCATED] 110s 110s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 110s 110s > plot(mytr) 110s 110s > foo() 110s 110s > plot(mytr, "c", FALSE) 110s 110s > foo() 110s 110s > plot(mytr, "u") 110s 110s > foo() 110s 110s > par(xpd = TRUE) 110s 110s > plot(mytr, "f") 110s 110s > foo() 110s 110s > box("outer") 110s 110s > tr <- compute.brlen(stree(8, "l"), 0.1) 110s 110s > tr$tip.label[] <- "" 110s 110s > foo <- function() { 110s + col <- "green" 110s + axis(1, col = col, col.ticks = col, col.axis = col) 110s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 110s 110s > layout(matrix(1:12, 6, 2)) 110s 110s > par(mar = c(2, 2, 0.3, 0)) 110s 110s > for (type in c("p", "c")) { 110s + plot(tr, type) 110s + foo() 110s + plot(tr, type, node.pos = 2) 110s + foo() 110s + plot(tr, type, FALSE) 110s + foo() 110s .... [TRUNCATED] 110s 110s > foo <- function() { 110s + col <- "green" 110s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 110s + las = 1) 110s + box(lty .... [TRUNCATED] 110s 110s > layout(matrix(1:4, 2, 2)) 110s 110s > par(las = 1) 110s 110s > plot(tr, "u") 110s 110s > foo() 110s 110s > plot(tr, "u", FALSE) 110s 110s > foo() 110s 110s > plot(tr, "f") 110s 110s > foo() 110s 110s > plot(tr, "f", FALSE) 110s 110s > foo() 110s 110s > args(node.depth.edgelength) 110s function (phy) 110s NULL 110s 110s > args(node.depth) 110s function (phy, method = 1) 110s NULL 110s 110s > args(node.height) 110s function (phy, clado.style = FALSE) 110s NULL 110s 110s > args(unrooted.xy) 110s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 110s NULL 110s 110s > args(phylogram.plot) 110s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 110s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 110s node.lty = NULL) 110s NULL 110s 110s > args(cladogram.plot) 110s function (edge, xx, yy, edge.color, edge.width, edge.lty) 110s NULL 110s 110s > args(circular.plot) 110s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 110s edge.lty) 110s NULL 110s 110s > args(plot.phylo) 110s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 110s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 110s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 110s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 110s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 110s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 110s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 110s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 110s ...) 110s NULL 110s 110s > geo <- factor(c("Africa", "World", "Africa")) 110s 110s > (mycol <- c("blue", "red")[geo]) 110s [1] "blue" "red" "blue" 110s 110s > plot(mytr, tip.color = mycol) 110s 110s > par(xpd = TRUE) 110s 110s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 110s 110s > args(def) 110s function (x, ..., default = NULL, regexp = FALSE) 110s NULL 110s 110s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 110s 110s > identical(mycol, mycol2) 110s [1] TRUE 110s 110s > (i <- which.edge(mytr, c("Homo", "Pan"))) 110s [1] 2 3 110s 110s > co <- rep("black", Nedge(mytr)) 110s 110s > co[i] <- "blue" 110s 110s > par(xpd = TRUE) 110s 110s > plot(mytr, edge.col = co) 110s 110s > edgelabels() 110s 110s > args(axisPhylo) 110s function (side = NULL, root.time = NULL, backward = TRUE, ...) 110s NULL 110s 110s > args(add.scale.bar) 110s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 110s ...) 110s NULL 110s 110s > plot(mytr) 110s 110s > add.scale.bar() 110s 110s > axisPhylo() 110s 110s > axis(3) 110s 110s > args(nodelabels) 110s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 110s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 110s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 110s ...) 110s NULL 110s 110s > args(tiplabels) 110s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 110s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 110s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 110s offset = 0, ...) 110s NULL 110s 110s > args(edgelabels) 110s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 110s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 110s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 110s date = NULL, ...) 110s NULL 110s 110s > par(xpd = TRUE) 110s 110s > plot(mytr) 110s 110s > nodelabels() 110s 110s > tiplabels() 110s 110s > edgelabels() 110s 110s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 110s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 110s 110s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 110s 110s > v <- c(0, 0.5, 1) 110s 110s > layout(matrix(1:9, 3, 3)) 110s 110s > par(mar = c(3, 3, 3, 0), las = 1) 110s 110s > for (i in v) { 110s + for (j in v) { 110s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 110s + ")")) 110s + abline(v = 0, h = .... [TRUNCATED] 110s 110s > plot(rep(0, 3), 0:2, "n", las = 1) 110s 110s > abline(v = 0, h = 0:2, lty = 3) 110s 110s > text(0, 0:2, mytr$tip.label, adj = -1) 110s 110s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 110s 110s > args(phydataplot) 110s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 110s width = NULL, legend = "below", funcol = rainbow, ...) 110s NULL 110s 110s > args(ring) 110s function (x, phy, style = "ring", offset = 1, ...) 110s NULL 110s 110s > x <- matrix(1:6, 3, 10) 110s 110s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 110s 110s > x 110s A B C D E F G H I J 110s Homo 1 4 1 4 1 4 1 4 1 4 110s Gorilla 2 5 2 5 2 5 2 5 2 5 110s Pan 3 6 3 6 3 6 3 6 3 6 110s 110s > mytr$tip.label 110s [1] "Pan" "Homo" "Gorilla" 110s 110s > par(mar = c(10, 2, 5, 5)) 110s 110s > plot(mytr, x.lim = 30) 110s 110s > phydataplot(x, mytr, "m", border = "white", offset = 2, 110s + width = 1) 110s 110s > phydataplot(x, mytr, "m", border = "white", offset = 15, 110s + width = 1, continuous = 2) 110s 110s > n <- 100 110s 110s > p <- 3 110s 110s > set.seed(3) 110s 110s > tr <- rcoal(n) 110s 110s > x <- matrix(runif(p * n), n, p) 110s 110s > rownames(x) <- tr$tip.label 110s 110s > COL <- c("red", "green", "blue") 110s 110s > par(xpd = TRUE) 110s 110s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 110s + no.margin = TRUE) 110s 110s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 110s + col = COL[j]) 110s 110s > tree <- rtree(10) 110s 110s > tree$edge.length[1] <- 1000 110s 110s > layout(matrix(1:2, 1)) 110s 110s > plot(tree) 110s 110s > axisPhylo() 110s 110s > plotBreakLongEdges(tree) 110s 110s > axisPhylo() 110s 110s > el <- tree$edge.length 110s 110s > sum(el > mean(el) + 2 * sd(el)) 110s [1] 1 110s 110s > tree$edge.length[8] <- 1000 110s 110s > el <- tree$edge.length 110s 110s > sum(el > mean(el) + 2 * sd(el)) 110s [1] 2 110s 110s > layout(matrix(1:2, 1)) 110s 110s > plotBreakLongEdges(tree) 110s 110s > plotBreakLongEdges(tree, n = 2) 110s 110s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 110s + simplify = FALSE) 110s 110s > kronoviz(TR, type = "c", show.tip.label = FALSE) 110s 110s > dates <- as.Date(.leap.seconds) 110s 110s > tr <- rcoal(length(dates)) 110s 110s > plotTreeTime(tr, dates) 110s 110s > par(oma = rep(2, 4)) 110s 110s > plot(mytr) 110s 110s > box(lty = 3) 110s 110s > box("figure", col = "blue") 110s 110s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 110s + font = 2, col = "blue") 110s 110s > box("outer") 110s 110s > layout(matrix(1:4, 2, 2)) 110s 110s > par(oma = rep(2, 4)) 110s 110s > for (i in 1:4) { 110s + par(mar = rep(i, 4)) 110s + plot(mytr) 110s + box(lty = 3) 110s + box("figure", col = "blue") 110s + } 110s 110s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 110s + font = 2, col = "blue") 110s 110s > box("outer") 110s 110s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 110s 110s > for (i in 1:3) plot(rtree(5)) 110s 110s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 110s $type 110s [1] "phylogram" 110s 110s $use.edge.length 110s [1] TRUE 110s 110s $node.pos 110s [1] 1 110s 110s $node.depth 110s [1] 1 110s 110s $show.tip.label 110s [1] TRUE 110s 110s $show.node.label 110s [1] FALSE 110s 110s $font 110s [1] 3 110s 110s $cex 110s [1] 0.83 110s 110s $adj 110s [1] 0 110s 110s $srt 110s [1] 0 110s 110s $no.margin 110s [1] FALSE 110s 110s $label.offset 110s [1] 0 110s 110s $x.lim 110s [1] 0.00000 3.13046 110s 110s $y.lim 110s [1] 1 5 110s 110s $direction 110s [1] "rightwards" 110s 110s $tip.color 110s [1] "black" 110s 110s $Ntip 110s [1] 5 110s 110s $Nnode 110s [1] 4 110s 110s $root.time 110s NULL 110s 110s $align.tip.label 110s [1] FALSE 110s 110s $edge 110s [,1] [,2] 110s [1,] 6 1 110s [2,] 6 7 110s [3,] 7 2 110s [4,] 7 8 110s [5,] 8 3 110s [6,] 8 9 110s [7,] 9 4 110s [8,] 9 5 110s 110s $xx 110s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 110s [8] 1.3631198 1.9857132 110s 110s $yy 110s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 110s 110s 110s > layout(matrix(1:2, 2)) 110s 110s > plot(rtree(4)) 110s 110s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 110s 110s > x <- pp$xx[1] 110s 110s > y <- pp$yy[1] 110s 110s > (pu <- par("usr")) 110s [1] -0.06364557 1.65478492 0.88000000 4.12000000 110s 110s > (x - pu[1])/(pu[2] - pu[1]) 110s [1] 0.9349839 110s 110s > (y - pu[3])/(pu[4] - pu[3]) 110s [1] 0.03703704 110s 110s > pi <- par("pin") 110s 110s > mi <- par("mai") 110s 110s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 110s 110s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 110s 110s > plot(rtree(4)) 110s 110s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 110s 110s > x <- pp$xx[5] 110s 110s > y <- pp$yy[5] 110s 110s > pu <- par("usr") 110s 110s > pi <- par("pin") 110s 110s > mi <- par("mai") 110s 110s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 110s 110s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 110s 110s > yi1 <- yi1 + par("fin")[2] 110s 110s > di <- par("din") 110s 110s > layout(1) 110s 110s > par(new = TRUE, mai = rep(0, 4)) 110s 110s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 110s + ylim = 0:1, xaxs = "i", yaxs = "i") 110s 110s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 110s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 110s 110s > foo <- function(phy1, phy2, from) { 110s + layout(matrix(1:2, 2)) 110s + plot(phy1, font = 1) 110s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 110s 110s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 110s 110s > par(xpd = TRUE) 110s 110s > foo(trb, mytr, "Primates") 110s 110s > plot(mytr, plot = FALSE) 110s 110s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 110s 110s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 110s + pp$yy[2] + 0.1, col = "yellow", border = NA) 110s 110s > par(new = TRUE) 110s 110s > plot(mytr) 110s > 111s 111s R version 4.4.3 (2025-02-28) -- "Trophy Case" 111s Copyright (C) 2025 The R Foundation for Statistical Computing 111s Platform: aarch64-unknown-linux-gnu 111s 111s R is free software and comes with ABSOLUTELY NO WARRANTY. 111s You are welcome to redistribute it under certain conditions. 111s Type 'license()' or 'licence()' for distribution details. 111s 111s R is a collaborative project with many contributors. 111s Type 'contributors()' for more information and 111s 'citation()' on how to cite R or R packages in publications. 111s 111s Type 'demo()' for some demos, 'help()' for on-line help, or 111s 'help.start()' for an HTML browser interface to help. 111s Type 'q()' to quit R. 111s 111s > Stangle("MoranI.Rnw") 111s Writing to file MoranI.R 111s > source("MoranI.R", echo=TRUE) 111s 111s > options(width = 80, prompt = "> ") 111s 111s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 111s 111s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 111s 111s > names(body) <- names(longevity) <- c("Homo", "Pongo", 111s + "Macaca", "Ateles", "Galago") 111s 111s > library(ape) 111s 111s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 111s 111s > trnwk[2] <- ":0.38,Galago:1.00);" 111s 111s > tr <- read.tree(text = trnwk) 111s 111s > plot(tr) 111s 111s > axisPhylo() 111s 111s > w <- 1/cophenetic(tr) 111s 111s > w 111s Homo Pongo Macaca Ateles Galago 111s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 111s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 111s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 111s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 111s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 111s 111s > diag(w) <- 0 111s 111s > Moran.I(body, w) 111s $observed 111s [1] -0.07312179 111s 111s $expected 111s [1] -0.25 111s 111s $sd 111s [1] 0.08910814 111s 111s $p.value 111s [1] 0.04714628 111s 111s 111s > Moran.I(body, w, alt = "greater") 111s $observed 111s [1] -0.07312179 111s 111s $expected 111s [1] -0.25 111s 111s $sd 111s [1] 0.08910814 111s 111s $p.value 111s [1] 0.02357314 111s 111s 111s > Moran.I(longevity, w) 111s $observed 111s [1] -0.1837739 111s 111s $expected 111s [1] -0.25 111s 111s $sd 111s [1] 0.09114549 111s 111s $p.value 111s [1] 0.4674727 111s 111s 111s > data(carnivora) 111s 111s > carnivora$log10SW <- log10(carnivora$SW) 111s 111s > carnivora$log10FW <- log10(carnivora$FW) 111s 111s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 111s 111s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 111s 111s > plot(co1) 111s 111s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 111s 111s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 111s 111s > print(plot(co2)) 111s 111s > plot(co2, FALSE) 111s > 111s 111s R version 4.4.3 (2025-02-28) -- "Trophy Case" 111s Copyright (C) 2025 The R Foundation for Statistical Computing 111s Platform: aarch64-unknown-linux-gnu 111s 111s R is free software and comes with ABSOLUTELY NO WARRANTY. 111s You are welcome to redistribute it under certain conditions. 111s Type 'license()' or 'licence()' for distribution details. 111s 111s R is a collaborative project with many contributors. 111s Type 'contributors()' for more information and 111s 'citation()' on how to cite R or R packages in publications. 111s 111s Type 'demo()' for some demos, 'help()' for on-line help, or 111s 'help.start()' for an HTML browser interface to help. 111s Type 'q()' to quit R. 111s 111s > Stangle("RandomTopologies.Rnw") 111s Writing to file RandomTopologies.R 111s > source("RandomTopologies.R", echo=TRUE) 111s 111s > options(width = 80, prompt = "> ") 111s 111s > library(ape) 111s 111s > n <- 1:10 111s 111s > data.frame(N.topo = sapply(n, howmanytrees)) 111s N.topo 111s 1 1 111s 2 1 111s 3 3 111s 4 15 111s 5 105 111s 6 945 111s 7 10395 111s 8 135135 111s 9 2027025 111s 10 34459425 111s 111s > howmanytrees(25) 111s [1] 1.192568e+30 111s 111s > howmanytrees(25) * 0.21 111s [1] 2.504393e+29 111s 111s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 111s N.topo 111s 1 1 111s 2 1 111s 3 1 111s 4 2 111s 5 3 111s 6 6 111s 7 11 111s 8 23 111s 9 46 111s 10 98 111s 111s > n2 <- c(50, 100, 200) 111s 111s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 111s + row.names = n2) 111s N.topo 111s 50 5.150149e+16 111s 100 1.019560e+36 111s 200 1.141703e+75 111s 111s > 1/howmanytrees(50) 111s [1] 3.632505e-77 111s 111s > 1/sapply(n, howmanytrees) 111s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 111s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 111s 111s > 1/sapply(n, howmanytrees, labeled = FALSE) 111s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 111s [7] 0.09090909 0.04347826 0.02173913 0.01020408 111s 111s > library(phangorn) 113s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 113s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 113s 113s > TR <- allTrees(4, rooted = TRUE) 113s 113s > TR 113s 15 phylogenetic trees 113s 113s > layout(matrix(1:15, 3, 5)) 113s 113s > par(mar = rep(1.5, 4), xpd = TRUE) 113s 113s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 113s 113s > K <- 100 113s 113s > n <- 50 113s 113s > N <- howmanytrees(n, labeled = FALSE) 113s 113s > p <- 1/N 113s 113s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 113s [1] 0 113s 113s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 113s [1] -5.431212e-17 113s 113s > f <- function(n, K) { 113s + N <- howmanytrees(n, labeled = FALSE) 113s + p <- 1/N 113s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 113s + } 113s 113s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 113s + 10000)) 113s 113s > DF$P <- mapply(f, n = DF$n, K = DF$K) 113s 113s > library(lattice) 113s 113s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 113s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 113s 113s > subset(DF, n == 20) 113s n K P 113s 17 20 2 1.160494e-11 113s 34 20 5 1.160491e-10 113s 51 20 10 5.222149e-10 113s 68 20 100 5.743191e-08 113s 85 20 1000 5.783570e-06 113s 102 20 10000 5.671842e-04 113s 113s > f(20, 1e+05) 113s [1] 0.04638755 113s 113s > f(30, 1e+06) 113s [1] 2.525152e-07 113s 113s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 113s 113s > TR5 <- read.tree(text = txt) 113s 113s > layout(matrix(1:3, 1)) 113s 113s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 113s 113s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 113s + labeled = FALSE) 113s [1] 2 113s 113s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 113s + labeled = FALSE) 113s [1] 1 113s 113s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 113s + labeled = FALSE) 113s [1] Inf 113s 113s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 113s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 113s 113s > foo.test <- function(x, labeled = TRUE) { 113s + uTR <- unique(x, use.tip.label = labeled) 113s + f <- integer(length(uTR)) 113s + for (j in seq_along( .... [TRUNCATED] 113s 113s > lapply(TR, foo.test) 117s [1] 64 62 80 70 75 64 59 64 62 68 69 65 63 56 79 119s [1] 128 75 67 101 52 46 103 69 44 42 64 52 48 63 46 121s [1] 40 39 158 38 169 33 53 175 42 44 42 42 43 41 41 121s [[1]] 121s 121s Chi-squared test for given probabilities 121s 121s data: f 121s X-squared = 10.07, df = 14, p-value = 0.757 121s 121s 121s [[2]] 121s 121s Chi-squared test for given probabilities 121s 121s data: f 121s X-squared = 136.67, df = 14, p-value < 2.2e-16 121s 121s 121s [[3]] 121s 121s Chi-squared test for given probabilities 121s 121s data: f 121s X-squared = 575.78, df = 14, p-value < 2.2e-16 121s 121s 121s 121s > lapply(TR, foo.test, labeled = FALSE) 122s [1] 810 190 122s [1] 332 668 123s [1] 498 502 123s [[1]] 123s 123s Chi-squared test for given probabilities 123s 123s data: f 123s X-squared = 384.4, df = 1, p-value < 2.2e-16 123s 123s 123s [[2]] 123s 123s Chi-squared test for given probabilities 123s 123s data: f 123s X-squared = 112.9, df = 1, p-value < 2.2e-16 123s 123s 123s [[3]] 123s 123s Chi-squared test for given probabilities 123s 123s data: f 123s X-squared = 0.016, df = 1, p-value = 0.8993 123s 123s 123s 123s > .Machine$double.xmax 123s [1] 1.797693e+308 123s 123s > howmanytrees(151) 123s [1] 3.753274e+306 123s 123s > howmanytrees(792, labeled = FALSE) 123s [1] 1.029038e+308 123s 123s > (N <- howmanytrees(2e+06)) 123s approximately 3.692364 * 10^12335524 123s 123s > N[2] + 1 123s n 123s 12335525 123s 123s > ceiling((N[2] + 1)/3000) 123s n 123s 4112 123s 123s > n <- 1:792 123s 123s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 123s 123s > lN <- log10(N) 123s 123s > summary(lm(lN ~ n)) 123s 123s Call: 123s lm(formula = lN ~ n) 123s 123s Residuals: 123s Min 1Q Median 3Q Max 123s -0.25968 -0.21424 -0.08311 0.12406 2.82605 123s 123s Coefficients: 123s Estimate Std. Error t value Pr(>|t|) 123s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 123s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 123s --- 123s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 123s 123s Residual standard error: 0.3175 on 790 degrees of freedom 123s Multiple R-squared: 1, Adjusted R-squared: 1 123s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 123s 123s 123s > s <- n > 700 123s 123s > summary(lm(lN[s] ~ n[s])) 123s 123s Call: 123s lm(formula = lN[s] ~ n[s]) 123s 123s Residuals: 123s Min 1Q Median 3Q Max 123s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 123s 123s Coefficients: 123s Estimate Std. Error t value Pr(>|t|) 123s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 123s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 123s --- 123s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 123s 123s Residual standard error: 0.0003738 on 90 degrees of freedom 123s Multiple R-squared: 1, Adjusted R-squared: 1 123s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 123s 123s 123s > n <- 788:792 123s 123s > log10(sapply(n, howmanytrees, labeled = FALSE)) 123s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 123s 123s > 0.3941 * n - 4.153 123s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 123s 123s > xi <- 2.477993 123s 123s > lxi <- log10(xi) 123s 123s > n <- 1000 123s 123s > (n - 1) * lxi 123s [1] 393.706 123s 123s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 123s + 1))))) 123s [1] 393.8532 123s [1] 393.9009 123s [1] 393.9187 123s [1] 393.9257 123s [1] 393.9285 123s [1] 393.9296 123s [1] 393.9301 123s [1] 393.9303 123s [1] 393.9304 123s [1] 393.9304 123s > 123s autopkgtest [07:12:11]: test run-unit-test: -----------------------] 124s autopkgtest [07:12:12]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 124s run-unit-test PASS 124s autopkgtest [07:12:12]: test pkg-r-autopkgtest: preparing testbed 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 125s The following NEW packages will be installed: 125s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 125s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 125s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 125s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 125s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 125s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 125s libjpeg-turbo8-dev libjpeg8-dev libjs-jquery liblapack-dev liblsan0 125s liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 125s libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev 125s libtirpc-dev libtsan2 libubsan1 node-html5shiv pkg-r-autopkgtest pkgconf 125s pkgconf-bin r-base-dev r-cran-expm r-cran-gee r-cran-xml2 zlib1g-dev 126s 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 93.6 MB of archives. 126s After this operation, 336 MB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 libisl23 arm64 0.27-1 [676 kB] 126s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 126s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [10.6 MB] 126s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14 arm64 14.2.0-19ubuntu2 [1026 B] 126s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 126s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 126s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libcc1-0 arm64 15-20250404-0ubuntu1 [49.1 kB] 126s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libitm1 arm64 15-20250404-0ubuntu1 [27.8 kB] 126s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libasan8 arm64 15-20250404-0ubuntu1 [2922 kB] 126s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 liblsan0 arm64 15-20250404-0ubuntu1 [1318 kB] 126s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 libtsan2 arm64 15-20250404-0ubuntu1 [2692 kB] 126s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libubsan1 arm64 15-20250404-0ubuntu1 [1177 kB] 126s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libhwasan0 arm64 15-20250404-0ubuntu1 [1640 kB] 126s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu2 [2593 kB] 126s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [20.9 MB] 127s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14 arm64 14.2.0-19ubuntu2 [529 kB] 127s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 127s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 127s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu2 [2501 kB] 127s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [12.1 MB] 127s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14 arm64 14.2.0-19ubuntu2 [23.0 kB] 127s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 127s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 127s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 build-essential arm64 12.12ubuntu1 [5082 B] 127s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 127s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran-14-dev arm64 14.2.0-19ubuntu2 [498 kB] 127s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [11.4 MB] 127s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-14 arm64 14.2.0-19ubuntu2 [14.2 kB] 127s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 127s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 127s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 127s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 127s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 127s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 127s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 127s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 127s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 127s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 127s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 127s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 128s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 128s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 128s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 128s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 128s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 128s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 128s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 128s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 libpng-dev arm64 1.6.47-1.1 [269 kB] 128s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 128s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 128s Get:51 http://ftpmaster.internal/ubuntu questing/main arm64 liblzma-dev arm64 5.6.4-1ubuntu1 [180 kB] 128s Get:52 http://ftpmaster.internal/ubuntu questing/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 128s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 128s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 128s Get:55 http://ftpmaster.internal/ubuntu questing/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 128s Get:56 http://ftpmaster.internal/ubuntu questing/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 128s Get:57 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-expm arm64 1.0-0-1 [225 kB] 128s Get:58 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-gee arm64 4.13-29-1 [72.8 kB] 128s Get:59 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-xml2 arm64 1.3.8-1 [326 kB] 128s Fetched 93.6 MB in 2s (42.3 MB/s) 128s Selecting previously unselected package libisl23:arm64. 128s (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 ... 90289 files and directories currently installed.) 128s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 128s Unpacking libisl23:arm64 (0.27-1) ... 128s Selecting previously unselected package libmpc3:arm64. 128s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 128s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 128s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 128s Preparing to unpack .../02-cpp-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 128s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 128s Selecting previously unselected package cpp-14. 128s Preparing to unpack .../03-cpp-14_14.2.0-19ubuntu2_arm64.deb ... 128s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 128s Selecting previously unselected package cpp-aarch64-linux-gnu. 128s Preparing to unpack .../04-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 128s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 128s Selecting previously unselected package cpp. 128s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 128s Unpacking cpp (4:14.2.0-1ubuntu1) ... 128s Selecting previously unselected package libcc1-0:arm64. 128s Preparing to unpack .../06-libcc1-0_15-20250404-0ubuntu1_arm64.deb ... 128s Unpacking libcc1-0:arm64 (15-20250404-0ubuntu1) ... 128s Selecting previously unselected package libitm1:arm64. 128s Preparing to unpack .../07-libitm1_15-20250404-0ubuntu1_arm64.deb ... 128s Unpacking libitm1:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libasan8:arm64. 129s Preparing to unpack .../08-libasan8_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking libasan8:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package liblsan0:arm64. 129s Preparing to unpack .../09-liblsan0_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking liblsan0:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libtsan2:arm64. 129s Preparing to unpack .../10-libtsan2_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking libtsan2:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libubsan1:arm64. 129s Preparing to unpack .../11-libubsan1_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking libubsan1:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libhwasan0:arm64. 129s Preparing to unpack .../12-libhwasan0_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking libhwasan0:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libgcc-14-dev:arm64. 129s Preparing to unpack .../13-libgcc-14-dev_14.2.0-19ubuntu2_arm64.deb ... 129s Unpacking libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 129s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 129s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 129s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 129s Selecting previously unselected package gcc-14. 129s Preparing to unpack .../15-gcc-14_14.2.0-19ubuntu2_arm64.deb ... 129s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 129s Selecting previously unselected package gcc-aarch64-linux-gnu. 129s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 129s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 129s Selecting previously unselected package gcc. 129s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 129s Unpacking gcc (4:14.2.0-1ubuntu1) ... 129s Selecting previously unselected package libstdc++-14-dev:arm64. 129s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-19ubuntu2_arm64.deb ... 129s Unpacking libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package g++-14-aarch64-linux-gnu. 130s Preparing to unpack .../19-g++-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 130s Unpacking g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package g++-14. 130s Preparing to unpack .../20-g++-14_14.2.0-19ubuntu2_arm64.deb ... 130s Unpacking g++-14 (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package g++-aarch64-linux-gnu. 130s Preparing to unpack .../21-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 130s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package g++. 130s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 130s Unpacking g++ (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package build-essential. 130s Preparing to unpack .../23-build-essential_12.12ubuntu1_arm64.deb ... 130s Unpacking build-essential (12.12ubuntu1) ... 130s Selecting previously unselected package dctrl-tools. 130s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 130s Unpacking dctrl-tools (2.24-3build3) ... 130s Selecting previously unselected package libgfortran-14-dev:arm64. 130s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-19ubuntu2_arm64.deb ... 130s Unpacking libgfortran-14-dev:arm64 (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 130s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 130s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package gfortran-14. 130s Preparing to unpack .../27-gfortran-14_14.2.0-19ubuntu2_arm64.deb ... 130s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 130s Selecting previously unselected package gfortran-aarch64-linux-gnu. 130s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 130s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package gfortran. 130s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 130s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package icu-devtools. 130s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 130s Unpacking icu-devtools (76.1-1ubuntu2) ... 130s Selecting previously unselected package libblas-dev:arm64. 130s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 130s Unpacking libblas-dev:arm64 (3.12.1-2) ... 130s Selecting previously unselected package libbz2-dev:arm64. 130s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 130s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 130s Selecting previously unselected package libdeflate-dev:arm64. 130s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 130s Unpacking libdeflate-dev:arm64 (1.23-1) ... 130s Selecting previously unselected package libicu-dev:arm64. 130s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 130s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 131s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 131s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 131s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 131s Selecting previously unselected package libjpeg8-dev:arm64. 131s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 131s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 131s Selecting previously unselected package libjpeg-dev:arm64. 131s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 131s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 131s Selecting previously unselected package libjs-jquery. 131s Preparing to unpack .../38-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 131s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 131s Selecting previously unselected package liblapack-dev:arm64. 131s Preparing to unpack .../39-liblapack-dev_3.12.1-2_arm64.deb ... 131s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 131s Selecting previously unselected package libncurses-dev:arm64. 131s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_arm64.deb ... 131s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 131s Selecting previously unselected package libpcre2-16-0:arm64. 131s Preparing to unpack .../41-libpcre2-16-0_10.45-1_arm64.deb ... 131s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 131s Selecting previously unselected package libpcre2-32-0:arm64. 131s Preparing to unpack .../42-libpcre2-32-0_10.45-1_arm64.deb ... 131s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 131s Selecting previously unselected package libpcre2-posix3:arm64. 131s Preparing to unpack .../43-libpcre2-posix3_10.45-1_arm64.deb ... 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libreadline-dev:arm64 (8.2-6) ... 132s Setting up libpcre2-16-0:arm64 (10.45-1) ... 132s Setting up libpcre2-32-0:arm64 (10.45-1) ... 132s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 132s Setting up libpkgconf3:arm64 (1.8.1-4) ... 132s Setting up libmpc3:arm64 (1.3.1-1build2) ... 132s Setting up icu-devtools (76.1-1ubuntu2) ... 132s Setting up pkgconf-bin (1.8.1-4) ... 132s Setting up liblzma-dev:arm64 (5.6.4-1ubuntu1) ... 132s Setting up libubsan1:arm64 (15-20250404-0ubuntu1) ... 132s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 132s Setting up libpcre2-posix3:arm64 (10.45-1) ... 132s Setting up libhwasan0:arm64 (15-20250404-0ubuntu1) ... 132s Setting up libasan8:arm64 (15-20250404-0ubuntu1) ... 132s Setting up libtsan2:arm64 (15-20250404-0ubuntu1) ... 132s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 132s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 132s Setting up r-cran-gee (4.13-29-1) ... 132s Setting up libisl23:arm64 (0.27-1) ... 132s Setting up libdeflate-dev:arm64 (1.23-1) ... 132s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 132s Setting up libcc1-0:arm64 (15-20250404-0ubuntu1) ... 132s Setting up liblsan0:arm64 (15-20250404-0ubuntu1) ... 132s Setting up libblas-dev:arm64 (3.12.1-2) ... 132s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 132s Setting up dctrl-tools (2.24-3build3) ... 132s Setting up libitm1:arm64 (15-20250404-0ubuntu1) ... 132s Setting up libbz2-dev:arm64 (1.0.8-6) ... 132s Setting up libpcre2-dev:arm64 (10.45-1) ... 132s Setting up r-cran-xml2 (1.3.8-1) ... 132s Setting up libpng-dev:arm64 (1.6.47-1.1) ... 132s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 132s Setting up pkgconf:arm64 (1.8.1-4) ... 132s Setting up liblapack-dev:arm64 (3.12.1-2) ... 132s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 132s Setting up cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 132s Setting up libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 132s Setting up libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 132s Setting up libgfortran-14-dev:arm64 (14.2.0-19ubuntu2) ... 132s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up cpp-14 (14.2.0-19ubuntu2) ... 132s Setting up cpp (4:14.2.0-1ubuntu1) ... 132s Setting up gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 132s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 132s Setting up gcc-14 (14.2.0-19ubuntu2) ... 132s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 132s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up g++-14 (14.2.0-19ubuntu2) ... 132s Setting up gfortran-14 (14.2.0-19ubuntu2) ... 132s Setting up gcc (4:14.2.0-1ubuntu1) ... 132s Setting up g++ (4:14.2.0-1ubuntu1) ... 132s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 132s Setting up build-essential (12.12ubuntu1) ... 132s Setting up gfortran (4:14.2.0-1ubuntu1) ... 132s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 132s 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 132s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 132s 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 132s Setting up r-base-dev (4.4.3-1) ... 132s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 132s Processing triggers for libc-bin (2.41-6ubuntu1) ... 132s Processing triggers for man-db (2.13.0-1) ... 133s Processing triggers for install-info (7.1.1-1) ... 134s autopkgtest [07:12:22]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 134s autopkgtest [07:12:22]: test pkg-r-autopkgtest: [----------------------- 134s Test: Try to load the R library ape 134s 134s R version 4.4.3 (2025-02-28) -- "Trophy Case" 134s Copyright (C) 2025 The R Foundation for Statistical Computing 134s Platform: aarch64-unknown-linux-gnu 134s 134s R is free software and comes with ABSOLUTELY NO WARRANTY. 134s You are welcome to redistribute it under certain conditions. 134s Type 'license()' or 'licence()' for distribution details. 134s 134s R is a collaborative project with many contributors. 134s Type 'contributors()' for more information and 134s 'citation()' on how to cite R or R packages in publications. 134s 134s Type 'demo()' for some demos, 'help()' for on-line help, or 134s 'help.start()' for an HTML browser interface to help. 134s Type 'q()' to quit R. 134s 134s > library('ape') 134s > 134s > 134s Other tests are currently unsupported! 134s They will be progressively added. 135s autopkgtest [07:12:23]: test pkg-r-autopkgtest: -----------------------] 135s autopkgtest [07:12:23]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 135s pkg-r-autopkgtest PASS 135s autopkgtest [07:12:23]: @@@@@@@@@@@@@@@@@@@@ summary 135s run-unit-test PASS 135s pkg-r-autopkgtest PASS 140s nova [W] Using flock in prodstack7-arm64 140s Creating nova instance adt-questing-arm64-r-cran-ape-20250502-071008-juju-7f2275-prod-proposed-migration-environment-2-26771ad1-b902-4af5-acca-1ed115005f42 from image adt/ubuntu-questing-arm64-server-20250501.img (UUID 137c3127-57d2-4bf2-a106-d904ad6e43f4)... 140s nova [W] Timed out waiting for 5ab4727e-487d-43c0-8b72-321a1a77ab35 to get deleted.