0s autopkgtest [18:49:28]: starting date and time: 2025-05-03 18:49:28+0000 0s autopkgtest [18:49:28]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [18:49:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xm8kwtrc/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-7.secgroup --name adt-questing-amd64-r-cran-ape-20250503-184928-juju-7f2275-prod-proposed-migration-environment-2-10d0f009-e2aa-4ebf-97a9-e431f5ed0064 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 72s autopkgtest [18:50:40]: testbed dpkg architecture: amd64 72s autopkgtest [18:50:40]: testbed apt version: 3.0.0 73s autopkgtest [18:50:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s autopkgtest [18:50:41]: testbed release detected to be: None 74s autopkgtest [18:50:42]: updating testbed package index (apt update) 74s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 74s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 74s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 74s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 74s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 74s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1442 kB] 75s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 75s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [203 kB] 75s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [146 kB] 75s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1424 kB] 75s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [576 kB] 75s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [48.6 kB] 75s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [23.1 kB] 75s Fetched 4155 kB in 1s (3747 kB/s) 76s Reading package lists... 77s autopkgtest [18:50:45]: upgrading testbed (apt dist-upgrade and autopurge) 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 78s Starting 2 pkgProblemResolver with broken count: 0 78s Done 78s Entering ResolveByKeep 78s 79s Calculating upgrade... 79s The following packages will be upgraded: 79s cloud-init cloud-init-base debianutils libmbim-glib4 libmbim-proxy 79s libnftnl11 libqmi-glib5 libqmi-proxy libsepol2 python3-lazr.restfulclient 79s sos 79s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 2693 kB of archives. 79s After this operation, 104 kB disk space will be freed. 79s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB] 79s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libsepol2 amd64 3.8.1-1 [327 kB] 79s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB] 79s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 79s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B] 79s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB] 79s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B] 79s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB] 79s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB] 79s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 sos all 4.9.1-1 [367 kB] 79s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 80s Preconfiguring packages ... 80s Fetched 2693 kB in 1s (4442 kB/s) 80s (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 ... 80514 files and directories currently installed.) 80s Preparing to unpack .../debianutils_5.22_amd64.deb ... 80s Unpacking debianutils (5.22) over (5.21) ... 80s Setting up debianutils (5.22) ... 80s (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 ... 80514 files and directories currently installed.) 80s Preparing to unpack .../libsepol2_3.8.1-1_amd64.deb ... 80s Unpacking libsepol2:amd64 (3.8.1-1) over (3.7-1) ... 80s Setting up libsepol2:amd64 (3.8.1-1) ... 81s (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 ... 80514 files and directories currently installed.) 81s Preparing to unpack .../0-libnftnl11_1.2.9-1_amd64.deb ... 81s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ... 81s Preparing to unpack .../1-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 81s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 81s Preparing to unpack .../2-libmbim-proxy_1.32.0-1_amd64.deb ... 81s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 81s Preparing to unpack .../3-libmbim-glib4_1.32.0-1_amd64.deb ... 81s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 81s Preparing to unpack .../4-libqmi-proxy_1.36.0-1_amd64.deb ... 81s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 81s Preparing to unpack .../5-libqmi-glib5_1.36.0-1_amd64.deb ... 81s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ... 81s Preparing to unpack .../6-python3-lazr.restfulclient_0.14.6-3_all.deb ... 81s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ... 81s Preparing to unpack .../7-sos_4.9.1-1_all.deb ... 82s Unpacking sos (4.9.1-1) over (4.9.0-6) ... 82s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 82s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 82s Setting up sos (4.9.1-1) ... 82s Setting up libnftnl11:amd64 (1.2.9-1) ... 82s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 84s Setting up python3-lazr.restfulclient (0.14.6-3) ... 84s Setting up libmbim-glib4:amd64 (1.32.0-1) ... 84s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 84s Setting up libmbim-proxy (1.32.0-1) ... 84s Setting up libqmi-glib5:amd64 (1.36.0-1) ... 84s Setting up libqmi-proxy (1.36.0-1) ... 84s Processing triggers for libc-bin (2.41-6ubuntu1) ... 84s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 84s Processing triggers for man-db (2.13.0-1) ... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 87s Solving dependencies... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s autopkgtest [18:50:55]: rebooting testbed after setup commands that affected boot 110s autopkgtest [18:51:18]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 113s autopkgtest [18:51:21]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 115s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 115s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 115s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 115s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 115s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 115s gpgv: issuer "plessy@debian.org" 115s gpgv: Can't check signature: No public key 115s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 115s autopkgtest [18:51:23]: testing package r-cran-ape version 5.8-1-1 115s autopkgtest [18:51:23]: build not needed 117s autopkgtest [18:51:25]: test run-unit-test: preparing testbed 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 118s Starting pkgProblemResolver with broken count: 0 118s Starting 2 pkgProblemResolver with broken count: 0 118s Done 118s The following NEW packages will be installed: 118s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 118s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 118s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 118s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 118s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 118s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 118s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 118s libxss1 libxt6t64 littler r-base-core r-cran-ape r-cran-cli r-cran-cpp11 118s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 118s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 118s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 118s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 118s xdg-utils zip 118s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 67.6 MB of archives. 118s After this operation, 136 MB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 119s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 119s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 119s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 119s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 119s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 119s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-3 [13.5 kB] 119s Get:8 http://ftpmaster.internal/ubuntu questing/universe amd64 libamd3 amd64 1:7.8.3+dfsg-3 [31.0 kB] 119s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 119s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 119s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 119s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 119s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 119s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 119s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-3 [19.5 kB] 119s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 119s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 119s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 119s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libltdl7 amd64 2.5.4-4 [46.5 kB] 119s Get:20 http://ftpmaster.internal/ubuntu questing/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 119s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 119s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 119s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 119s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 119s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 119s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 119s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 119s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 119s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 119s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 119s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 119s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 119s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 119s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 119s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 119s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 119s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 119s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 119s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 119s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 119s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 119s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 119s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 119s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 119s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 119s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 119s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 119s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 119s Get:49 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 120s Get:50 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 120s Get:51 http://ftpmaster.internal/ubuntu questing/universe amd64 littler all 0.3.20-2 [2554 B] 120s Get:52 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 120s Get:53 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 120s Get:54 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 120s Get:55 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 120s Get:56 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 120s Get:57 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-ape amd64 5.8-1-1 [2918 kB] 120s Get:58 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 120s Get:59 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB] 120s Get:60 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-fastmatch amd64 1.1-6-1 [37.0 kB] 120s Get:61 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 120s Get:62 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 120s Get:63 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 120s Get:64 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 120s Get:65 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 120s Get:66 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 120s Get:67 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 120s Get:68 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 120s Get:69 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-igraph amd64 2.1.4-1 [5357 kB] 121s Get:70 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-quadprog amd64 1.5-8-1build1 [30.9 kB] 121s Get:71 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-phangorn amd64 2.12.1+dfsg-1 [1831 kB] 121s Preconfiguring packages ... 121s Fetched 67.6 MB in 2s (27.7 MB/s) 121s Selecting previously unselected package fonts-dejavu-mono. 121s (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 ... 80518 files and directories currently installed.) 121s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 121s Unpacking fonts-dejavu-mono (2.37-8) ... 121s Selecting previously unselected package fonts-dejavu-core. 121s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 121s Unpacking fonts-dejavu-core (2.37-8) ... 121s Selecting previously unselected package fontconfig-config. 121s Preparing to unpack .../02-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 122s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 122s Selecting previously unselected package libfontconfig1:amd64. 122s Preparing to unpack .../03-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 122s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 122s Selecting previously unselected package fontconfig. 122s Preparing to unpack .../04-fontconfig_2.15.0-2.2ubuntu1_amd64.deb ... 122s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 122s Selecting previously unselected package libgomp1:amd64. 122s Preparing to unpack .../05-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 122s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 122s Selecting previously unselected package libsuitesparseconfig7:amd64. 122s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_amd64.deb ... 122s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 122s Selecting previously unselected package libamd3:amd64. 122s Preparing to 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package libltdl7:amd64. 122s Preparing to unpack .../18-libltdl7_2.5.4-4_amd64.deb ... 122s Unpacking libltdl7:amd64 (2.5.4-4) ... 122s Selecting previously unselected package libglpk40:amd64. 122s Preparing to unpack .../19-libglpk40_5.0-1build2_amd64.deb ... 122s Unpacking libglpk40:amd64 (5.0-1build2) ... 122s Selecting previously unselected package libgraphite2-3:amd64. 122s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 122s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 122s Selecting previously unselected package libharfbuzz0b:amd64. 122s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_amd64.deb ... 122s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 122s Selecting previously unselected package x11-common. 122s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu4_all.deb ... 122s Unpacking x11-common (1:7.7+23ubuntu4) ... 122s Selecting previously unselected package libice6:amd64. 122s Preparing to unpack .../23-libice6_2%3a1.1.1-1_amd64.deb ... 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unselected package libthai0:amd64. 123s Preparing to unpack .../29-libthai0_0.1.29-2build1_amd64.deb ... 123s Unpacking libthai0:amd64 (0.1.29-2build1) ... 123s Selecting previously unselected package libpango-1.0-0:amd64. 123s Preparing to unpack .../30-libpango-1.0-0_1.56.3-1_amd64.deb ... 123s Unpacking libpango-1.0-0:amd64 (1.56.3-1) ... 123s Selecting previously unselected package libpangoft2-1.0-0:amd64. 123s Preparing to unpack .../31-libpangoft2-1.0-0_1.56.3-1_amd64.deb ... 123s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-1) ... 123s Selecting previously unselected package libpangocairo-1.0-0:amd64. 123s Preparing to unpack .../32-libpangocairo-1.0-0_1.56.3-1_amd64.deb ... 123s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-1) ... 123s Selecting previously unselected package libpaper2:amd64. 123s Preparing to unpack .../33-libpaper2_2.2.5-0.3_amd64.deb ... 123s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 123s Selecting previously unselected package libpaper-utils. 123s Preparing to 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libgomp1:amd64 (15-20250404-0ubuntu1) ... 125s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 125s Setting up zip (3.0-14ubuntu2) ... 125s Setting up libblas3:amd64 (3.12.1-2) ... 126s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 126s Setting up fonts-dejavu-mono (2.37-8) ... 126s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 126s Setting up fonts-dejavu-core (2.37-8) ... 126s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 126s Setting up libltdl7:amd64 (2.5.4-4) ... 126s Setting up libgfortran5:amd64 (15-20250404-0ubuntu1) ... 126s Setting up libwebp7:amd64 (1.5.0-0.1) ... 126s Setting up libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 126s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 126s Setting up libthai-data (0.1.29-2build1) ... 126s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 126s Setting up libpaper2:amd64 (2.2.5-0.3) ... 126s Setting up xdg-utils 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128s Setting up libxft2:amd64 (2.3.6-1build1) ... 128s Setting up libtk8.6:amd64 (8.6.16-1) ... 128s Setting up libpango-1.0-0:amd64 (1.56.3-1) ... 128s Setting up libcairo2:amd64 (1.18.4-1) ... 128s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 128s Setting up libpangoft2-1.0-0:amd64 (1.56.3-1) ... 128s Setting up libpangocairo-1.0-0:amd64 (1.56.3-1) ... 128s Setting up r-base-core (4.4.3-1) ... 128s Creating config file /etc/R/Renviron with new version 128s Setting up r-cran-fastmatch (1.1-6-1) ... 128s Setting up r-cran-lattice (0.22-6-1) ... 128s Setting up r-cran-nlme (3.1.168-1) ... 128s Setting up r-cran-pkgkitten (0.2.4-1) ... 128s Setting up r-cran-magrittr (2.0.3-1) ... 128s Setting up r-cran-quadprog (1.5-8-1build1) ... 128s Setting up r-cran-littler (0.3.20-2) ... 128s Setting up r-cran-rcpp (1.0.14-1) ... 128s Setting up r-cran-rlang (1.1.5-1) ... 128s Setting up littler (0.3.20-2) ... 128s Setting up r-cran-generics (0.1.3-1) ... 128s Setting up r-cran-digest (0.6.37-1) ... 128s Setting up r-cran-ape (5.8-1-1) ... 128s Setting up r-cran-glue (1.8.0-1) ... 128s Setting up r-cran-cli (3.6.4-1) ... 128s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 128s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 128s Setting up r-cran-cpp11 (0.5.2-1) ... 128s Setting up r-cran-matrix (1.7-3-1) ... 128s Setting up r-cran-vctrs (0.6.5-1) ... 128s Setting up r-cran-igraph (2.1.4-1) ... 128s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 128s Processing triggers for libc-bin (2.41-6ubuntu1) ... 128s Processing triggers for man-db (2.13.0-1) ... 129s Processing triggers for install-info (7.1.1-1) ... 131s autopkgtest [18:51:39]: test run-unit-test: [----------------------- 131s 131s R version 4.4.3 (2025-02-28) -- "Trophy Case" 131s Copyright (C) 2025 The R Foundation for Statistical Computing 131s Platform: x86_64-pc-linux-gnu 131s 131s R is free software and comes with ABSOLUTELY NO WARRANTY. 131s You are welcome to redistribute it under certain conditions. 131s Type 'license()' or 'licence()' for distribution details. 131s 131s R is a collaborative project with many contributors. 131s Type 'contributors()' for more information and 131s 'citation()' on how to cite R or R packages in publications. 131s 131s Type 'demo()' for some demos, 'help()' for on-line help, or 131s 'help.start()' for an HTML browser interface to help. 131s Type 'q()' to quit R. 131s 131s > Stangle("DrawingPhylogenies.Rnw") 131s Writing to file DrawingPhylogenies.R 131s > source("DrawingPhylogenies.R", echo=TRUE) 131s 131s > options(width = 80, prompt = "> ") 131s 131s > library(ape) 131s 131s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 131s 131s > foo <- function() { 131s + col <- "green" 131s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 131s + las = 1) 131s + box(lty .... [TRUNCATED] 131s 131s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 131s 131s > plot(mytr) 131s 131s > foo() 131s 131s > plot(mytr, "c", FALSE) 131s 131s > foo() 132s 132s > plot(mytr, "u") 132s 132s > foo() 132s 132s > par(xpd = TRUE) 132s 132s > plot(mytr, "f") 132s 132s > foo() 132s 132s > box("outer") 132s 132s > tr <- compute.brlen(stree(8, "l"), 0.1) 132s 132s > tr$tip.label[] <- "" 132s 132s > foo <- function() { 132s + col <- "green" 132s + axis(1, col = col, col.ticks = col, col.axis = col) 132s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 132s 132s > layout(matrix(1:12, 6, 2)) 132s 132s > par(mar = c(2, 2, 0.3, 0)) 132s 132s > for (type in c("p", "c")) { 132s + plot(tr, type) 132s + foo() 132s + plot(tr, type, node.pos = 2) 132s + foo() 132s + plot(tr, type, FALSE) 132s + foo() 132s .... [TRUNCATED] 132s 132s > foo <- function() { 132s + col <- "green" 132s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 132s + las = 1) 132s + box(lty .... [TRUNCATED] 132s 132s > layout(matrix(1:4, 2, 2)) 132s 132s > par(las = 1) 132s 132s > plot(tr, "u") 132s 132s > foo() 132s 132s > plot(tr, "u", FALSE) 132s 132s > foo() 132s 132s > plot(tr, "f") 132s 132s > foo() 132s 132s > plot(tr, "f", FALSE) 132s 132s > foo() 132s 132s > args(node.depth.edgelength) 132s function (phy) 132s NULL 132s 132s > args(node.depth) 132s function (phy, method = 1) 132s NULL 132s 132s > args(node.height) 132s function (phy, clado.style = FALSE) 132s NULL 132s 132s > args(unrooted.xy) 132s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 132s NULL 132s 132s > args(phylogram.plot) 132s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 132s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 132s node.lty = NULL) 132s NULL 132s 132s > args(cladogram.plot) 132s function (edge, xx, yy, edge.color, edge.width, edge.lty) 132s NULL 132s 132s > args(circular.plot) 132s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 132s edge.lty) 132s NULL 132s 132s > args(plot.phylo) 132s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 132s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 132s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 132s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 132s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 132s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 132s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 132s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 132s ...) 132s NULL 132s 132s > geo <- factor(c("Africa", "World", "Africa")) 132s 132s > (mycol <- c("blue", "red")[geo]) 132s [1] "blue" "red" "blue" 132s 132s > plot(mytr, tip.color = mycol) 132s 132s > par(xpd = TRUE) 132s 132s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 132s 132s > args(def) 132s function (x, ..., default = NULL, regexp = FALSE) 132s NULL 132s 132s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 132s 132s > identical(mycol, mycol2) 132s [1] TRUE 132s 132s > (i <- which.edge(mytr, c("Homo", "Pan"))) 132s [1] 2 3 132s 132s > co <- rep("black", Nedge(mytr)) 132s 132s > co[i] <- "blue" 132s 132s > par(xpd = TRUE) 132s 132s > plot(mytr, edge.col = co) 132s 132s > edgelabels() 132s 132s > args(axisPhylo) 132s function (side = NULL, root.time = NULL, backward = TRUE, ...) 132s NULL 132s 132s > args(add.scale.bar) 132s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 132s ...) 132s NULL 132s 132s > plot(mytr) 132s 132s > add.scale.bar() 132s 132s > axisPhylo() 132s 132s > axis(3) 132s 132s > args(nodelabels) 132s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 132s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 132s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 132s ...) 132s NULL 132s 132s > args(tiplabels) 132s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 132s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 132s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 132s offset = 0, ...) 132s NULL 132s 132s > args(edgelabels) 132s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 132s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 132s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 132s date = NULL, ...) 132s NULL 132s 132s > par(xpd = TRUE) 132s 132s > plot(mytr) 132s 132s > nodelabels() 132s 132s > tiplabels() 132s 132s > edgelabels() 132s 132s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 132s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 132s 132s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 132s 132s > v <- c(0, 0.5, 1) 132s 132s > layout(matrix(1:9, 3, 3)) 132s 132s > par(mar = c(3, 3, 3, 0), las = 1) 132s 132s > for (i in v) { 132s + for (j in v) { 132s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 132s + ")")) 132s + abline(v = 0, h = .... [TRUNCATED] 132s 132s > plot(rep(0, 3), 0:2, "n", las = 1) 132s 132s > abline(v = 0, h = 0:2, lty = 3) 132s 132s > text(0, 0:2, mytr$tip.label, adj = -1) 132s 132s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 132s 132s > args(phydataplot) 132s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 132s width = NULL, legend = "below", funcol = rainbow, ...) 132s NULL 132s 132s > args(ring) 132s function (x, phy, style = "ring", offset = 1, ...) 132s NULL 132s 132s > x <- matrix(1:6, 3, 10) 132s 132s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 132s 132s > x 132s A B C D E F G H I J 132s Homo 1 4 1 4 1 4 1 4 1 4 132s Gorilla 2 5 2 5 2 5 2 5 2 5 132s Pan 3 6 3 6 3 6 3 6 3 6 132s 132s > mytr$tip.label 132s [1] "Pan" "Homo" "Gorilla" 132s 132s > par(mar = c(10, 2, 5, 5)) 132s 132s > plot(mytr, x.lim = 30) 132s 132s > phydataplot(x, mytr, "m", border = "white", offset = 2, 132s + width = 1) 132s 132s > phydataplot(x, mytr, "m", border = "white", offset = 15, 132s + width = 1, continuous = 2) 132s 132s > n <- 100 132s 132s > p <- 3 132s 132s > set.seed(3) 132s 132s > tr <- rcoal(n) 132s 132s > x <- matrix(runif(p * n), n, p) 132s 132s > rownames(x) <- tr$tip.label 132s 132s > COL <- c("red", "green", "blue") 132s 132s > par(xpd = TRUE) 132s 132s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 132s + no.margin = TRUE) 132s 132s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 132s + col = COL[j]) 132s 132s > tree <- rtree(10) 132s 132s > tree$edge.length[1] <- 1000 132s 132s > layout(matrix(1:2, 1)) 132s 132s > plot(tree) 132s 132s > axisPhylo() 132s 132s > plotBreakLongEdges(tree) 132s 132s > axisPhylo() 132s 132s > el <- tree$edge.length 132s 132s > sum(el > mean(el) + 2 * sd(el)) 132s [1] 1 132s 132s > tree$edge.length[8] <- 1000 132s 132s > el <- tree$edge.length 132s 132s > sum(el > mean(el) + 2 * sd(el)) 132s [1] 2 132s 132s > layout(matrix(1:2, 1)) 132s 132s > plotBreakLongEdges(tree) 132s 132s > plotBreakLongEdges(tree, n = 2) 132s 132s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 132s + simplify = FALSE) 132s 132s > kronoviz(TR, type = "c", show.tip.label = FALSE) 132s 132s > dates <- as.Date(.leap.seconds) 132s 132s > tr <- rcoal(length(dates)) 132s 132s > plotTreeTime(tr, dates) 132s 132s > par(oma = rep(2, 4)) 132s 132s > plot(mytr) 132s 132s > box(lty = 3) 132s 132s > box("figure", col = "blue") 132s 132s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 132s + font = 2, col = "blue") 132s 132s > box("outer") 132s 132s > layout(matrix(1:4, 2, 2)) 132s 132s > par(oma = rep(2, 4)) 132s 132s > for (i in 1:4) { 132s + par(mar = rep(i, 4)) 132s + plot(mytr) 132s + box(lty = 3) 132s + box("figure", col = "blue") 132s + } 132s 132s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 132s + font = 2, col = "blue") 132s 132s > box("outer") 132s 132s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 132s 132s > for (i in 1:3) plot(rtree(5)) 132s 132s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 132s $type 132s [1] "phylogram" 132s 132s $use.edge.length 132s [1] TRUE 132s 132s $node.pos 132s [1] 1 132s 132s $node.depth 132s [1] 1 132s 132s $show.tip.label 132s [1] TRUE 132s 132s $show.node.label 132s [1] FALSE 132s 132s $font 132s [1] 3 132s 132s $cex 132s [1] 0.83 132s 132s $adj 132s [1] 0 132s 132s $srt 132s [1] 0 132s 132s $no.margin 132s [1] FALSE 132s 132s $label.offset 132s [1] 0 132s 132s $x.lim 132s [1] 0.00000 3.13046 132s 132s $y.lim 132s [1] 1 5 132s 132s $direction 132s [1] "rightwards" 132s 132s $tip.color 132s [1] "black" 132s 132s $Ntip 132s [1] 5 132s 132s $Nnode 132s [1] 4 132s 132s $root.time 132s NULL 132s 132s $align.tip.label 132s [1] FALSE 132s 132s $edge 132s [,1] [,2] 132s [1,] 6 1 132s [2,] 6 7 132s [3,] 7 2 132s [4,] 7 8 132s [5,] 8 3 132s [6,] 8 9 132s [7,] 9 4 132s [8,] 9 5 132s 132s $xx 132s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 132s [8] 1.3631198 1.9857132 132s 132s $yy 132s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 132s 132s 132s > layout(matrix(1:2, 2)) 132s 132s > plot(rtree(4)) 132s 132s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 132s 132s > x <- pp$xx[1] 132s 132s > y <- pp$yy[1] 132s 132s > (pu <- par("usr")) 132s [1] -0.06364557 1.65478492 0.88000000 4.12000000 132s 132s > (x - pu[1])/(pu[2] - pu[1]) 132s [1] 0.9349839 132s 132s > (y - pu[3])/(pu[4] - pu[3]) 132s [1] 0.03703704 132s 132s > pi <- par("pin") 132s 132s > mi <- par("mai") 132s 132s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 132s 132s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 132s 132s > plot(rtree(4)) 132s 132s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 132s 132s > x <- pp$xx[5] 132s 132s > y <- pp$yy[5] 132s 132s > pu <- par("usr") 132s 132s > pi <- par("pin") 132s 132s > mi <- par("mai") 132s 132s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 132s 132s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 132s 132s > yi1 <- yi1 + par("fin")[2] 132s 132s > di <- par("din") 132s 132s > layout(1) 132s 132s > par(new = TRUE, mai = rep(0, 4)) 132s 132s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 132s + ylim = 0:1, xaxs = "i", yaxs = "i") 132s 132s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 132s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 132s 132s > foo <- function(phy1, phy2, from) { 132s + layout(matrix(1:2, 2)) 132s + plot(phy1, font = 1) 132s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 132s 132s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 132s 132s > par(xpd = TRUE) 132s 132s > foo(trb, mytr, "Primates") 132s 132s > plot(mytr, plot = FALSE) 132s 132s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 132s 132s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 132s + pp$yy[2] + 0.1, col = "yellow", border = NA) 132s 132s > par(new = TRUE) 132s 132s > plot(mytr) 132s > 132s 132s R version 4.4.3 (2025-02-28) -- "Trophy Case" 132s Copyright (C) 2025 The R Foundation for Statistical Computing 132s Platform: x86_64-pc-linux-gnu 132s 132s R is free software and comes with ABSOLUTELY NO WARRANTY. 132s You are welcome to redistribute it under certain conditions. 132s Type 'license()' or 'licence()' for distribution details. 132s 132s R is a collaborative project with many contributors. 132s Type 'contributors()' for more information and 132s 'citation()' on how to cite R or R packages in publications. 132s 132s Type 'demo()' for some demos, 'help()' for on-line help, or 132s 'help.start()' for an HTML browser interface to help. 132s Type 'q()' to quit R. 132s 132s > Stangle("MoranI.Rnw") 132s Writing to file MoranI.R 132s > source("MoranI.R", echo=TRUE) 132s 132s > options(width = 80, prompt = "> ") 132s 132s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 132s 132s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 132s 132s > names(body) <- names(longevity) <- c("Homo", "Pongo", 132s + "Macaca", "Ateles", "Galago") 132s 132s > library(ape) 132s 132s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 132s 132s > trnwk[2] <- ":0.38,Galago:1.00);" 132s 132s > tr <- read.tree(text = trnwk) 132s 132s > plot(tr) 132s 132s > axisPhylo() 132s 132s > w <- 1/cophenetic(tr) 132s 132s > w 132s Homo Pongo Macaca Ateles Galago 132s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 132s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 132s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 132s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 132s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 132s 132s > diag(w) <- 0 132s 132s > Moran.I(body, w) 132s $observed 132s [1] -0.07312179 132s 132s $expected 132s [1] -0.25 132s 132s $sd 132s [1] 0.08910814 132s 132s $p.value 132s [1] 0.04714628 132s 132s 132s > Moran.I(body, w, alt = "greater") 132s $observed 132s [1] -0.07312179 132s 132s $expected 132s [1] -0.25 132s 132s $sd 132s [1] 0.08910814 132s 132s $p.value 132s [1] 0.02357314 132s 132s 132s > Moran.I(longevity, w) 132s $observed 132s [1] -0.1837739 132s 132s $expected 132s [1] -0.25 132s 132s $sd 132s [1] 0.09114549 132s 132s $p.value 132s [1] 0.4674727 132s 132s 132s > data(carnivora) 132s 132s > carnivora$log10SW <- log10(carnivora$SW) 132s 132s > carnivora$log10FW <- log10(carnivora$FW) 132s 132s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 132s 132s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 132s 132s > plot(co1) 132s 132s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 132s 132s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 133s 133s > print(plot(co2)) 133s 133s > plot(co2, FALSE) 133s > 133s 133s R version 4.4.3 (2025-02-28) -- "Trophy Case" 133s Copyright (C) 2025 The R Foundation for Statistical Computing 133s Platform: x86_64-pc-linux-gnu 133s 133s R is free software and comes with ABSOLUTELY NO WARRANTY. 133s You are welcome to redistribute it under certain conditions. 133s Type 'license()' or 'licence()' for distribution details. 133s 133s R is a collaborative project with many contributors. 133s Type 'contributors()' for more information and 133s 'citation()' on how to cite R or R packages in publications. 133s 133s Type 'demo()' for some demos, 'help()' for on-line help, or 133s 'help.start()' for an HTML browser interface to help. 133s Type 'q()' to quit R. 133s 133s > Stangle("RandomTopologies.Rnw") 133s Writing to file RandomTopologies.R 133s > source("RandomTopologies.R", echo=TRUE) 133s 133s > options(width = 80, prompt = "> ") 133s 133s > library(ape) 133s 133s > n <- 1:10 133s 133s > data.frame(N.topo = sapply(n, howmanytrees)) 133s N.topo 133s 1 1 133s 2 1 133s 3 3 133s 4 15 133s 5 105 133s 6 945 133s 7 10395 133s 8 135135 133s 9 2027025 133s 10 34459425 133s 133s > howmanytrees(25) 133s [1] 1.192568e+30 133s 133s > howmanytrees(25) * 0.21 133s [1] 2.504393e+29 133s 133s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 133s N.topo 133s 1 1 133s 2 1 133s 3 1 133s 4 2 133s 5 3 133s 6 6 133s 7 11 133s 8 23 133s 9 46 133s 10 98 133s 133s > n2 <- c(50, 100, 200) 133s 133s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 133s + row.names = n2) 133s N.topo 133s 50 5.150149e+16 133s 100 1.019560e+36 133s 200 1.141703e+75 133s 133s > 1/howmanytrees(50) 133s [1] 3.632505e-77 133s 133s > 1/sapply(n, howmanytrees) 133s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 133s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 133s 133s > 1/sapply(n, howmanytrees, labeled = FALSE) 133s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 133s [7] 0.09090909 0.04347826 0.02173913 0.01020408 133s 133s > library(phangorn) 134s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 134s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 134s 134s > TR <- allTrees(4, rooted = TRUE) 134s 134s > TR 134s 15 phylogenetic trees 134s 134s > layout(matrix(1:15, 3, 5)) 134s 134s > par(mar = rep(1.5, 4), xpd = TRUE) 134s 134s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 134s 134s > K <- 100 134s 134s > n <- 50 134s 134s > N <- howmanytrees(n, labeled = FALSE) 134s 134s > p <- 1/N 134s 134s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 134s [1] 0 134s 134s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 134s [1] -5.431212e-17 134s 134s > f <- function(n, K) { 134s + N <- howmanytrees(n, labeled = FALSE) 134s + p <- 1/N 134s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 134s + } 134s 134s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 134s + 10000)) 134s 134s > DF$P <- mapply(f, n = DF$n, K = DF$K) 134s 134s > library(lattice) 134s 134s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 134s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 134s 134s > subset(DF, n == 20) 134s n K P 134s 17 20 2 1.160494e-11 134s 34 20 5 1.160491e-10 134s 51 20 10 5.222149e-10 134s 68 20 100 5.743191e-08 134s 85 20 1000 5.783570e-06 134s 102 20 10000 5.671842e-04 134s 134s > f(20, 1e+05) 134s [1] 0.04638755 134s 134s > f(30, 1e+06) 134s [1] 2.525152e-07 134s 134s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 134s 134s > TR5 <- read.tree(text = txt) 134s 134s > layout(matrix(1:3, 1)) 134s 134s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 134s 134s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 134s + labeled = FALSE) 134s [1] 2 134s 134s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 134s + labeled = FALSE) 134s [1] 1 134s 134s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 134s + labeled = FALSE) 134s [1] Inf 134s 134s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 134s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 135s 135s > foo.test <- function(x, labeled = TRUE) { 135s + uTR <- unique(x, use.tip.label = labeled) 135s + f <- integer(length(uTR)) 135s + for (j in seq_along( .... [TRUNCATED] 135s 135s > lapply(TR, foo.test) 138s [1] 59 58 70 73 66 73 69 71 70 68 59 72 68 64 60 140s [1] 56 101 130 54 62 45 49 107 66 48 55 57 58 58 54 142s [1] 161 163 41 40 187 55 40 27 50 40 40 42 36 44 34 142s [[1]] 142s 142s Chi-squared test for given probabilities 142s 142s data: f 142s X-squared = 6.05, df = 14, p-value = 0.9652 142s 142s 142s [[2]] 142s 142s Chi-squared test for given probabilities 142s 142s data: f 142s X-squared = 131.75, df = 14, p-value < 2.2e-16 142s 142s 142s [[3]] 142s 142s Chi-squared test for given probabilities 142s 142s data: f 142s X-squared = 619.19, df = 14, p-value < 2.2e-16 142s 142s 142s 142s > lapply(TR, foo.test, labeled = FALSE) 143s [1] 793 207 143s [1] 662 338 144s [1] 511 489 144s [[1]] 144s 144s Chi-squared test for given probabilities 144s 144s data: f 144s X-squared = 343.4, df = 1, p-value < 2.2e-16 144s 144s 144s [[2]] 144s 144s Chi-squared test for given probabilities 144s 144s data: f 144s X-squared = 104.98, df = 1, p-value < 2.2e-16 144s 144s 144s [[3]] 144s 144s Chi-squared test for given probabilities 144s 144s data: f 144s X-squared = 0.484, df = 1, p-value = 0.4866 144s 144s 144s 144s > .Machine$double.xmax 144s [1] 1.797693e+308 144s 144s > howmanytrees(151) 144s [1] 3.753274e+306 144s 144s > howmanytrees(792, labeled = FALSE) 144s [1] 1.029038e+308 144s 144s > (N <- howmanytrees(2e+06)) 144s approximately 3.692364 * 10^12335524 144s 144s > N[2] + 1 144s n 144s 12335525 144s 144s > ceiling((N[2] + 1)/3000) 144s n 144s 4112 144s 144s > n <- 1:792 144s 144s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 144s 144s > lN <- log10(N) 144s 144s > summary(lm(lN ~ n)) 144s 144s Call: 144s lm(formula = lN ~ n) 144s 144s Residuals: 144s Min 1Q Median 3Q Max 144s -0.25968 -0.21424 -0.08311 0.12406 2.82605 144s 144s Coefficients: 144s Estimate Std. Error t value Pr(>|t|) 144s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 144s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 144s --- 144s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 144s 144s Residual standard error: 0.3175 on 790 degrees of freedom 144s Multiple R-squared: 1, Adjusted R-squared: 1 144s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 144s 144s 144s > s <- n > 700 144s 144s > summary(lm(lN[s] ~ n[s])) 144s 144s Call: 144s lm(formula = lN[s] ~ n[s]) 144s 144s Residuals: 144s Min 1Q Median 3Q Max 144s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 144s 144s Coefficients: 144s Estimate Std. Error t value Pr(>|t|) 144s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 144s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 144s --- 144s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 144s 144s Residual standard error: 0.0003738 on 90 degrees of freedom 144s Multiple R-squared: 1, Adjusted R-squared: 1 144s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 144s 144s 144s > n <- 788:792 144s 144s > log10(sapply(n, howmanytrees, labeled = FALSE)) 144s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 144s 144s > 0.3941 * n - 4.153 144s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 144s 144s > xi <- 2.477993 144s 144s > lxi <- log10(xi) 144s 144s > n <- 1000 144s 144s > (n - 1) * lxi 144s [1] 393.706 144s 144s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 144s + 1))))) 144s [1] 393.8532 144s [1] 393.9009 144s [1] 393.9187 144s [1] 393.9257 144s [1] 393.9285 144s [1] 393.9296 144s [1] 393.9301 144s [1] 393.9303 144s [1] 393.9304 144s [1] 393.9304 144s > 144s autopkgtest [18:51:52]: test run-unit-test: -----------------------] 145s run-unit-test PASS 145s autopkgtest [18:51:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 145s autopkgtest [18:51:53]: test pkg-r-autopkgtest: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 146s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 146s The following NEW packages will be installed: 146s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 146s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 146s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 146s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 146s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 146s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 146s libjpeg-turbo8-dev libjpeg8-dev libjs-jquery liblapack-dev liblsan0 146s liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 146s libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 libreadline-dev 146s libstdc++-14-dev libtirpc-dev libtsan2 libubsan1 node-html5shiv 146s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-expm r-cran-gee 146s r-cran-xml2 zlib1g-dev 146s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 104 MB of archives. 146s After this operation, 365 MB of additional disk space will be used. 146s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 libisl23 amd64 0.27-1 [685 kB] 147s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 147s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [11.9 MB] 147s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14 amd64 14.2.0-19ubuntu2 [1030 B] 147s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 147s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 147s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libcc1-0 amd64 15-20250404-0ubuntu1 [47.1 kB] 147s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libitm1 amd64 15-20250404-0ubuntu1 [29.5 kB] 147s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libasan8 amd64 15-20250404-0ubuntu1 [3076 kB] 147s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 liblsan0 amd64 15-20250404-0ubuntu1 [1362 kB] 147s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libtsan2 amd64 15-20250404-0ubuntu1 [2760 kB] 147s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libubsan1 amd64 15-20250404-0ubuntu1 [1211 kB] 147s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libhwasan0 amd64 15-20250404-0ubuntu1 [1687 kB] 147s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libquadmath0 amd64 15-20250404-0ubuntu1 [153 kB] 147s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu2 [2815 kB] 147s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [23.3 MB] 148s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14 amd64 14.2.0-19ubuntu2 [540 kB] 148s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 148s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 148s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu2 [2510 kB] 148s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [13.4 MB] 148s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14 amd64 14.2.0-19ubuntu2 [23.0 kB] 148s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 148s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 148s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 148s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 148s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran-14-dev amd64 14.2.0-19ubuntu2 [967 kB] 148s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [12.5 MB] 148s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14 amd64 14.2.0-19ubuntu2 [14.2 kB] 148s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 148s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 148s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 149s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 149s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 149s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate-dev amd64 1.23-2 [56.8 kB] 149s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 149s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 149s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 149s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 149s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 149s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 149s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 149s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 149s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 149s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 149s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 149s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 149s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 149s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 libpng-dev amd64 1.6.47-1.1 [298 kB] 149s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 149s Get:51 http://ftpmaster.internal/ubuntu questing/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 149s Get:52 http://ftpmaster.internal/ubuntu questing/main amd64 liblzma-dev amd64 5.6.4-1ubuntu1 [189 kB] 149s Get:53 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 149s Get:54 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 149s Get:55 http://ftpmaster.internal/ubuntu questing/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 149s Get:56 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 149s Get:57 http://ftpmaster.internal/ubuntu questing/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 149s Get:58 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-expm amd64 1.0-0-1 [226 kB] 149s Get:59 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-gee amd64 4.13-29-1 [84.2 kB] 149s Get:60 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-xml2 amd64 1.3.8-1 [333 kB] 149s Fetched 104 MB in 3s (33.2 MB/s) 150s Selecting previously unselected package libisl23:amd64. 150s (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 ... 85625 files and directories currently installed.) 150s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 150s Unpacking libisl23:amd64 (0.27-1) ... 150s Selecting previously unselected package libmpc3:amd64. 150s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 150s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 150s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 150s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 150s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 150s Selecting previously unselected package cpp-14. 150s Preparing to unpack .../03-cpp-14_14.2.0-19ubuntu2_amd64.deb ... 150s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 150s Selecting previously unselected package cpp-x86-64-linux-gnu. 150s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 150s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 150s Selecting previously unselected package cpp. 150s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 150s Unpacking cpp (4:14.2.0-1ubuntu1) ... 150s Selecting previously unselected package libcc1-0:amd64. 150s Preparing to unpack .../06-libcc1-0_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libcc1-0:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libitm1:amd64. 150s Preparing to unpack .../07-libitm1_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libitm1:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libasan8:amd64. 150s Preparing to unpack .../08-libasan8_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libasan8:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package liblsan0:amd64. 150s Preparing to unpack .../09-liblsan0_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking liblsan0:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libtsan2:amd64. 150s Preparing to unpack .../10-libtsan2_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libtsan2:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libubsan1:amd64. 150s Preparing to unpack .../11-libubsan1_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libubsan1:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libhwasan0:amd64. 150s Preparing to unpack .../12-libhwasan0_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libhwasan0:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libquadmath0:amd64. 150s Preparing to unpack .../13-libquadmath0_15-20250404-0ubuntu1_amd64.deb ... 150s Unpacking libquadmath0:amd64 (15-20250404-0ubuntu1) ... 150s Selecting previously unselected package libgcc-14-dev:amd64. 150s Preparing to unpack .../14-libgcc-14-dev_14.2.0-19ubuntu2_amd64.deb ... 150s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 151s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 151s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package gcc-14. 151s Preparing to unpack .../16-gcc-14_14.2.0-19ubuntu2_amd64.deb ... 151s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package gcc-x86-64-linux-gnu. 151s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 151s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 151s Selecting previously unselected package gcc. 151s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 151s Unpacking gcc (4:14.2.0-1ubuntu1) ... 151s Selecting previously unselected package libstdc++-14-dev:amd64. 151s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-19ubuntu2_amd64.deb ... 151s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package g++-14-x86-64-linux-gnu. 151s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 151s Unpacking g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package g++-14. 151s Preparing to unpack .../21-g++-14_14.2.0-19ubuntu2_amd64.deb ... 151s Unpacking g++-14 (14.2.0-19ubuntu2) ... 151s Selecting previously unselected package g++-x86-64-linux-gnu. 151s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 151s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 151s Selecting previously unselected package g++. 151s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 151s Unpacking g++ (4:14.2.0-1ubuntu1) ... 151s Selecting previously unselected package build-essential. 152s Preparing to unpack .../24-build-essential_12.12ubuntu1_amd64.deb ... 152s Unpacking build-essential (12.12ubuntu1) ... 152s Selecting previously unselected package dctrl-tools. 152s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 152s Unpacking dctrl-tools (2.24-3build3) ... 152s Selecting previously unselected package libgfortran-14-dev:amd64. 152s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-19ubuntu2_amd64.deb ... 152s Unpacking libgfortran-14-dev:amd64 (14.2.0-19ubuntu2) ... 152s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 152s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 152s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 152s Selecting previously unselected package gfortran-14. 152s Preparing to unpack .../28-gfortran-14_14.2.0-19ubuntu2_amd64.deb ... 152s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 152s Selecting previously unselected package gfortran-x86-64-linux-gnu. 152s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 152s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 152s Selecting previously unselected package gfortran. 152s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 152s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 152s Selecting previously unselected package icu-devtools. 152s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 152s Unpacking icu-devtools (76.1-1ubuntu2) ... 152s Selecting previously unselected package libblas-dev:amd64. 152s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 152s Unpacking libblas-dev:amd64 (3.12.1-2) ... 152s Selecting previously unselected package libbz2-dev:amd64. 152s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 152s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 152s Selecting previously unselected package libdeflate-dev:amd64. 152s Preparing to unpack .../34-libdeflate-dev_1.23-2_amd64.deb ... 152s Unpacking libdeflate-dev:amd64 (1.23-2) ... 152s Selecting previously unselected package libicu-dev:amd64. 152s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 152s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 152s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 152s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 152s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 152s Selecting previously unselected package libjpeg8-dev:amd64. 152s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 152s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 152s Selecting previously unselected package libjpeg-dev:amd64. 152s Preparing 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libtsan2:amd64 (15-20250404-0ubuntu1) ... 153s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 153s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 153s Setting up r-cran-gee (4.13-29-1) ... 153s Setting up libisl23:amd64 (0.27-1) ... 153s Setting up libdeflate-dev:amd64 (1.23-2) ... 153s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 153s Setting up libcc1-0:amd64 (15-20250404-0ubuntu1) ... 153s Setting up liblsan0:amd64 (15-20250404-0ubuntu1) ... 153s Setting up libblas-dev:amd64 (3.12.1-2) ... 153s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 153s Setting up dctrl-tools (2.24-3build3) ... 153s Setting up libitm1:amd64 (15-20250404-0ubuntu1) ... 153s Setting up libbz2-dev:amd64 (1.0.8-6) ... 153s Setting up libpcre2-dev:amd64 (10.45-1) ... 153s Setting up r-cran-xml2 (1.3.8-1) ... 153s Setting up libpng-dev:amd64 (1.6.47-1.1) ... 153s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 153s Setting up pkgconf:amd64 (1.8.1-4) ... 153s Setting up liblapack-dev:amd64 (3.12.1-2) ... 153s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 153s Setting up cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 153s Setting up cpp-14 (14.2.0-19ubuntu2) ... 153s Setting up libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 153s Setting up libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 153s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 153s Setting up libgfortran-14-dev:amd64 (14.2.0-19ubuntu2) ... 153s Setting up cpp (4:14.2.0-1ubuntu1) ... 153s Setting up gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 153s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 153s Setting up gcc-14 (14.2.0-19ubuntu2) ... 153s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 153s Setting up g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 153s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 153s Setting up g++-14 (14.2.0-19ubuntu2) ... 153s Setting up gfortran-14 (14.2.0-19ubuntu2) ... 153s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 153s Setting up gcc (4:14.2.0-1ubuntu1) ... 153s Setting up g++ (4:14.2.0-1ubuntu1) ... 153s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 153s Setting up build-essential (12.12ubuntu1) ... 153s Setting up gfortran (4:14.2.0-1ubuntu1) ... 153s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 153s 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 153s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 153s 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 153s Setting up r-base-dev (4.4.3-1) ... 153s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 153s Processing triggers for libc-bin (2.41-6ubuntu1) ... 153s Processing triggers for man-db (2.13.0-1) ... 154s Processing triggers for install-info (7.1.1-1) ... 155s autopkgtest [18:52:03]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 155s autopkgtest [18:52:03]: test pkg-r-autopkgtest: [----------------------- 156s Test: Try to load the R library ape 156s 156s R version 4.4.3 (2025-02-28) -- "Trophy Case" 156s Copyright (C) 2025 The R Foundation for Statistical Computing 156s Platform: x86_64-pc-linux-gnu 156s 156s R is free software and comes with ABSOLUTELY NO WARRANTY. 156s You are welcome to redistribute it under certain conditions. 156s Type 'license()' or 'licence()' for distribution details. 156s 156s R is a collaborative project with many contributors. 156s Type 'contributors()' for more information and 156s 'citation()' on how to cite R or R packages in publications. 156s 156s Type 'demo()' for some demos, 'help()' for on-line help, or 156s 'help.start()' for an HTML browser interface to help. 156s Type 'q()' to quit R. 156s 156s > library('ape') 156s > 156s > 156s Other tests are currently unsupported! 156s They will be progressively added. 156s autopkgtest [18:52:04]: test pkg-r-autopkgtest: -----------------------] 157s pkg-r-autopkgtest PASS 157s autopkgtest [18:52:05]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 157s autopkgtest [18:52:05]: @@@@@@@@@@@@@@@@@@@@ summary 157s run-unit-test PASS 157s pkg-r-autopkgtest PASS 175s nova [W] Skipping flock for amd64 175s Creating nova instance adt-questing-amd64-r-cran-ape-20250503-184928-juju-7f2275-prod-proposed-migration-environment-2-10d0f009-e2aa-4ebf-97a9-e431f5ed0064 from image adt/ubuntu-questing-amd64-server-20250503.img (UUID 57b7c1b6-ad80-4bdb-b031-36f045f7f3b3)... 175s nova [W] Timed out waiting for 59a4024a-8ba8-405f-8efd-c6d8b33e66a3 to get deleted.