0s autopkgtest [01:37:15]: starting date and time: 2025-03-04 01:37:15+0000 0s autopkgtest [01:37:15]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:37:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qyscxueh/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-mass,src:r-cran-bayestestr,src:r-cran-dendextend,src:r-cran-glmmtmb,src:r-cran-rmpfr --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-cran-mass/7.3-65-1 r-cran-bayestestr/0.15.2-1 r-cran-dendextend/1.19.0+dfsg-1 r-cran-glmmtmb/1.1.10+dfsg-1 r-cran-rmpfr/1.0-0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-3.secgroup --name adt-plucky-ppc64el-r-cran-vegan-20250304-013715-juju-7f2275-prod-proposed-migration-environment-20-c05ccc62-9fe4-407d-88bf-10fc43a0c4f3 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 75s autopkgtest [01:38:30]: testbed dpkg architecture: ppc64el 75s autopkgtest [01:38:30]: testbed apt version: 2.9.31ubuntu1 75s autopkgtest [01:38:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s autopkgtest [01:38:30]: testbed release detected to be: None 76s autopkgtest [01:38:31]: updating testbed package index (apt update) 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 77s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.4 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [472 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [51.1 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [2420 B] 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [89.5 kB] 77s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [434 kB] 77s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [17.0 kB] 77s Fetched 1195 kB in 1s (1316 kB/s) 78s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 79s Calculating upgrade... 79s The following packages will be upgraded: 79s wireless-regdb 80s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 7290 B of archives. 80s After this operation, 1024 B of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el wireless-regdb all 2024.10.07-0ubuntu2 [7290 B] 80s Fetched 7290 B in 0s (43.7 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 ... 106532 files and directories currently installed.) 80s Preparing to unpack .../wireless-regdb_2024.10.07-0ubuntu2_all.deb ... 80s Unpacking wireless-regdb (2024.10.07-0ubuntu2) over (2024.10.07-0ubuntu1) ... 80s Setting up wireless-regdb (2024.10.07-0ubuntu2) ... 80s Processing triggers for man-db (2.13.0-1) ... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 81s autopkgtest [01:38:36]: upgrading testbed (apt dist-upgrade and autopurge) 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 82s Starting 2 pkgProblemResolver with broken count: 0 82s Done 82s Entering ResolveByKeep 83s 83s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 84s Solving dependencies... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s autopkgtest [01:38:41]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP Fri Feb 14 16:16:28 UTC 2025 86s autopkgtest [01:38:41]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 88s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (dsc) [2204 B] 88s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (tar) [1205 kB] 88s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (diff) [6312 B] 89s gpgv: Signature made Sun Sep 1 23:45:51 2024 UTC 89s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 89s gpgv: issuer "plessy@debian.org" 89s gpgv: Can't check signature: No public key 89s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-8+dfsg-1.dsc: no acceptable signature found 89s autopkgtest [01:38:44]: testing package r-cran-vegan version 2.6-8+dfsg-1 89s autopkgtest [01:38:44]: build not needed 92s autopkgtest [01:38:47]: test run-unit-test: preparing testbed 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Starting pkgProblemResolver with broken count: 0 92s Starting 2 pkgProblemResolver with broken count: 0 92s Done 92s The following NEW packages will be installed: 92s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 92s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 92s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 92s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 92s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 92s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 92s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 92s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 92s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 92s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 92s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 92s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 92s x11-common xdg-utils zip 93s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 93s Need to get 68.8 MB of archives. 93s After this operation, 170 MB of additional disk space will be used. 93s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 93s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-2ubuntu1 [37.5 kB] 93s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-2ubuntu1 [188 kB] 93s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-2ubuntu1 [192 kB] 93s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 93s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 93s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.1-2 [239 kB] 93s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 93s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 93s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 93s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 93s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 93s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB] 93s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.23-1 [63.4 kB] 93s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250213-1ubuntu1 [613 kB] 93s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 15-20250213-1ubuntu1 [168 kB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 94s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.2.0-1 [598 kB] 94s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 94s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB] 94s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB] 94s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 94s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 94s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 94s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 94s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 94s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.1-2 [2813 kB] 94s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 94s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB] 94s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB] 94s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.56.1-1 [277 kB] 94s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.56.1-1 [58.6 kB] 94s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.56.1-1 [30.6 kB] 94s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper2 ppc64el 2.2.5-0.3 [18.0 kB] 94s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper-utils ppc64el 2.2.5-0.3 [15.6 kB] 94s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 94s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsm6 ppc64el 2:1.2.4-1 [18.4 kB] 94s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.16+dfsg-1 [1201 kB] 94s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 94s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 94s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 94s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 94s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 94s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.16-1 [946 kB] 94s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 94s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el node-normalize.css all 8.0.1-5 [10.8 kB] 94s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el zip ppc64el 3.0-14ubuntu2 [196 kB] 94s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el unzip ppc64el 6.0-28ubuntu6 [200 kB] 94s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 94s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-core ppc64el 4.4.2-1build1 [28.9 MB] 95s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-cluster ppc64el 2.1.8-1 [586 kB] 95s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-commonmark ppc64el 1.9.2-2 [141 kB] 95s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-evaluate all 1.0.3-1 [114 kB] 95s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-xfun ppc64el 0.50+dfsg-1 [569 kB] 95s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 95s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 95s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 95s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-knitr all 1.49+dfsg-1 [859 kB] 95s Get:60 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-lattice ppc64el 0.22-6-1 [1340 kB] 95s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-markdown all 1.13-1 [162 kB] 95s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 95s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-matrix ppc64el 1.7-2-1 [4536 kB] 95s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-nlme ppc64el 3.1.167-1 [2329 kB] 95s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 95s Get:66 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-permute all 0.9-7-1 [228 kB] 95s Get:67 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-vegan ppc64el 2.6-8+dfsg-1 [3147 kB] 96s Preconfiguring packages ... 96s Fetched 68.8 MB in 3s (23.0 MB/s) 96s Selecting previously unselected package fonts-dejavu-mono. 96s (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 ... 106532 files and directories currently installed.) 96s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 96s Unpacking fonts-dejavu-mono (2.37-8) ... 96s Selecting previously unselected package fonts-dejavu-core. 96s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 96s Unpacking fonts-dejavu-core (2.37-8) ... 96s Selecting previously unselected package fontconfig-config. 96s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_ppc64el.deb ... 96s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 96s Selecting previously unselected package libfontconfig1:ppc64el. 96s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_ppc64el.deb ... 96s Unpacking libfontconfig1:ppc64el (2.15.0-2ubuntu1) ... 96s Selecting previously unselected package fontconfig. 96s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_ppc64el.deb ... 96s Unpacking fontconfig (2.15.0-2ubuntu1) ... 96s Selecting previously unselected package fonts-glyphicons-halflings. 96s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 96s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 96s Selecting previously unselected package fonts-mathjax. 96s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 96s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 96s Selecting previously unselected package libblas3:ppc64el. 96s Preparing to unpack .../07-libblas3_3.12.1-2_ppc64el.deb ... 96s Unpacking libblas3:ppc64el (3.12.1-2) ... 96s Selecting previously unselected package libpixman-1-0:ppc64el. 96s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_ppc64el.deb ... 96s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ... 96s Selecting previously unselected package libxcb-render0:ppc64el. 96s Preparing to unpack .../09-libxcb-render0_1.17.0-2_ppc64el.deb ... 96s Unpacking libxcb-render0:ppc64el (1.17.0-2) ... 97s Selecting previously unselected package libxcb-shm0:ppc64el. 97s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_ppc64el.deb ... 97s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ... 97s Selecting previously unselected package libxrender1:ppc64el. 97s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ... 97s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ... 97s Selecting previously unselected package libcairo2:ppc64el. 97s Preparing to unpack .../12-libcairo2_1.18.2-2_ppc64el.deb ... 97s Unpacking libcairo2:ppc64el (1.18.2-2) ... 97s Selecting previously unselected package libdatrie1:ppc64el. 97s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_ppc64el.deb ... 97s Unpacking libdatrie1:ppc64el (0.2.13-3build1) ... 97s Selecting previously unselected package libdeflate0:ppc64el. 97s Preparing to unpack .../14-libdeflate0_1.23-1_ppc64el.deb ... 97s Unpacking libdeflate0:ppc64el (1.23-1) ... 97s Selecting previously unselected package libgfortran5:ppc64el. 97s Preparing to unpack .../15-libgfortran5_15-20250213-1ubuntu1_ppc64el.deb ... 97s Unpacking libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 97s Selecting previously unselected package libgomp1:ppc64el. 97s Preparing to unpack .../16-libgomp1_15-20250213-1ubuntu1_ppc64el.deb ... 97s Unpacking libgomp1:ppc64el (15-20250213-1ubuntu1) ... 97s Selecting previously unselected package libgraphite2-3:ppc64el. 97s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ... 97s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ... 97s Selecting previously unselected package libharfbuzz0b:ppc64el. 97s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_ppc64el.deb ... 97s Unpacking libharfbuzz0b:ppc64el (10.2.0-1) ... 97s Selecting previously unselected package x11-common. 97s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 97s Unpacking x11-common (1:7.7+23ubuntu3) ... 97s Selecting previously unselected package libice6:ppc64el. 97s Preparing to unpack .../20-libice6_2%3a1.1.1-1_ppc64el.deb ... 97s Unpacking libice6:ppc64el (2:1.1.1-1) ... 97s Selecting previously unselected package libjpeg-turbo8:ppc64el. 97s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_ppc64el.deb ... 97s Unpacking libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ... 97s Selecting previously unselected package libjpeg8:ppc64el. 97s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 97s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 97s Selecting previously unselected package libjs-bootstrap. 97s Preparing to unpack .../23-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 97s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 97s Selecting previously unselected package libjs-highlight.js. 97s Preparing to unpack .../24-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 97s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 97s Selecting previously unselected package libjs-jquery. 97s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 97s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 97s Selecting previously unselected package libjs-jquery-datatables. 97s Preparing to unpack .../26-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 97s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 97s Selecting previously unselected package liblapack3:ppc64el. 97s Preparing to unpack .../27-liblapack3_3.12.1-2_ppc64el.deb ... 97s Unpacking liblapack3:ppc64el (3.12.1-2) ... 97s Selecting previously unselected package liblerc4:ppc64el. 97s Preparing to unpack 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(2.40-4ubuntu1) ... 102s Processing triggers for man-db (2.13.0-1) ... 103s Processing triggers for install-info (7.1.1-1) ... 104s autopkgtest [01:38:59]: test run-unit-test: [----------------------- 104s 104s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 104s Copyright (C) 2024 The R Foundation for Statistical Computing 104s Platform: powerpc64le-unknown-linux-gnu 104s 104s R is free software and comes with ABSOLUTELY NO WARRANTY. 104s You are welcome to redistribute it under certain conditions. 104s Type 'license()' or 'licence()' for distribution details. 104s 104s R is a collaborative project with many contributors. 104s Type 'contributors()' for more information and 104s 'citation()' on how to cite R or R packages in publications. 104s 104s Type 'demo()' for some demos, 'help()' for on-line help, or 104s 'help.start()' for an HTML browser interface to help. 104s Type 'q()' to quit R. 104s 104s > Stangle("decision-vegan.Rnw") 105s Writing to file decision-vegan.R 105s > source("decision-vegan.R", echo=TRUE) 105s 105s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 105s 105s > options(SweaveHooks = list(fig = figset)) 105s 105s > options(prompt = "> ", continue = " ") 105s 105s > options(width = 55) 105s 105s > require(vegan) 105s Loading required package: vegan 105s Loading required package: permute 105s Loading required package: lattice 106s This is vegan 2.6-8 106s 106s > data(sipoo) 106s 106s > mod <- nestedtemp(sipoo) 106s 106s > plot(mod, "i") 106s 106s > x <- mod$c["Falcsubb"] 106s 106s > y <- 1 - mod$r["Svartholm"] 106s 106s > points(x, y, pch = 16, cex = 1.5) 106s 106s > abline(x + y, -1, lty = 2) 106s 106s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 106s 106s > cross <- function(x, a, p) f(x, p) - a + x 106s 106s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 106s 106s > arrows(x, y, r, f(r, mod$p), lwd = 4) 106s 106s > library(vegan) 106s 106s > data(varespec) 106s 106s > data(varechem) 106s 106s > orig <- cca(varespec ~ Al + K, varechem) 106s 106s > plot(orig, dis = c("lc", "bp")) 106s 106s > plot(orig, dis = c("lc", "bp")) 106s 106s > i <- sample(nrow(varespec)) 106s 106s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 106s 106s > plot(shuff, dis = c("lc", "bp")) 106s 106s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 106s + dis = "lc"))) 106s 106s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 106s + dis = "lc"))) 106s 106s > tmp1 <- rda(varespec ~ Al + K, varechem) 106s 106s > i <- sample(nrow(varespec)) 106s 106s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 106s 106s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 106s + dis = "lc"))) 106s 106s > orig 106s Call: cca(formula = varespec ~ Al + K, data = 106s varechem) 106s 106s -- Model Summary -- 106s 106s Inertia Proportion Rank 106s Total 2.0832 1.0000 106s Constrained 0.4760 0.2285 2 106s Unconstrained 1.6072 0.7715 21 106s 106s Inertia is scaled Chi-square 106s 106s -- Eigenvalues -- 106s 106s Eigenvalues for constrained axes: 106s CCA1 CCA2 106s 0.3608 0.1152 106s 106s Eigenvalues for unconstrained axes: 106s CA1 CA2 CA3 CA4 CA5 CA6 CA7 106s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 106s CA8 106s 0.0757 106s (Showing 8 of 21 unconstrained eigenvalues) 106s 106s 106s > shuff 106s Call: cca(formula = varespec[i, ] ~ Al + K, data = 106s varechem) 106s 106s -- Model Summary -- 106s 106s Inertia Proportion Rank 106s Total 2.08320 1.00000 106s Constrained 0.20804 0.09987 2 106s Unconstrained 1.87516 0.90013 21 106s 106s Inertia is scaled Chi-square 106s 106s -- Eigenvalues -- 106s 106s Eigenvalues for constrained axes: 106s CCA1 CCA2 106s 0.15513 0.05291 106s 106s Eigenvalues for unconstrained axes: 106s CA1 CA2 CA3 CA4 CA5 CA6 CA7 106s 0.4226 0.3403 0.2260 0.1783 0.1728 0.1162 0.0967 106s CA8 106s 0.0742 106s (Showing 8 of 21 unconstrained eigenvalues) 106s 106s 106s > plot(procrustes(orig, shuff)) 106s 106s > tmp1 <- rda(varespec ~ ., varechem) 106s 106s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 106s 106s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 106s + scores(tmp2, dis = "lc", choi = 1:14)) 106s 106s > max(residuals(proc)) 106s [1] 3.138515e-14 106s 106s > data(dune) 106s 106s > data(dune.env) 106s 106s > orig <- cca(dune ~ Moisture, dune.env) 106s 106s > plot(orig, dis = "lc") 106s 106s > plot(orig, display = "wa", type = "points") 106s 106s > ordispider(orig, col = "red") 106s 106s > text(orig, dis = "cn", col = "blue") 106s 106s > plot(orig, display = "wa", type = "points") 106s 106s > ordispider(orig, col = "red") 106s 106s > text(orig, dis = "cn", col = "blue") 106s > 106s 106s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 106s Copyright (C) 2024 The R Foundation for Statistical Computing 106s Platform: powerpc64le-unknown-linux-gnu 106s 106s R is free software and comes with ABSOLUTELY NO WARRANTY. 106s You are welcome to redistribute it under certain conditions. 106s Type 'license()' or 'licence()' for distribution details. 106s 106s R is a collaborative project with many contributors. 106s Type 'contributors()' for more information and 106s 'citation()' on how to cite R or R packages in publications. 106s 106s Type 'demo()' for some demos, 'help()' for on-line help, or 106s 'help.start()' for an HTML browser interface to help. 106s Type 'q()' to quit R. 106s 106s > Stangle("diversity-vegan.Rnw") 106s Writing to file diversity-vegan.R 106s > source("diversity-vegan.R", echo=TRUE) 106s 106s > par(mfrow = c(1, 1)) 106s 106s > options(width = 55) 106s 106s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 106s 106s > options(SweaveHooks = list(fig = figset)) 106s 106s > options(prompt = "> ", continue = " ") 106s 106s > library(vegan) 106s Loading required package: permute 106s Loading required package: lattice 107s This is vegan 2.6-8 107s 107s > data(BCI) 107s 107s > H <- diversity(BCI) 107s 107s > J <- H/log(specnumber(BCI)) 107s 107s > k <- sample(nrow(BCI), 6) 107s 107s > R <- renyi(BCI[k, ]) 107s 107s > print(plot(R)) 107s 107s > alpha <- fisher.alpha(BCI) 107s 107s > quantile(rowSums(BCI)) 107s 0% 25% 50% 75% 100% 107s 340.0 409.0 428.0 443.5 601.0 107s 107s > Srar <- rarefy(BCI, min(rowSums(BCI))) 107s 107s > S2 <- rarefy(BCI, 2) 107s 107s > all(rank(Srar) == rank(S2)) 107s [1] FALSE 107s 107s > range(diversity(BCI, "simp") - (S2 - 1)) 107s [1] -0.002868298 -0.001330663 107s 107s > data(dune) 107s 107s > data(dune.taxon) 107s 107s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 107s 107s > mod <- taxondive(dune, taxdis) 107s 107s > plot(mod) 107s 107s > tr <- hclust(taxdis, "aver") 107s 107s > mod <- treedive(dune, tr) 107s forced matching of 'tree' labels and 'comm' names 107s 107s > k <- sample(nrow(BCI), 1) 107s 107s > fish <- fisherfit(BCI[k, ]) 107s 107s > fish 107s 107s Fisher log series model 107s No. of species: 100 107s Fisher alpha: 40.99634 107s 107s 107s > plot(fish) 107s 107s > prestondistr(BCI[k, ]) 107s 107s Preston lognormal model 107s Method: maximized likelihood to log2 abundances 107s No. of species: 100 107s 107s mode width S0 107s 0.9849822 1.6642110 27.1323499 107s 107s Frequencies by Octave 107s 0 1 2 3 4 107s Observed 19.00000 29.00000 22.00000 12.500 13.500000 107s Fitted 22.77303 27.13125 22.52739 13.036 5.257389 107s 5 6 107s Observed 3.000000 1.0000000 107s Fitted 1.477706 0.2894664 107s 107s 107s > rad <- radfit(BCI[k, ]) 107s 107s > rad 107s 107s RAD models, family poisson 107s No. of species 100, total abundance 429 107s 107s par1 par2 par3 Deviance AIC 107s Null 45.067 331.756 107s Preemption 0.039794 33.728 322.417 107s Lognormal 0.93253 1.0384 19.018 309.707 107s Zipf 0.11174 -0.76181 42.503 333.192 107s Mandelbrot 8.5711 -1.7894 14.87 7.286 299.975 107s BIC 107s Null 331.756 107s Preemption 325.022 107s Lognormal 314.917 107s Zipf 338.402 107s Mandelbrot 307.790 107s 107s > print(radlattice(rad)) 108s 108s > sac <- specaccum(BCI) 108s 108s > plot(sac, ci.type = "polygon", ci.col = "yellow") 108s 108s > sac <- specaccum(BCI) 108s 108s > plot(sac, ci.type = "polygon", ci.col = "yellow") 108s 108s > ncol(BCI)/mean(specnumber(BCI)) - 1 108s [1] 1.478519 108s 108s > beta <- vegdist(BCI, binary = TRUE) 108s 108s > mean(beta) 108s [1] 0.3399075 108s 108s > betadiver(help = TRUE) 108s 1 "w" = (b+c)/(2*a+b+c) 108s 2 "-1" = (b+c)/(2*a+b+c) 108s 3 "c" = (b+c)/2 108s 4 "wb" = b+c 108s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 108s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 108s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 108s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 108s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 108s (2*a+b+c))-1 108s 8 "t" = (b+c)/(2*a+b+c) 108s 9 "me" = (b+c)/(2*a+b+c) 108s 10 "j" = a/(a+b+c) 108s 11 "sor" = 2*a/(2*a+b+c) 108s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 108s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 108s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 108s 15 "cc" = (b+c)/(a+b+c) 108s 16 "g" = (b+c)/(a+b+c) 108s 17 "-3" = pmin.int(b,c)/(a+b+c) 108s 18 "l" = (b+c)/2 108s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 108s 20 "hk" = (b+c)/(2*a+b+c) 108s 21 "rlb" = a/(a+c) 108s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 108s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 108s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 108s 108s > z <- betadiver(BCI, "z") 108s 108s > quantile(z) 108s 0% 25% 50% 75% 100% 108s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 108s 108s > data(dune) 108s 108s > data(dune.env) 108s 108s > z <- betadiver(dune, "z") 108s 108s > mod <- with(dune.env, betadisper(z, Management)) 108s 108s > mod 108s 108s Homogeneity of multivariate dispersions 108s 108s Call: betadisper(d = z, group = Management) 108s 108s No. of Positive Eigenvalues: 12 108s No. of Negative Eigenvalues: 7 108s 108s Average distance to median: 108s BF HF NM SF 108s 0.2532 0.2512 0.4406 0.3635 108s 108s Eigenvalues for PCoA axes: 108s (Showing 8 of 19 eigenvalues) 108s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 108s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 108s PCoA7 PCoA8 108s 0.16128 0.08099 108s 108s > boxplot(mod) 108s 108s > specpool(BCI) 108s Species chao chao.se jack1 jack1.se jack2 108s All 225 236.3732 6.54361 245.58 5.650522 247.8722 108s boot boot.se n 108s All 235.6862 3.468888 50 108s 108s > s <- sample(nrow(BCI), 25) 108s 108s > specpool(BCI[s, ]) 108s Species chao chao.se jack1 jack1.se jack2 108s All 207 247.96 19.7607 237.72 9.12421 256.58 108s boot boot.se n 108s All 220.6784 4.743108 25 108s 108s > estimateR(BCI[k, ]) 108s 20 108s S.obs 100.000000 108s S.chao1 133.476190 108s se.chao1 14.332699 108s S.ACE 147.592810 108s se.ACE 6.621289 108s 108s > veiledspec(prestondistr(BCI[k, ])) 108s Extrapolated Observed Veiled 108s 113.18418 100.00000 13.18418 108s 108s > veiledspec(BCI[k, ]) 108s Extrapolated Observed Veiled 108s 122.24639 100.00000 22.24639 108s 108s > smo <- beals(BCI) 108s 108s > j <- which(colnames(BCI) == "Ceiba.pentandra") 108s 108s > plot(beals(BCI, species = j, include = FALSE), BCI[, 108s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 108s 108s > j <- which(colnames(BCI) == "Ceiba.pentandra") 108s 108s > plot(beals(BCI, species = j, include = FALSE), BCI[, 108s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 108s Warning messages: 108s 1: In cor(x > 0) : the standard deviation is zero 108s 2: In cor(x > 0) : the standard deviation is zero 108s 3: In betadisper(z, Management) : 108s some squared distances are negative and changed to zero 108s > 108s 108s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 108s Copyright (C) 2024 The R Foundation for Statistical Computing 108s Platform: powerpc64le-unknown-linux-gnu 108s 108s R is free software and comes with ABSOLUTELY NO WARRANTY. 108s You are welcome to redistribute it under certain conditions. 108s Type 'license()' or 'licence()' for distribution details. 108s 108s R is a collaborative project with many contributors. 108s Type 'contributors()' for more information and 108s 'citation()' on how to cite R or R packages in publications. 108s 108s Type 'demo()' for some demos, 'help()' for on-line help, or 108s 'help.start()' for an HTML browser interface to help. 108s Type 'q()' to quit R. 108s 108s > Stangle("intro-vegan.Rnw") 108s Writing to file intro-vegan.R 108s > source("intro-vegan.R", echo=TRUE) 108s 108s > par(mfrow = c(1, 1)) 108s 108s > options(width = 72) 108s 108s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 108s 108s > options(SweaveHooks = list(fig = figset)) 108s 108s > options(prompt = "> ", continue = " ") 108s 108s > library(vegan) 108s Loading required package: permute 108s Loading required package: lattice 109s 109s > data(dune) 109s This is vegan 2.6-8 109s 109s > ord <- decorana(dune) 109s 109s > ord 109s 109s Call: 109s decorana(veg = dune) 109s 109s Detrended correspondence analysis with 26 segments. 109s Rescaling of axes with 4 iterations. 109s Total inertia (scaled Chi-square): 2.1153 109s 109s DCA1 DCA2 DCA3 DCA4 109s Eigenvalues 0.5117 0.3036 0.12125 0.14267 109s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 109s Decorana values 0.5360 0.2869 0.08136 0.04814 109s Axis lengths 3.7004 3.1166 1.30055 1.47888 109s 109s 109s > ord <- metaMDS(dune, trace = FALSE) 109s 109s > ord 109s 109s Call: 109s metaMDS(comm = dune, trace = FALSE) 109s 109s global Multidimensional Scaling using monoMDS 109s 109s Data: dune 109s Distance: bray 109s 109s Dimensions: 2 109s Stress: 0.1183186 109s Stress type 1, weak ties 109s Best solution was repeated 3 times in 20 tries 109s The best solution was from try 18 (random start) 109s Scaling: centring, PC rotation, halfchange scaling 109s Species: expanded scores based on ‘dune’ 109s 109s 109s > plot(ord) 109s 109s > plot(ord) 109s 109s > plot(ord, type = "n") 109s 109s > points(ord, display = "sites", cex = 0.8, pch = 21, 109s + col = "red", bg = "yellow") 109s 109s > text(ord, display = "species", cex = 0.7, col = "blue") 109s 109s > plot(ord, type = "n") 109s 109s > points(ord, display = "sites", cex = 0.8, pch = 21, 109s + col = "red", bg = "yellow") 109s 109s > text(ord, display = "species", cex = 0.7, col = "blue") 109s 109s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 109s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 109s + col = "blue") 109s 109s > data(dune.env) 109s 109s > attach(dune.env) 109s 109s > plot(ord, disp = "sites", type = "n") 109s 109s > ordihull(ord, Management, col = 1:4, lwd = 3) 109s 109s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 109s + lwd = 3) 109s 109s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 109s 109s > ordispider(ord, Management, col = 1:4, label = TRUE) 109s 109s > points(ord, disp = "sites", pch = 21, col = "red", 109s + bg = "yellow", cex = 1.3) 109s 109s > plot(ord, disp = "sites", type = "n") 109s 109s > ordihull(ord, Management, col = 1:4, lwd = 3) 109s 109s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 109s + lwd = 3) 109s 109s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 109s 109s > ordispider(ord, Management, col = 1:4, label = TRUE) 109s 109s > points(ord, disp = "sites", pch = 21, col = "red", 109s + bg = "yellow", cex = 1.3) 109s 109s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 109s + perm = 999) 109s 109s > ord.fit 109s 109s ***VECTORS 109s 109s NMDS1 NMDS2 r2 Pr(>r) 109s A1 0.96473 0.26323 0.3649 0.017 * 109s --- 109s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 109s Permutation: free 109s Number of permutations: 999 109s 109s ***FACTORS: 109s 109s Centroids: 109s NMDS1 NMDS2 109s ManagementBF -0.4534 -0.0102 109s ManagementHF -0.2636 -0.1282 109s ManagementNM 0.2958 0.5790 109s ManagementSF 0.1506 -0.4670 109s 109s Goodness of fit: 109s r2 Pr(>r) 109s Management 0.4134 0.006 ** 109s --- 109s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 109s Permutation: free 109s Number of permutations: 999 109s 109s 109s 109s > plot(ord, dis = "site") 109s 109s > plot(ord.fit) 109s 109s > ordisurf(ord, A1, add = TRUE) 109s 109s Family: gaussian 109s Link function: identity 109s 109s Formula: 109s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 109s 109s Estimated degrees of freedom: 109s 1.59 total = 2.59 109s 109s REML score: 41.58727 109s 109s > plot(ord, dis = "site") 109s 109s > plot(ord.fit) 109s 109s > ordisurf(ord, A1, add = TRUE) 110s 110s Family: gaussian 110s Link function: identity 110s 110s Formula: 110s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 110s 110s Estimated degrees of freedom: 110s 1.59 total = 2.59 110s 110s REML score: 41.58727 110s 110s > ord <- cca(dune ~ A1 + Management, data = dune.env) 110s 110s > ord 110s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 110s 110s -- Model Summary -- 110s 110s Inertia Proportion Rank 110s Total 2.1153 1.0000 110s Constrained 0.7798 0.3686 4 110s Unconstrained 1.3355 0.6314 15 110s 110s Inertia is scaled Chi-square 110s 110s -- Eigenvalues -- 110s 110s Eigenvalues for constrained axes: 110s CCA1 CCA2 CCA3 CCA4 110s 0.3187 0.2372 0.1322 0.0917 110s 110s Eigenvalues for unconstrained axes: 110s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 110s Some constraints or conditions were aliased because they were 110s redundant. This can happen if terms are linearly dependent (collinear): 110s ‘Manure^4’ 110s 110s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 110s CA11 CA12 CA13 CA14 CA15 110s 0.0317 0.0178 0.0116 0.0087 0.0047 110s 110s 110s > plot(ord) 110s 110s > plot(ord) 110s 110s > cca(dune ~ ., data = dune.env) 110s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 110s Manure, data = dune.env) 110s 110s -- Model Summary -- 110s 110s Inertia Proportion Rank 110s Total 2.1153 1.0000 110s Constrained 1.5032 0.7106 12 110s Unconstrained 0.6121 0.2894 7 110s 110s Inertia is scaled Chi-square 110s 110s -- Note -- 110s 110s Some constraints or conditions were aliased because they were 110s redundant. This can happen if terms are linearly dependent 110s (collinear): ‘Manure^4’ 110s 110s -- Eigenvalues -- 110s 110s Eigenvalues for constrained axes: 110s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 110s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 110s CCA11 CCA12 110s 0.0228 0.0108 110s 110s Eigenvalues for unconstrained axes: 110s CA1 CA2 CA3 CA4 CA5 CA6 CA7 110s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 110s 110s 110s > anova(ord) 110s Permutation test for cca under reduced model 110s Permutation: free 110s Number of permutations: 999 110s 110s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 110s Df ChiSquare F Pr(>F) 110s Model 4 0.77978 2.1896 0.001 *** 110s Residual 15 1.33549 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > anova(ord, by = "term", permutations = 199) 110s Permutation test for cca under reduced model 110s Terms added sequentially (first to last) 110s Permutation: free 110s Number of permutations: 199 110s 110s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 110s Df ChiSquare F Pr(>F) 110s A1 1 0.22476 2.5245 0.015 * 110s Management 3 0.55502 2.0780 0.005 ** 110s Residual 15 1.33549 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > anova(ord, by = "mar", permutations = 199) 110s Permutation test for cca under reduced model 110s Marginal effects of terms 110s Permutation: free 110s Number of permutations: 199 110s 110s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 110s Df ChiSquare F Pr(>F) 110s A1 1 0.17594 1.9761 0.020 * 110s Management 3 0.55502 2.0780 0.005 ** 110s Residual 15 1.33549 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > anova(ord, by = "axis", permutations = 499) 110s Permutation test for cca under reduced model 110s Forward tests for axes 110s Permutation: free 110s Number of permutations: 499 110s 110s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 110s Df ChiSquare F Pr(>F) 110s CCA1 1 0.31875 3.5801 0.008 ** 110s CCA2 1 0.23718 2.6640 0.142 110s CCA3 1 0.13217 1.4845 0.844 110s CCA4 1 0.09168 1.0297 1.000 110s Residual 15 1.33549 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 110s + data = dune.env) 110s 110s > ord 110s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 110s data = dune.env) 110s 110s -- Model Summary -- 110s 110s Inertia Proportion Rank 110s Total 2.1153 1.0000 110s Conditional 0.6283 0.2970 3 110s Constrained 0.5109 0.2415 4 110s Unconstrained 0.9761 0.4615 12 110s 110s Inertia is scaled Chi-square 110s 110s -- Eigenvalues -- 110s 110s Eigenvalues for constrained axes: 110s CCA1 CCA2 CCA3 CCA4 110s 0.24932 0.12090 0.08160 0.05904 110s 110s Eigenvalues for unconstrained axes: 110s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 110s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 110s CA10 CA11 CA12 110s 0.02102 0.01254 0.00928 110s 110s 110s > anova(ord, by = "term", permutations = 499) 110s Permutation test for cca under reduced model 110s Terms added sequentially (first to last) 110s Permutation: free 110s Number of permutations: 499 110s 110s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 110s Df ChiSquare F Pr(>F) 110s A1 1 0.11543 1.4190 1.000 110s Management 3 0.39543 1.6205 0.002 ** 110s Residual 12 0.97610 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 110s 110s > anova(ord, by = "term", permutations = how) 110s Permutation test for cca under reduced model 110s Terms added sequentially (first to last) 110s Plots: dune.env$Moisture, plot permutation: none 110s Permutation: free 110s Number of permutations: 499 110s 110s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 110s Df ChiSquare F Pr(>F) 110s A1 1 0.11543 1.4190 1.000 110s Management 3 0.39543 1.6205 0.002 ** 110s Residual 12 0.97610 110s --- 110s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 110s 110s > detach(dune.env) 110s > 110s 110s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 110s Copyright (C) 2024 The R Foundation for Statistical Computing 110s Platform: powerpc64le-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("partitioning.Rnw") 110s Writing to file partitioning.R 110s > source("partitioning.R", echo=TRUE) 110s 110s > par(mfrow = c(1, 1)) 110s 110s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 110s 110s > options(SweaveHooks = list(fig = figset)) 110s 110s > library(vegan) 110s Loading required package: permute 110s Loading required package: lattice 111s This is vegan 2.6-8 111s 111s > labs <- paste("Table", 1:4) 111s 111s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 111s 111s > showvarparts(2, bg = cls, Xnames = labs) 111s 111s > showvarparts(3, bg = cls, Xnames = labs) 111s 111s > showvarparts(4, bg = cls, Xnames = labs) 111s > 118s Test cca-object-tests passed 120s Test oecosimu-tests passed 123s Test vegan-tests passed 124s autopkgtest [01:39:19]: test run-unit-test: -----------------------] 124s autopkgtest [01:39:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 124s run-unit-test PASS 125s autopkgtest [01:39:20]: test pkg-r-autopkgtest: preparing testbed 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 126s The following NEW packages will be installed: 126s build-essential cpp cpp-14 cpp-14-powerpc64le-linux-gnu 126s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-14 126s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 126s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-14 126s gfortran-14-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 126s icu-devtools libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev 126s libgcc-14-dev libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 126s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 126s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 126s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 126s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 126s r-base-dev zlib1g-dev 126s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 93.6 MB of archives. 126s After this operation, 350 MB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 126s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu3 [10.5 MB] 127s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-17ubuntu3 [1036 B] 127s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [5566 B] 127s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.2.0-1ubuntu1 [22.4 kB] 127s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 15-20250213-1ubuntu1 [48.7 kB] 127s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 15-20250213-1ubuntu1 [32.4 kB] 127s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 15-20250213-1ubuntu1 [3009 kB] 127s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 15-20250213-1ubuntu1 [1377 kB] 127s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 15-20250213-1ubuntu1 [2734 kB] 127s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 15-20250213-1ubuntu1 [1234 kB] 127s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 15-20250213-1ubuntu1 [160 kB] 127s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-17ubuntu3 [1619 kB] 127s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu3 [20.6 MB] 127s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-17ubuntu3 [536 kB] 127s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [1226 B] 127s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.2.0-1ubuntu1 [5012 B] 127s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-17ubuntu3 [2678 kB] 128s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu3 [12.0 MB] 128s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-17ubuntu3 [21.8 kB] 128s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [966 B] 128s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.2.0-1ubuntu1 [1088 B] 128s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 128s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el dctrl-tools ppc64el 2.24-3build3 [109 kB] 128s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran-14-dev ppc64el 14.2.0-17ubuntu3 [621 kB] 128s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu3 [11.3 MB] 128s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-14 ppc64el 14.2.0-17ubuntu3 [13.6 kB] 128s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [1024 B] 128s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran ppc64el 4:14.2.0-1ubuntu1 [1166 B] 128s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el icu-devtools ppc64el 76.1-1ubuntu2 [251 kB] 128s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas-dev ppc64el 3.12.1-2 [318 kB] 128s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbz2-dev ppc64el 1.0.8-6 [50.2 kB] 128s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate-dev ppc64el 1.23-1 [70.8 kB] 128s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libicu-dev ppc64el 76.1-1ubuntu2 [12.9 MB] 128s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-3ubuntu2 [358 kB] 128s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 128s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 128s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack-dev ppc64el 3.12.1-2 [6076 kB] 129s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libncurses-dev ppc64el 6.5+20250216-1 [484 kB] 129s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-16-0 ppc64el 10.45-1 [286 kB] 129s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-32-0 ppc64el 10.45-1 [269 kB] 129s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-posix3 ppc64el 10.45-1 [7390 B] 129s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-dev ppc64el 10.45-1 [921 kB] 129s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpkgconf3 ppc64el 1.8.1-4 [37.1 kB] 129s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 129s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpng-dev ppc64el 1.6.47-1 [323 kB] 129s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libreadline-dev ppc64el 8.2-6 [230 kB] 129s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblzma-dev ppc64el 5.6.3-1 [208 kB] 129s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf-bin ppc64el 1.8.1-4 [22.5 kB] 129s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf ppc64el 1.8.1-4 [16.7 kB] 129s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.3 [223 kB] 129s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-dev all 4.4.2-1build1 [4342 B] 129s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 129s Fetched 93.6 MB in 3s (28.9 MB/s) 129s Selecting previously unselected package libisl23:ppc64el. 129s (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 ... 114505 files and directories currently installed.) 129s Preparing to unpack .../00-libisl23_0.27-1_ppc64el.deb ... 129s Unpacking libisl23:ppc64el (0.27-1) ... 129s Selecting previously unselected package libmpc3:ppc64el. 129s Preparing to unpack .../01-libmpc3_1.3.1-1build2_ppc64el.deb ... 129s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 129s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 129s Preparing to unpack .../02-cpp-14-powerpc64le-linux-gnu_14.2.0-17ubuntu3_ppc64el.deb ... 129s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 129s Selecting previously unselected package cpp-14. 129s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_ppc64el.deb ... 129s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 129s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 129s Preparing to unpack .../04-cpp-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 129s Unpacking cpp-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 129s Selecting previously unselected package cpp. 129s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 129s Unpacking cpp (4:14.2.0-1ubuntu1) ... 129s Selecting previously unselected package libcc1-0:ppc64el. 129s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_ppc64el.deb ... 129s Unpacking libcc1-0:ppc64el (15-20250213-1ubuntu1) ... 129s Selecting previously unselected package libitm1:ppc64el. 129s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_ppc64el.deb ... 129s Unpacking libitm1:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package libasan8:ppc64el. 130s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_ppc64el.deb ... 130s Unpacking libasan8:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package liblsan0:ppc64el. 130s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_ppc64el.deb ... 130s Unpacking liblsan0:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package libtsan2:ppc64el. 130s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_ppc64el.deb ... 130s Unpacking libtsan2:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package libubsan1:ppc64el. 130s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_ppc64el.deb ... 130s Unpacking libubsan1:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package libquadmath0:ppc64el. 130s Preparing to unpack .../12-libquadmath0_15-20250213-1ubuntu1_ppc64el.deb ... 130s Unpacking libquadmath0:ppc64el (15-20250213-1ubuntu1) ... 130s Selecting previously unselected package libgcc-14-dev:ppc64el. 130s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu3_ppc64el.deb ... 130s Unpacking libgcc-14-dev:ppc64el (14.2.0-17ubuntu3) ... 130s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 130s Preparing to unpack .../14-gcc-14-powerpc64le-linux-gnu_14.2.0-17ubuntu3_ppc64el.deb ... 130s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 130s Selecting previously unselected package gcc-14. 130s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu3_ppc64el.deb ... 130s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 130s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 130s Preparing to unpack .../16-gcc-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 130s Unpacking gcc-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package gcc. 130s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 130s Unpacking gcc (4:14.2.0-1ubuntu1) ... 130s Selecting previously unselected package libstdc++-14-dev:ppc64el. 130s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu3_ppc64el.deb ... 130s Unpacking libstdc++-14-dev:ppc64el (14.2.0-17ubuntu3) ... 130s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 130s Preparing to unpack .../19-g++-14-powerpc64le-linux-gnu_14.2.0-17ubuntu3_ppc64el.deb ... 130s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 131s Selecting previously unselected package g++-14. 131s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu3_ppc64el.deb ... 131s Unpacking g++-14 (14.2.0-17ubuntu3) ... 131s Selecting previously unselected package g++-powerpc64le-linux-gnu. 131s Preparing to unpack .../21-g++-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 131s Unpacking g++-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 131s Selecting previously unselected package g++. 131s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 131s Unpacking g++ (4:14.2.0-1ubuntu1) ... 131s Selecting previously unselected package build-essential. 131s Preparing to unpack .../23-build-essential_12.10ubuntu1_ppc64el.deb ... 131s Unpacking build-essential (12.10ubuntu1) ... 131s Selecting previously unselected package dctrl-tools. 131s Preparing to unpack .../24-dctrl-tools_2.24-3build3_ppc64el.deb ... 131s Unpacking dctrl-tools (2.24-3build3) ... 131s Selecting previously unselected package libgfortran-14-dev:ppc64el. 131s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu3_ppc64el.deb ... 131s Unpacking libgfortran-14-dev:ppc64el (14.2.0-17ubuntu3) ... 131s Selecting previously unselected package gfortran-14-powerpc64le-linux-gnu. 131s Preparing to unpack .../26-gfortran-14-powerpc64le-linux-gnu_14.2.0-17ubuntu3_ppc64el.deb ... 131s Unpacking gfortran-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 131s Selecting previously unselected package gfortran-14. 131s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu3_ppc64el.deb ... 131s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 131s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 131s Preparing to unpack .../28-gfortran-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 131s Unpacking gfortran-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 131s Selecting previously unselected package gfortran. 131s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 131s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 131s Selecting previously unselected package icu-devtools. 131s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_ppc64el.deb ... 131s Unpacking icu-devtools (76.1-1ubuntu2) ... 131s Selecting previously unselected package libblas-dev:ppc64el. 131s Preparing to unpack .../31-libblas-dev_3.12.1-2_ppc64el.deb ... 131s Unpacking libblas-dev:ppc64el (3.12.1-2) ... 131s Selecting previously unselected package libbz2-dev:ppc64el. 131s Preparing to unpack .../32-libbz2-dev_1.0.8-6_ppc64el.deb ... 131s Unpacking libbz2-dev:ppc64el (1.0.8-6) ... 131s Selecting previously unselected package libdeflate-dev:ppc64el. 131s Preparing to unpack .../33-libdeflate-dev_1.23-1_ppc64el.deb ... 131s Unpacking libdeflate-dev:ppc64el (1.23-1) ... 131s Selecting previously unselected package libicu-dev:ppc64el. 131s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_ppc64el.deb ... 131s Unpacking libicu-dev:ppc64el (76.1-1ubuntu2) ... 131s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 131s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_ppc64el.deb ... 131s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-3ubuntu2) ... 131s Selecting previously unselected package libjpeg8-dev:ppc64el. 131s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 131s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 131s Selecting previously unselected package libjpeg-dev:ppc64el. 131s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 131s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 131s Selecting previously unselected package liblapack-dev:ppc64el. 131s Preparing to unpack .../38-liblapack-dev_3.12.1-2_ppc64el.deb ... 131s Unpacking liblapack-dev:ppc64el (3.12.1-2) ... 131s Selecting previously unselected package libncurses-dev:ppc64el. 131s Preparing to unpack .../39-libncurses-dev_6.5+20250216-1_ppc64el.deb ... 131s Unpacking libncurses-dev:ppc64el (6.5+20250216-1) ... 131s Selecting previously unselected package libpcre2-16-0:ppc64el. 132s Preparing to unpack .../40-libpcre2-16-0_10.45-1_ppc64el.deb ... 132s Unpacking libpcre2-16-0:ppc64el (10.45-1) ... 132s Selecting previously unselected package libpcre2-32-0:ppc64el. 132s Preparing to unpack .../41-libpcre2-32-0_10.45-1_ppc64el.deb ... 132s Unpacking libpcre2-32-0:ppc64el (10.45-1) ... 132s Selecting previously unselected package libpcre2-posix3:ppc64el. 132s Preparing to unpack .../42-libpcre2-posix3_10.45-1_ppc64el.deb ... 132s Unpacking libpcre2-posix3:ppc64el (10.45-1) ... 132s Selecting previously unselected package libpcre2-dev:ppc64el. 132s Preparing to unpack .../43-libpcre2-dev_10.45-1_ppc64el.deb ... 132s Unpacking libpcre2-dev:ppc64el (10.45-1) ... 132s Selecting previously unselected package libpkgconf3:ppc64el. 132s Preparing to unpack .../44-libpkgconf3_1.8.1-4_ppc64el.deb ... 132s Unpacking libpkgconf3:ppc64el (1.8.1-4) ... 132s Selecting previously unselected package zlib1g-dev:ppc64el. 132s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 132s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 132s Selecting previously unselected package libpng-dev:ppc64el. 132s Preparing to unpack .../46-libpng-dev_1.6.47-1_ppc64el.deb ... 132s Unpacking libpng-dev:ppc64el (1.6.47-1) ... 132s Selecting previously unselected package libreadline-dev:ppc64el. 132s Preparing to unpack .../47-libreadline-dev_8.2-6_ppc64el.deb ... 132s Unpacking libreadline-dev:ppc64el (8.2-6) ... 132s Selecting previously unselected package liblzma-dev:ppc64el. 132s Preparing to unpack .../48-liblzma-dev_5.6.3-1_ppc64el.deb ... 132s Unpacking liblzma-dev:ppc64el (5.6.3-1) ... 132s Selecting previously unselected package pkgconf-bin. 132s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_ppc64el.deb ... 132s Unpacking pkgconf-bin (1.8.1-4) ... 132s Selecting previously unselected package pkgconf:ppc64el. 132s Preparing to unpack .../50-pkgconf_1.8.1-4_ppc64el.deb ... 132s Unpacking pkgconf:ppc64el (1.8.1-4) ... 132s Selecting previously unselected package libtirpc-dev:ppc64el. 132s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_ppc64el.deb ... 132s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1.3) ... 132s Selecting previously unselected package r-base-dev. 132s Preparing to unpack .../52-r-base-dev_4.4.2-1build1_all.deb ... 132s Unpacking r-base-dev (4.4.2-1build1) ... 132s Selecting previously unselected package pkg-r-autopkgtest. 132s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 132s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 132s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-3ubuntu2) ... 132s Setting up libncurses-dev:ppc64el (6.5+20250216-1) ... 132s Setting up libreadline-dev:ppc64el (8.2-6) ... 132s Setting up libpcre2-16-0:ppc64el (10.45-1) ... 132s Setting up libpcre2-32-0:ppc64el (10.45-1) ... 132s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.3) ... 132s Setting up libpkgconf3:ppc64el (1.8.1-4) ... 132s Setting up libquadmath0:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up libmpc3:ppc64el (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:ppc64el (5.6.3-1) ... 132s Setting up libubsan1:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 132s Setting up libpcre2-posix3:ppc64el (10.45-1) ... 132s Setting up libasan8:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up libtsan2:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 132s Setting up libisl23:ppc64el (0.27-1) ... 132s Setting up libdeflate-dev:ppc64el (1.23-1) ... 132s Setting up libicu-dev:ppc64el (76.1-1ubuntu2) ... 132s Setting up libcc1-0:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up liblsan0:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up libblas-dev:ppc64el (3.12.1-2) ... 132s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 132s Setting up dctrl-tools (2.24-3build3) ... 132s Setting up libitm1:ppc64el (15-20250213-1ubuntu1) ... 132s Setting up libbz2-dev:ppc64el (1.0.8-6) ... 132s Setting up libpcre2-dev:ppc64el (10.45-1) ... 132s Setting up libpng-dev:ppc64el (1.6.47-1) ... 132s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 132s Setting up pkgconf:ppc64el (1.8.1-4) ... 132s Setting up liblapack-dev:ppc64el (3.12.1-2) ... 132s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 132s Setting up cpp-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 132s Setting up cpp-14 (14.2.0-17ubuntu3) ... 132s Setting up libgcc-14-dev:ppc64el (14.2.0-17ubuntu3) ... 132s Setting up libstdc++-14-dev:ppc64el (14.2.0-17ubuntu3) ... 132s Setting up cpp-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up gcc-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 132s Setting up libgfortran-14-dev:ppc64el (14.2.0-17ubuntu3) ... 132s Setting up g++-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 132s Setting up gcc-14 (14.2.0-17ubuntu3) ... 132s Setting up gcc-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up cpp (4:14.2.0-1ubuntu1) ... 132s Setting up g++-14 (14.2.0-17ubuntu3) ... 132s Setting up gfortran-14-powerpc64le-linux-gnu (14.2.0-17ubuntu3) ... 132s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 132s Setting up g++-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 132s Setting up gcc (4:14.2.0-1ubuntu1) ... 132s Setting up gfortran-powerpc64le-linux-gnu (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 (12.10ubuntu1) ... 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 (4.4.2-1build1) ... 132s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 132s Processing triggers for libc-bin (2.40-4ubuntu1) ... 132s Processing triggers for man-db (2.13.0-1) ... 133s Processing triggers for install-info (7.1.1-1) ... 134s autopkgtest [01:39:29]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 134s autopkgtest [01:39:29]: test pkg-r-autopkgtest: [----------------------- 134s Test: Try to load the R library vegan 135s 135s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 135s Copyright (C) 2024 The R Foundation for Statistical Computing 135s Platform: powerpc64le-unknown-linux-gnu 135s 135s R is free software and comes with ABSOLUTELY NO WARRANTY. 135s You are welcome to redistribute it under certain conditions. 135s Type 'license()' or 'licence()' for distribution details. 135s 135s R is a collaborative project with many contributors. 135s Type 'contributors()' for more information and 135s 'citation()' on how to cite R or R packages in publications. 135s 135s Type 'demo()' for some demos, 'help()' for on-line help, or 135s 'help.start()' for an HTML browser interface to help. 135s Type 'q()' to quit R. 135s 135s > library('vegan') 135s Loading required package: permute 135s Loading required package: lattice 136s This is vegan 2.6-8 136s > 136s > 136s Other tests are currently unsupported! 136s They will be progressively added. 136s autopkgtest [01:39:31]: test pkg-r-autopkgtest: -----------------------] 136s pkg-r-autopkgtest PASS 136s autopkgtest [01:39:31]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 137s autopkgtest [01:39:32]: @@@@@@@@@@@@@@@@@@@@ summary 137s run-unit-test PASS 137s pkg-r-autopkgtest PASS 154s nova [W] Using flock in prodstack6-ppc64el 154s Creating nova instance adt-plucky-ppc64el-r-cran-vegan-20250304-013715-juju-7f2275-prod-proposed-migration-environment-20-c05ccc62-9fe4-407d-88bf-10fc43a0c4f3 from image adt/ubuntu-plucky-ppc64el-server-20250303.img (UUID 777713ce-30ca-4c46-9290-ed7ac175e17c)... 154s nova [W] Timed out waiting for f8c69e09-0ff7-4b4a-884c-428180b563fc to get deleted.