0s autopkgtest [04:22:29]: starting date and time: 2025-02-19 04:22:29+0000 0s autopkgtest [04:22:29]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [04:22:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a8yq0_sn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-vegan --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-vegan/2.6-10+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-20.secgroup --name adt-plucky-amd64-r-cran-vegan-20250219-042229-juju-7f2275-prod-proposed-migration-environment-2-63949d84-7618-4902-bfe0-802227f0e06b --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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/ 62s autopkgtest [04:23:31]: testbed dpkg architecture: amd64 62s autopkgtest [04:23:31]: testbed apt version: 2.9.29 62s autopkgtest [04:23:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s autopkgtest [04:23:32]: testbed release detected to be: None 64s autopkgtest [04:23:33]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [79.1 kB] 65s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 65s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [788 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [106 kB] 65s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [84.0 kB] 65s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 65s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 65s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [271 kB] 65s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [712 kB] 65s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3440 B] 65s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [12.4 kB] 65s Fetched 2194 kB in 1s (2174 kB/s) 66s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [04:23:38]: upgrading testbed (apt dist-upgrade and autopurge) 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 70s Entering ResolveByKeep 70s 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [04:23:43]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 74s autopkgtest [04:23:43]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 77s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (dsc) [2211 B] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (tar) [1207 kB] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (diff) [6328 B] 77s gpgv: Signature made Sun Feb 2 23:43:24 2025 UTC 77s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 77s gpgv: issuer "plessy@debian.org" 77s gpgv: Can't check signature: No public key 77s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1.dsc: no acceptable signature found 77s autopkgtest [04:23:46]: testing package r-cran-vegan version 2.6-10+dfsg-1 78s autopkgtest [04:23:47]: build not needed 87s autopkgtest [04:23:56]: test run-unit-test: preparing testbed 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s Starting pkgProblemResolver with broken count: 0 88s Starting 2 pkgProblemResolver with broken count: 0 88s Done 88s The following NEW packages will be installed: 88s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 88s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 88s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 88s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 88s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 88s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 88s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 88s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 88s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 88s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 88s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 88s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 88s x11-common xdg-utils zip 89s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 68.7 MB of archives. 89s After this operation, 165 MB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 89s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 89s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 89s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 89s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 89s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 89s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 89s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 89s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 89s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 89s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 89s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 89s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 89s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 89s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 89s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 89s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 89s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 89s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 90s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 90s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 90s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 90s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 90s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 90s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 90s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 90s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 90s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 90s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 90s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 90s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 90s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 90s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 90s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 90s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 90s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 90s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 90s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 90s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 90s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 90s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 90s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 90s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 90s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1build1 [28.9 MB] 91s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.8-1 [579 kB] 91s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.2-2 [137 kB] 91s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 91s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.50+dfsg-1 [568 kB] 91s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 91s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 91s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 91s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 91s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 91s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-markdown all 1.13-1 [162 kB] 91s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 92s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-2-1 [4456 kB] 92s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 92s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 93s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-permute all 0.9-7-1 [228 kB] 93s Get:67 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 r-cran-vegan amd64 2.6-10+dfsg-1 [3146 kB] 94s Preconfiguring packages ... 94s Fetched 68.7 MB in 5s (13.7 MB/s) 94s Selecting previously unselected package fonts-dejavu-mono. 94s (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 ... 108925 files and directories currently installed.) 94s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 94s Unpacking fonts-dejavu-mono (2.37-8) ... 94s Selecting previously unselected package fonts-dejavu-core. 94s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 94s Unpacking fonts-dejavu-core (2.37-8) ... 94s Selecting previously unselected package fontconfig-config. 94s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 94s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 94s Selecting previously unselected package libfontconfig1:amd64. 94s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 94s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 94s Selecting previously unselected package fontconfig. 94s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 94s Unpacking fontconfig (2.15.0-2ubuntu1) ... 94s Selecting previously unselected package fonts-glyphicons-halflings. 94s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 94s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 94s Selecting previously unselected package fonts-mathjax. 94s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 94s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 94s Selecting previously unselected package libblas3:amd64. 94s Preparing to unpack .../07-libblas3_3.12.1-2_amd64.deb ... 94s Unpacking libblas3:amd64 (3.12.1-2) ... 94s Selecting previously unselected package libpixman-1-0:amd64. 94s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_amd64.deb ... 94s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 94s Selecting previously unselected package libxcb-render0:amd64. 94s Preparing to unpack .../09-libxcb-render0_1.17.0-2_amd64.deb ... 94s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 94s Selecting previously unselected package libxcb-shm0:amd64. 94s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_amd64.deb ... 94s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 95s Selecting previously unselected package libxrender1:amd64. 95s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 95s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 95s Selecting previously unselected package libcairo2:amd64. 95s Preparing to unpack .../12-libcairo2_1.18.2-2_amd64.deb ... 95s Unpacking libcairo2:amd64 (1.18.2-2) ... 95s Selecting previously unselected package libdatrie1:amd64. 95s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_amd64.deb ... 95s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 95s Selecting previously unselected package libdeflate0:amd64. 95s Preparing to unpack .../14-libdeflate0_1.23-1_amd64.deb ... 95s Unpacking libdeflate0:amd64 (1.23-1) ... 95s Selecting previously unselected package libgfortran5:amd64. 95s Preparing to unpack .../15-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 95s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 95s Selecting previously unselected package libgomp1:amd64. 95s Preparing to unpack .../16-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 95s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 95s Selecting previously unselected package libgraphite2-3:amd64. 95s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 95s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 95s Selecting previously unselected package libharfbuzz0b:amd64. 95s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_amd64.deb ... 95s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 95s Selecting previously unselected package x11-common. 95s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 95s Unpacking x11-common (1:7.7+23ubuntu3) ... 95s Selecting previously unselected package libice6:amd64. 95s Preparing to unpack .../20-libice6_2%3a1.1.1-1_amd64.deb ... 95s Unpacking libice6:amd64 (2:1.1.1-1) ... 95s Selecting previously unselected package libjpeg-turbo8:amd64. 95s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 95s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 95s Selecting previously unselected package libjpeg8:amd64. 95s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_amd64.deb ... 95s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 95s Selecting previously unselected package libjs-bootstrap. 95s Preparing to unpack .../23-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 95s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 95s Selecting previously unselected package libjs-highlight.js. 95s Preparing to unpack .../24-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 95s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 95s Selecting previously unselected package libjs-jquery. 95s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 95s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 95s Selecting previously unselected package libjs-jquery-datatables. 95s Preparing to unpack .../26-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 95s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 95s Selecting previously unselected package liblapack3:amd64. 95s Preparing to unpack .../27-liblapack3_3.12.1-2_amd64.deb ... 95s Unpacking liblapack3:amd64 (3.12.1-2) ... 95s Selecting previously unselected package liblerc4:amd64. 95s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 95s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 95s Selecting previously unselected package libthai-data. 95s Preparing to unpack .../29-libthai-data_0.1.29-2build1_all.deb ... 95s Unpacking libthai-data (0.1.29-2build1) ... 95s Selecting previously unselected package libthai0:amd64. 95s Preparing to unpack .../30-libthai0_0.1.29-2build1_amd64.deb ... 95s Unpacking libthai0:amd64 (0.1.29-2build1) ... 95s Selecting previously unselected package libpango-1.0-0:amd64. 95s Preparing to unpack .../31-libpango-1.0-0_1.56.1-1_amd64.deb ... 95s Unpacking libpango-1.0-0:amd64 (1.56.1-1) ... 95s Selecting previously unselected package libpangoft2-1.0-0:amd64. 95s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.1-1_amd64.deb ... 95s Unpacking libpangoft2-1.0-0:amd64 (1.56.1-1) ... 95s Selecting previously unselected package libpangocairo-1.0-0:amd64. 95s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.1-1_amd64.deb ... 95s Unpacking libpangocairo-1.0-0:amd64 (1.56.1-1) ... 95s Selecting previously unselected package libpaper2:amd64. 95s Preparing to 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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") 104s Writing to file decision-vegan.R 104s > source("decision-vegan.R", echo=TRUE) 104s 104s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 104s 104s > options(SweaveHooks = list(fig = figset)) 104s 104s > options(prompt = "> ", continue = " ") 104s 104s > options(width = 55) 104s 104s > require(vegan) 104s Loading required package: vegan 104s Loading required package: permute 104s Loading required package: lattice 104s 104s > data(sipoo) 104s 104s > mod <- nestedtemp(sipoo) 105s 105s > plot(mod, "i") 105s 105s > x <- mod$c["Falcsubb"] 105s 105s > y <- 1 - mod$r["Svartholm"] 105s 105s > points(x, y, pch = 16, cex = 1.5) 105s 105s > abline(x + y, -1, lty = 2) 105s 105s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 105s 105s > cross <- function(x, a, p) f(x, p) - a + x 105s 105s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 105s 105s > arrows(x, y, r, f(r, mod$p), lwd = 4) 105s 105s > library(vegan) 105s 105s > data(varespec) 105s 105s > data(varechem) 105s 105s > orig <- cca(varespec ~ Al + K, varechem) 105s 105s > plot(orig, dis = c("lc", "bp")) 105s 105s > plot(orig, dis = c("lc", "bp")) 105s 105s > i <- sample(nrow(varespec)) 105s 105s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 105s 105s > plot(shuff, dis = c("lc", "bp")) 105s 105s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 105s + dis = "lc"))) 105s 105s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 105s + dis = "lc"))) 105s 105s > tmp1 <- rda(varespec ~ Al + K, varechem) 105s 105s > i <- sample(nrow(varespec)) 105s 105s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 105s 105s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 105s + dis = "lc"))) 105s 105s > orig 105s Call: cca(formula = varespec ~ Al + K, data = 105s varechem) 105s 105s -- Model Summary -- 105s 105s Inertia Proportion Rank 105s Total 2.0832 1.0000 105s Constrained 0.4760 0.2285 2 105s Unconstrained 1.6072 0.7715 21 105s 105s Inertia is scaled Chi-square 105s 105s -- Eigenvalues -- 105s 105s Eigenvalues for constrained axes: 105s CCA1 CCA2 105s 0.3608 0.1152 105s 105s Eigenvalues for unconstrained axes: 105s CA1 CA2 CA3 CA4 CA5 CA6 CA7 105s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 105s CA8 105s 0.0757 105s (Showing 8 of 21 unconstrained eigenvalues) 105s 105s 105s > shuff 105s Call: cca(formula = varespec[i, ] ~ Al + K, data = 105s varechem) 105s 105s -- Model Summary -- 105s 105s Inertia Proportion Rank 105s Total 2.08320 1.00000 105s Constrained 0.08920 0.04282 2 105s Unconstrained 1.99400 0.95718 21 105s 105s Inertia is scaled Chi-square 105s 105s -- Eigenvalues -- 105s 105s Eigenvalues for constrained axes: 105s CCA1 CCA2 105s 0.06179 0.02741 105s 105s Eigenvalues for unconstrained axes: 105s CA1 CA2 CA3 CA4 CA5 CA6 CA7 105s 0.5230 0.3527 0.2300 0.1826 0.1716 0.1095 0.0996 105s CA8 105s 0.0772 105s (Showing 8 of 21 unconstrained eigenvalues) 105s 105s 105s > plot(procrustes(orig, shuff)) 105s 105s > tmp1 <- rda(varespec ~ ., varechem) 105s 105s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 105s 105s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 105s + scores(tmp2, dis = "lc", choi = 1:14)) 105s 105s > max(residuals(proc)) 105s [1] 3.148515e-14 105s 105s > data(dune) 105s 105s > data(dune.env) 105s 105s > orig <- cca(dune ~ Moisture, dune.env) 105s 105s > plot(orig, dis = "lc") 105s 105s > plot(orig, display = "wa", type = "points") 105s 105s > ordispider(orig, col = "red") 105s 105s > text(orig, dis = "cn", col = "blue") 105s 105s > plot(orig, display = "wa", type = "points") 105s 105s > ordispider(orig, col = "red") 105s 105s > text(orig, dis = "cn", col = "blue") 105s > 105s 105s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 105s Copyright (C) 2024 The R Foundation for Statistical Computing 105s Platform: x86_64-pc-linux-gnu 105s 105s R is free software and comes with ABSOLUTELY NO WARRANTY. 105s You are welcome to redistribute it under certain conditions. 105s Type 'license()' or 'licence()' for distribution details. 105s 105s R is a collaborative project with many contributors. 105s Type 'contributors()' for more information and 105s 'citation()' on how to cite R or R packages in publications. 105s 105s Type 'demo()' for some demos, 'help()' for on-line help, or 105s 'help.start()' for an HTML browser interface to help. 105s Type 'q()' to quit R. 105s 105s > Stangle("diversity-vegan.Rnw") 105s Writing to file diversity-vegan.R 105s > source("diversity-vegan.R", echo=TRUE) 105s 105s > par(mfrow = c(1, 1)) 105s 105s > options(width = 55) 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 > library(vegan) 105s Loading required package: permute 105s Loading required package: lattice 106s 106s > data(BCI) 106s 106s > H <- diversity(BCI) 106s 106s > J <- H/log(specnumber(BCI)) 106s 106s > k <- sample(nrow(BCI), 6) 106s 106s > R <- renyi(BCI[k, ]) 106s 106s > print(plot(R)) 106s 106s > alpha <- fisher.alpha(BCI) 106s 106s > quantile(rowSums(BCI)) 106s 0% 25% 50% 75% 100% 106s 340.0 409.0 428.0 443.5 601.0 106s 106s > Srar <- rarefy(BCI, min(rowSums(BCI))) 106s 106s > S2 <- rarefy(BCI, 2) 106s 106s > all(rank(Srar) == rank(S2)) 106s [1] FALSE 106s 106s > range(diversity(BCI, "simp") - (S2 - 1)) 106s [1] -0.002868298 -0.001330663 106s 106s > data(dune) 106s 106s > data(dune.taxon) 106s 106s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 106s 106s > mod <- taxondive(dune, taxdis) 106s 106s > plot(mod) 106s 106s > tr <- hclust(taxdis, "aver") 106s 106s > mod <- treedive(dune, tr) 106s 106s > k <- sample(nrow(BCI), 1) 106s 106s > fish <- fisherfit(BCI[k, ]) 106s 106s > fish 106s 106s Fisher log series model 106s No. of species: 82 106s Fisher alpha: 30.58383 106s 106s 106s > plot(fish) 106s 106s > prestondistr(BCI[k, ]) 106s forced matching of 'tree' labels and 'comm' names 106s 106s Preston lognormal model 106s Method: maximized likelihood to log2 abundances 106s No. of species: 82 106s 106s mode width S0 106s 1.184636 1.724112 21.142298 106s 106s Frequencies by Octave 106s 0 1 2 3 4 106s Observed 14.0000 21.50000 16.00000 17.00000 6.500000 106s Fitted 16.6969 21.02141 18.90544 12.14537 5.573573 106s 5 6 106s Observed 6.000000 1.0000000 106s Fitted 1.827072 0.4278351 106s 106s 106s > rad <- radfit(BCI[k, ]) 106s 106s > rad 106s 106s RAD models, family poisson 106s No. of species 82, total abundance 416 106s 106s par1 par2 par3 Deviance 106s Null 44.1321 106s Preemption 0.050871 35.5813 106s Lognormal 1.0473 1.0934 15.0446 106s Zipf 0.1343 -0.81154 37.1297 106s Mandelbrot 4.4331 -1.6963 9.5855 6.8295 106s AIC BIC 106s Null 288.5829 288.5829 106s Preemption 282.0320 284.4388 106s Lognormal 263.4954 268.3088 106s Zipf 285.5805 290.3940 106s Mandelbrot 257.2803 264.5004 106s 106s > print(radlattice(rad)) 106s 106s > sac <- specaccum(BCI) 106s 106s > plot(sac, ci.type = "polygon", ci.col = "yellow") 106s 106s > sac <- specaccum(BCI) 106s 106s > plot(sac, ci.type = "polygon", ci.col = "yellow") 106s 106s > ncol(BCI)/mean(specnumber(BCI)) - 1 106s [1] 1.478519 106s 106s > beta <- vegdist(BCI, binary = TRUE) 106s 106s > mean(beta) 106s [1] 0.3399075 106s 106s > betadiver(help = TRUE) 106s 1 "w" = (b+c)/(2*a+b+c) 106s 2 "-1" = (b+c)/(2*a+b+c) 106s 3 "c" = (b+c)/2 106s 4 "wb" = b+c 106s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 106s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 106s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 106s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 106s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 106s (2*a+b+c))-1 106s 8 "t" = (b+c)/(2*a+b+c) 106s 9 "me" = (b+c)/(2*a+b+c) 106s 10 "j" = a/(a+b+c) 106s 11 "sor" = 2*a/(2*a+b+c) 106s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 106s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 106s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 106s 15 "cc" = (b+c)/(a+b+c) 106s 16 "g" = (b+c)/(a+b+c) 106s 17 "-3" = pmin.int(b,c)/(a+b+c) 106s 18 "l" = (b+c)/2 106s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 106s 20 "hk" = (b+c)/(2*a+b+c) 106s 21 "rlb" = a/(a+c) 106s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 106s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 106s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 106s 106s > z <- betadiver(BCI, "z") 106s 106s > quantile(z) 106s 0% 25% 50% 75% 100% 106s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 106s 106s > data(dune) 106s 106s > data(dune.env) 106s 106s > z <- betadiver(dune, "z") 106s 106s > mod <- with(dune.env, betadisper(z, Management)) 106s 106s > mod 106s 106s Homogeneity of multivariate dispersions 106s 106s Call: betadisper(d = z, group = Management) 106s 106s No. of Positive Eigenvalues: 12 106s No. of Negative Eigenvalues: 7 106s 106s Average distance to median: 106s BF HF NM SF 106s 0.2532 0.2512 0.4406 0.3635 106s 106s Eigenvalues for PCoA axes: 106s (Showing 8 of 19 eigenvalues) 106s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 106s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 106s PCoA7 PCoA8 106s 0.16128 0.08099 106s 106s > boxplot(mod) 106s 106s > specpool(BCI) 106s Species chao chao.se jack1 jack1.se jack2 106s All 225 236.3732 6.54361 245.58 5.650522 247.8722 106s boot boot.se n 106s All 235.6862 3.468888 50 106s 106s > s <- sample(nrow(BCI), 25) 106s 106s > specpool(BCI[s, ]) 106s Species chao chao.se jack1 jack1.se jack2 106s All 208 223.36 8.233395 231.04 6.86137 237.25 106s boot boot.se n 106s All 219.5849 4.268497 25 106s 106s > estimateR(BCI[k, ]) 106s 7 106s S.obs 82.000000 106s S.chao1 105.625000 106s se.chao1 11.789446 106s S.ACE 108.315823 106s se.ACE 4.913317 106s 106s > veiledspec(prestondistr(BCI[k, ])) 106s Extrapolated Observed Veiled 106s 91.370848 82.000000 9.370848 106s 106s > veiledspec(BCI[k, ]) 106s Extrapolated Observed Veiled 106s 97.93917 82.00000 15.93917 106s 106s > smo <- beals(BCI) 106s 106s > j <- which(colnames(BCI) == "Ceiba.pentandra") 106s 106s > plot(beals(BCI, species = j, include = FALSE), BCI[, 106s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 106s 106s > j <- which(colnames(BCI) == "Ceiba.pentandra") 106s 106s > plot(beals(BCI, species = j, include = FALSE), BCI[, 106s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 106s > 106s Warning messages: 106s 1: In cor(x > 0) : the standard deviation is zero 106s 2: In cor(x > 0) : the standard deviation is zero 106s 3: In betadisper(z, Management) : 106s some squared distances are negative and changed to zero 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: x86_64-pc-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("intro-vegan.Rnw") 106s Writing to file intro-vegan.R 106s > source("intro-vegan.R", echo=TRUE) 106s 106s > par(mfrow = c(1, 1)) 106s 106s > options(width = 72) 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 107s > data(dune) 107s 107s > ord <- decorana(dune) 107s 107s > ord 107s 107s Call: 107s decorana(veg = dune) 107s 107s Detrended correspondence analysis with 26 segments. 107s Rescaling of axes with 4 iterations. 107s Total inertia (scaled Chi-square): 2.1153 107s 107s DCA1 DCA2 DCA3 DCA4 107s Eigenvalues 0.5117 0.3036 0.12125 0.14267 107s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 107s Decorana values 0.5360 0.2869 0.08136 0.04814 107s Axis lengths 3.7004 3.1166 1.30055 1.47888 107s 107s 107s > ord <- metaMDS(dune, trace = FALSE) 107s 107s > ord 107s 107s Call: 107s metaMDS(comm = dune, trace = FALSE) 107s 107s global Multidimensional Scaling using monoMDS 107s 107s Data: dune 107s Distance: bray 107s 107s Dimensions: 2 107s Stress: 0.1183186 107s Stress type 1, weak ties 107s Best solution was repeated 4 times in 20 tries 107s The best solution was from try 13 (random start) 107s Scaling: centring, PC rotation, halfchange scaling 107s Species: expanded scores based on ‘dune’ 107s 107s 107s > plot(ord) 107s 107s > plot(ord) 107s 107s > plot(ord, type = "n") 107s 107s > points(ord, display = "sites", cex = 0.8, pch = 21, 107s + col = "red", bg = "yellow") 107s 107s > text(ord, display = "species", cex = 0.7, col = "blue") 107s 107s > plot(ord, type = "n") 107s 107s > points(ord, display = "sites", cex = 0.8, pch = 21, 107s + col = "red", bg = "yellow") 107s 107s > text(ord, display = "species", cex = 0.7, col = "blue") 107s 107s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 107s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 107s + col = "blue") 107s 107s > data(dune.env) 107s 107s > attach(dune.env) 107s 107s > plot(ord, disp = "sites", type = "n") 107s 107s > ordihull(ord, Management, col = 1:4, lwd = 3) 107s 107s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 107s + lwd = 3) 107s 107s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 107s 107s > ordispider(ord, Management, col = 1:4, label = TRUE) 107s 107s > points(ord, disp = "sites", pch = 21, col = "red", 107s + bg = "yellow", cex = 1.3) 107s 107s > plot(ord, disp = "sites", type = "n") 107s 107s > ordihull(ord, Management, col = 1:4, lwd = 3) 107s 107s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 107s + lwd = 3) 107s 107s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 107s 107s > ordispider(ord, Management, col = 1:4, label = TRUE) 107s 107s > points(ord, disp = "sites", pch = 21, col = "red", 107s + bg = "yellow", cex = 1.3) 107s 107s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 107s + perm = 999) 107s 107s > ord.fit 107s 107s ***VECTORS 107s 107s NMDS1 NMDS2 r2 Pr(>r) 107s A1 0.96474 0.26322 0.3649 0.022 * 107s --- 107s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 107s Permutation: free 107s Number of permutations: 999 107s 107s ***FACTORS: 107s 107s Centroids: 107s NMDS1 NMDS2 107s ManagementBF -0.4534 -0.0102 107s ManagementHF -0.2636 -0.1282 107s ManagementNM 0.2958 0.5790 107s ManagementSF 0.1506 -0.4670 107s 107s Goodness of fit: 107s r2 Pr(>r) 107s Management 0.4134 0.005 ** 107s --- 107s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 107s Permutation: free 107s Number of permutations: 999 107s 107s 107s 107s > plot(ord, dis = "site") 107s 107s > plot(ord.fit) 107s 107s > ordisurf(ord, A1, add = TRUE) 108s 108s Family: gaussian 108s Link function: identity 108s 108s Formula: 108s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 108s 108s Estimated degrees of freedom: 108s 1.59 total = 2.59 108s 108s REML score: 41.58727 108s 108s > plot(ord, dis = "site") 108s 108s > plot(ord.fit) 108s 108s > ordisurf(ord, A1, add = TRUE) 108s 108s Family: gaussian 108s Link function: identity 108s 108s Formula: 108s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 108s 108s Estimated degrees of freedom: 108s 1.59 total = 2.59 108s 108s REML score: 41.58727 108s 108s > ord <- cca(dune ~ A1 + Management, data = dune.env) 108s 108s > ord 108s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 108s 108s -- Model Summary -- 108s 108s Inertia Proportion Rank 108s Total 2.1153 1.0000 108s Constrained 0.7798 0.3686 4 108s Unconstrained 1.3355 0.6314 15 108s 108s Inertia is scaled Chi-square 108s 108s -- Eigenvalues -- 108s 108s Eigenvalues for constrained axes: 108s CCA1 CCA2 CCA3 CCA4 108s 0.3187 0.2372 0.1322 0.0917 108s 108s Eigenvalues for unconstrained axes: 108s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 108s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 108s CA11 CA12 CA13 CA14 CA15 108s 0.0317 0.0178 0.0116 0.0087 0.0047 108s 108s 108s > plot(ord) 108s 108s > plot(ord) 108s 108s > cca(dune ~ ., data = dune.env) 108s 108s Some constraints or conditions were aliased because they were 108s redundant. This can happen if terms are linearly dependent (collinear): 108s ‘Manure^4’ 108s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 108s Manure, data = dune.env) 108s 108s -- Model Summary -- 108s 108s Inertia Proportion Rank 108s Total 2.1153 1.0000 108s Constrained 1.5032 0.7106 12 108s Unconstrained 0.6121 0.2894 7 108s 108s Inertia is scaled Chi-square 108s 108s -- Note -- 108s 108s Some constraints or conditions were aliased because they were 108s redundant. This can happen if terms are linearly dependent 108s (collinear): ‘Manure^4’ 108s 108s -- Eigenvalues -- 108s 108s Eigenvalues for constrained axes: 108s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 108s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 108s CCA11 CCA12 108s 0.0228 0.0108 108s 108s Eigenvalues for unconstrained axes: 108s CA1 CA2 CA3 CA4 CA5 CA6 CA7 108s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 108s 108s 108s > anova(ord) 108s Permutation test for cca under reduced model 108s Permutation: free 108s Number of permutations: 999 108s 108s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 108s Df ChiSquare F Pr(>F) 108s Model 4 0.77978 2.1896 0.001 *** 108s Residual 15 1.33549 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > anova(ord, by = "term", permutations = 199) 108s Permutation test for cca under reduced model 108s Terms added sequentially (first to last) 108s Permutation: free 108s Number of permutations: 199 108s 108s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 108s Df ChiSquare F Pr(>F) 108s A1 1 0.22476 2.5245 0.015 * 108s Management 3 0.55502 2.0780 0.010 ** 108s Residual 15 1.33549 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > anova(ord, by = "mar", permutations = 199) 108s Permutation test for cca under reduced model 108s Marginal effects of terms 108s Permutation: free 108s Number of permutations: 199 108s 108s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 108s Df ChiSquare F Pr(>F) 108s A1 1 0.17594 1.9761 0.020 * 108s Management 3 0.55502 2.0780 0.005 ** 108s Residual 15 1.33549 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > anova(ord, by = "axis", permutations = 499) 108s Permutation test for cca under reduced model 108s Forward tests for axes 108s Permutation: free 108s Number of permutations: 499 108s 108s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 108s Df ChiSquare F Pr(>F) 108s CCA1 1 0.31875 3.5801 0.014 * 108s CCA2 1 0.23718 2.6640 0.144 108s CCA3 1 0.13217 1.4845 0.834 108s CCA4 1 0.09168 1.0297 1.000 108s Residual 15 1.33549 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 108s + data = dune.env) 108s 108s > ord 108s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 108s data = dune.env) 108s 108s -- Model Summary -- 108s 108s Inertia Proportion Rank 108s Total 2.1153 1.0000 108s Conditional 0.6283 0.2970 3 108s Constrained 0.5109 0.2415 4 108s Unconstrained 0.9761 0.4615 12 108s 108s Inertia is scaled Chi-square 108s 108s -- Eigenvalues -- 108s 108s Eigenvalues for constrained axes: 108s CCA1 CCA2 CCA3 CCA4 108s 0.24932 0.12090 0.08160 0.05904 108s 108s Eigenvalues for unconstrained axes: 108s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 108s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 108s CA10 CA11 CA12 108s 0.02102 0.01254 0.00928 108s 108s 108s > anova(ord, by = "term", permutations = 499) 108s Permutation test for cca under reduced model 108s Terms added sequentially (first to last) 108s Permutation: free 108s Number of permutations: 499 108s 108s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 108s Df ChiSquare F Pr(>F) 108s A1 1 0.11543 1.4190 1.000 108s Management 3 0.39543 1.6205 0.002 ** 108s Residual 12 0.97610 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 108s 108s > anova(ord, by = "term", permutations = how) 108s Permutation test for cca under reduced model 108s Terms added sequentially (first to last) 108s Plots: dune.env$Moisture, plot permutation: none 108s Permutation: free 108s Number of permutations: 499 108s 108s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 108s Df ChiSquare F Pr(>F) 108s A1 1 0.11543 1.4190 1.000 108s Management 3 0.39543 1.6205 0.002 ** 108s Residual 12 0.97610 108s --- 108s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 108s 108s > detach(dune.env) 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: x86_64-pc-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("partitioning.Rnw") 108s Writing to file partitioning.R 108s > source("partitioning.R", echo=TRUE) 108s 108s > par(mfrow = c(1, 1)) 108s 108s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 108s 108s > options(SweaveHooks = list(fig = figset)) 108s 108s > library(vegan) 108s Loading required package: permute 108s Loading required package: lattice 109s 109s > labs <- paste("Table", 1:4) 109s 109s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 109s 109s > showvarparts(2, bg = cls, Xnames = labs) 109s 109s > showvarparts(3, bg = cls, Xnames = labs) 109s 109s > showvarparts(4, bg = cls, Xnames = labs) 109s > 116s --- cca-object-tests.Rout.save_ 2025-02-19 04:24:24.947605331 +0000 116s +++ cca-object-tests.Rout_ 2025-02-19 04:24:24.950604583 +0000 116s @@ -1,4 +1,4 @@ 116s - 116s + 116s 116s R is free software and comes with ABSOLUTELY NO WARRANTY. 116s You are welcome to redistribute it under certain conditions. 116s autopkgtest [04:24:25]: test run-unit-test: -----------------------] 117s autopkgtest [04:24:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 117s run-unit-test FAIL non-zero exit status 1 117s autopkgtest [04:24:26]: test pkg-r-autopkgtest: 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 build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 118s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 118s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 118s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 118s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 118s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 118s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 118s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 118s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 118s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 118s r-base-dev zlib1g-dev 119s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 103 MB of archives. 119s After this operation, 363 MB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 120s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 120s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [11.9 MB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu1 [1032 B] 123s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 123s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 123s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250213-1ubuntu1 [47.0 kB] 123s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250213-1ubuntu1 [28.5 kB] 123s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250213-1ubuntu1 [3059 kB] 124s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250213-1ubuntu1 [1356 kB] 125s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250213-1ubuntu1 [2757 kB] 126s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250213-1ubuntu1 [1206 kB] 126s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250213-1ubuntu1 [1678 kB] 127s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250213-1ubuntu1 [152 kB] 127s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu1 [2814 kB] 128s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [23.3 MB] 133s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu1 [536 kB] 133s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 133s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 133s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu1 [2507 kB] 133s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [13.4 MB] 135s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu1 [21.8 kB] 135s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 135s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 135s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 135s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 135s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu1 [966 kB] 135s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu1 [12.5 MB] 137s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu1 [13.6 kB] 137s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 137s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 137s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 137s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 137s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 137s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 137s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 138s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 138s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 138s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 138s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 138s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250125-2 [425 kB] 138s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.42-4ubuntu3 [214 kB] 138s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.42-4ubuntu3 [201 kB] 138s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.42-4ubuntu3 [6768 B] 138s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.42-4ubuntu3 [747 kB] 138s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 138s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 138s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.46-4 [304 kB] 138s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 138s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.3-1 [189 kB] 138s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 138s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 138s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 138s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.2-1build1 [4342 B] 138s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 139s Fetched 103 MB in 20s (5031 kB/s) 139s Selecting previously unselected package libisl23:amd64. 139s (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 ... 116940 files and directories currently installed.) 139s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 139s Unpacking libisl23:amd64 (0.27-1) ... 139s Selecting previously unselected package libmpc3:amd64. 139s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 139s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 139s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 139s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 139s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 139s Selecting previously unselected package cpp-14. 139s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu1_amd64.deb ... 139s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 139s Selecting previously unselected package cpp-x86-64-linux-gnu. 139s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 139s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 139s Selecting previously unselected package cpp. 139s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 139s Unpacking cpp (4:14.2.0-1ubuntu1) ... 139s Selecting previously unselected package libcc1-0:amd64. 139s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking libcc1-0:amd64 (15-20250213-1ubuntu1) ... 139s Selecting previously unselected package libitm1:amd64. 139s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking libitm1:amd64 (15-20250213-1ubuntu1) ... 139s Selecting previously unselected package libasan8:amd64. 139s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking libasan8:amd64 (15-20250213-1ubuntu1) ... 139s Selecting previously unselected package liblsan0:amd64. 139s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking liblsan0:amd64 (15-20250213-1ubuntu1) ... 139s Selecting previously unselected package libtsan2:amd64. 139s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking libtsan2:amd64 (15-20250213-1ubuntu1) ... 139s Selecting previously unselected package libubsan1:amd64. 139s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_amd64.deb ... 139s Unpacking libubsan1:amd64 (15-20250213-1ubuntu1) ... 140s Selecting previously unselected package libhwasan0:amd64. 140s Preparing to unpack .../12-libhwasan0_15-20250213-1ubuntu1_amd64.deb ... 140s Unpacking libhwasan0:amd64 (15-20250213-1ubuntu1) ... 140s Selecting previously unselected package libquadmath0:amd64. 140s Preparing to unpack .../13-libquadmath0_15-20250213-1ubuntu1_amd64.deb ... 140s Unpacking libquadmath0:amd64 (15-20250213-1ubuntu1) ... 140s Selecting previously unselected package libgcc-14-dev:amd64. 140s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu1_amd64.deb ... 140s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 140s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 140s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 140s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 140s Selecting previously unselected package gcc-14. 140s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu1_amd64.deb ... 140s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 140s Selecting previously unselected package gcc-x86-64-linux-gnu. 140s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 140s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 140s Selecting previously unselected package gcc. 140s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 140s Unpacking gcc (4:14.2.0-1ubuntu1) ... 140s Selecting previously unselected package libstdc++-14-dev:amd64. 140s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu1_amd64.deb ... 140s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu1) ... 140s Selecting previously unselected package g++-14-x86-64-linux-gnu. 140s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 140s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package g++-14. 141s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu1_amd64.deb ... 141s Unpacking g++-14 (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package g++-x86-64-linux-gnu. 141s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 141s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 141s Selecting previously unselected package g++. 141s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 141s Unpacking g++ (4:14.2.0-1ubuntu1) ... 141s Selecting previously unselected package build-essential. 141s Preparing to unpack .../24-build-essential_12.10ubuntu1_amd64.deb ... 141s Unpacking build-essential (12.10ubuntu1) ... 141s Selecting previously unselected package dctrl-tools. 141s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 141s Unpacking dctrl-tools (2.24-3build3) ... 141s Selecting previously unselected package libgfortran-14-dev:amd64. 141s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu1_amd64.deb ... 141s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 141s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu1_amd64.deb ... 141s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package gfortran-14. 141s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu1_amd64.deb ... 141s Unpacking gfortran-14 (14.2.0-17ubuntu1) ... 141s Selecting previously unselected package gfortran-x86-64-linux-gnu. 141s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 141s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 141s Selecting previously unselected package gfortran. 141s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 141s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 141s Selecting previously unselected package icu-devtools. 141s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 141s Unpacking icu-devtools (76.1-1ubuntu2) ... 141s Selecting previously unselected package libblas-dev:amd64. 141s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 141s Unpacking libblas-dev:amd64 (3.12.1-2) ... 141s Selecting previously unselected package libbz2-dev:amd64. 141s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 141s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 141s Selecting previously unselected package libdeflate-dev:amd64. 141s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 141s Unpacking libdeflate-dev:amd64 (1.23-1) ... 141s Selecting previously unselected package libicu-dev:amd64. 141s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 141s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 142s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 142s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 142s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 142s Selecting previously unselected package libjpeg8-dev:amd64. 142s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 142s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 142s Selecting previously unselected package libjpeg-dev:amd64. 142s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 142s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 142s Selecting previously unselected package liblapack-dev:amd64. 142s Preparing to unpack .../39-liblapack-dev_3.12.1-2_amd64.deb ... 142s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 142s Selecting previously unselected package libncurses-dev:amd64. 142s Preparing to unpack .../40-libncurses-dev_6.5+20250125-2_amd64.deb ... 142s Unpacking libncurses-dev:amd64 (6.5+20250125-2) ... 142s Selecting previously unselected package libpcre2-16-0:amd64. 142s Preparing to unpack .../41-libpcre2-16-0_10.42-4ubuntu3_amd64.deb ... 142s Unpacking libpcre2-16-0:amd64 (10.42-4ubuntu3) ... 142s Selecting previously unselected package libpcre2-32-0:amd64. 142s Preparing to unpack .../42-libpcre2-32-0_10.42-4ubuntu3_amd64.deb ... 142s Unpacking libpcre2-32-0:amd64 (10.42-4ubuntu3) ... 142s Selecting previously unselected package libpcre2-posix3:amd64. 142s Preparing to unpack .../43-libpcre2-posix3_10.42-4ubuntu3_amd64.deb ... 142s Unpacking libpcre2-posix3:amd64 (10.42-4ubuntu3) ... 142s Selecting previously unselected package libpcre2-dev:amd64. 142s Preparing to unpack .../44-libpcre2-dev_10.42-4ubuntu3_amd64.deb ... 142s Unpacking libpcre2-dev:amd64 (10.42-4ubuntu3) ... 142s Selecting previously unselected package libpkgconf3:amd64. 142s Preparing to unpack .../45-libpkgconf3_1.8.1-4_amd64.deb ... 142s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 142s Selecting previously unselected package zlib1g-dev:amd64. 142s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 142s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 142s Selecting previously unselected package libpng-dev:amd64. 142s Preparing to unpack .../47-libpng-dev_1.6.46-4_amd64.deb ... 142s Unpacking libpng-dev:amd64 (1.6.46-4) ... 142s Selecting previously unselected package libreadline-dev:amd64. 142s Preparing to unpack .../48-libreadline-dev_8.2-6_amd64.deb ... 142s Unpacking libreadline-dev:amd64 (8.2-6) ... 142s Selecting previously unselected package liblzma-dev:amd64. 142s Preparing to unpack .../49-liblzma-dev_5.6.3-1_amd64.deb ... 142s Unpacking liblzma-dev:amd64 (5.6.3-1) ... 142s Selecting previously unselected package pkgconf-bin. 142s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_amd64.deb ... 142s Unpacking pkgconf-bin (1.8.1-4) ... 142s Selecting previously unselected package pkgconf:amd64. 142s Preparing to unpack .../51-pkgconf_1.8.1-4_amd64.deb ... 142s Unpacking pkgconf:amd64 (1.8.1-4) ... 142s Selecting previously unselected package libtirpc-dev:amd64. 142s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 142s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 142s Selecting previously unselected package r-base-dev. 142s Preparing to unpack .../53-r-base-dev_4.4.2-1build1_all.deb ... 142s Unpacking r-base-dev (4.4.2-1build1) ... 142s Selecting previously unselected package pkg-r-autopkgtest. 142s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 142s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 142s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 142s Setting up libncurses-dev:amd64 (6.5+20250125-2) ... 142s Setting up libreadline-dev:amd64 (8.2-6) ... 142s Setting up libpcre2-16-0:amd64 (10.42-4ubuntu3) ... 142s Setting up libpcre2-32-0:amd64 (10.42-4ubuntu3) ... 142s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 142s Setting up libpkgconf3:amd64 (1.8.1-4) ... 142s Setting up libquadmath0:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libmpc3:amd64 (1.3.1-1build2) ... 142s Setting up icu-devtools (76.1-1ubuntu2) ... 142s Setting up pkgconf-bin (1.8.1-4) ... 142s Setting up liblzma-dev:amd64 (5.6.3-1) ... 142s Setting up libubsan1:amd64 (15-20250213-1ubuntu1) ... 142s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 142s Setting up libpcre2-posix3:amd64 (10.42-4ubuntu3) ... 142s Setting up libhwasan0:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libasan8:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libtsan2:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 142s Setting up libisl23:amd64 (0.27-1) ... 142s Setting up libdeflate-dev:amd64 (1.23-1) ... 142s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 142s Setting up libcc1-0:amd64 (15-20250213-1ubuntu1) ... 142s Setting up liblsan0:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libblas-dev:amd64 (3.12.1-2) ... 142s 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 142s Setting up dctrl-tools (2.24-3build3) ... 142s Setting up libitm1:amd64 (15-20250213-1ubuntu1) ... 142s Setting up libbz2-dev:amd64 (1.0.8-6) ... 142s Setting up libpcre2-dev:amd64 (10.42-4ubuntu3) ... 142s Setting up libpng-dev:amd64 (1.6.46-4) ... 143s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 143s Setting up pkgconf:amd64 (1.8.1-4) ... 143s Setting up liblapack-dev:amd64 (3.12.1-2) ... 143s 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 143s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 143s Setting up cpp-14 (14.2.0-17ubuntu1) ... 143s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu1) ... 143s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu1) ... 143s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 143s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu1) ... 143s Setting up cpp (4:14.2.0-1ubuntu1) ... 143s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 143s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 143s Setting up gcc-14 (14.2.0-17ubuntu1) ... 143s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 143s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu1) ... 143s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 143s Setting up g++-14 (14.2.0-17ubuntu1) ... 143s Setting up gfortran-14 (14.2.0-17ubuntu1) ... 143s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 143s Setting up gcc (4:14.2.0-1ubuntu1) ... 143s Setting up g++ (4:14.2.0-1ubuntu1) ... 143s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 143s Setting up build-essential (12.10ubuntu1) ... 143s Setting up gfortran (4:14.2.0-1ubuntu1) ... 143s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 143s 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 143s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 143s 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 143s Setting up r-base-dev (4.4.2-1build1) ... 143s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 143s Processing triggers for libc-bin (2.40-4ubuntu1) ... 143s Processing triggers for man-db (2.13.0-1) ... 144s Processing triggers for install-info (7.1.1-1) ... 145s autopkgtest [04:24:54]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 145s autopkgtest [04:24:54]: test pkg-r-autopkgtest: [----------------------- 145s Test: Try to load the R library vegan 145s 145s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 145s Copyright (C) 2024 The R Foundation for Statistical Computing 145s Platform: x86_64-pc-linux-gnu 145s 145s R is free software and comes with ABSOLUTELY NO WARRANTY. 145s You are welcome to redistribute it under certain conditions. 145s Type 'license()' or 'licence()' for distribution details. 145s 145s R is a collaborative project with many contributors. 145s Type 'contributors()' for more information and 145s 'citation()' on how to cite R or R packages in publications. 145s 145s Type 'demo()' for some demos, 'help()' for on-line help, or 145s 'help.start()' for an HTML browser interface to help. 145s Type 'q()' to quit R. 145s 145s > library('vegan') 145s Loading required package: permute 145s Loading required package: lattice 146s > 146s > 146s Other tests are currently unsupported! 146s They will be progressively added. 146s autopkgtest [04:24:55]: test pkg-r-autopkgtest: -----------------------] 147s autopkgtest [04:24:56]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 147s pkg-r-autopkgtest PASS 147s autopkgtest [04:24:56]: @@@@@@@@@@@@@@@@@@@@ summary 147s run-unit-test FAIL non-zero exit status 1 147s pkg-r-autopkgtest PASS 167s nova [W] Skipping flock for amd64 167s Creating nova instance adt-plucky-amd64-r-cran-vegan-20250219-042229-juju-7f2275-prod-proposed-migration-environment-2-63949d84-7618-4902-bfe0-802227f0e06b from image adt/ubuntu-plucky-amd64-server-20250219.img (UUID 90711abf-916f-4a80-845a-825250a78697)... 167s nova [W] Timed out waiting for 5205c9ab-8bea-46df-8563-47da93b99f93 to get deleted.