0s autopkgtest [11:09:43]: starting date and time: 2025-03-15 11:09:43+0000 0s autopkgtest [11:09:43]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [11:09:43]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gmf97m78/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.142 lxd-armhf-10.145.243.142:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [11:10:04]: testbed dpkg architecture: armhf 23s autopkgtest [11:10:06]: testbed apt version: 2.9.33 27s autopkgtest [11:10:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [11:10:12]: testbed release detected to be: None 36s autopkgtest [11:10:19]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [46.2 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [410 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [80.8 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1860 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [332 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1388 kB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 68s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1379 kB] 70s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [14.9 MB] 88s Fetched 40.3 MB in 49s (819 kB/s) 89s Reading package lists... 94s autopkgtest [11:11:17]: upgrading testbed (apt dist-upgrade and autopurge) 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 98s Entering ResolveByKeep 98s 98s Calculating upgrade... 99s The following packages will be upgraded: 99s libc-bin libc6 locales python3-jinja2 strace 99s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Need to get 8277 kB of archives. 99s After this operation, 23.6 kB of additional disk space will be used. 99s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 108s Preconfiguring packages ... 109s Fetched 8277 kB in 9s (899 kB/s) 109s (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 ... 64655 files and directories currently installed.) 109s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 109s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc6:armhf (2.41-1ubuntu2) ... 109s (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 ... 64655 files and directories currently installed.) 109s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 109s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 109s Setting up libc-bin (2.41-1ubuntu2) ... 110s (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 ... 64655 files and directories currently installed.) 110s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 110s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 110s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 110s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 110s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 110s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 110s Setting up locales (2.41-1ubuntu2) ... 111s Generating locales (this might take a while)... 113s en_US.UTF-8... done 113s Generation complete. 113s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 113s Setting up strace (6.13+ds-1ubuntu1) ... 113s Processing triggers for man-db (2.13.0-1) ... 114s Processing triggers for systemd (257.3-1ubuntu3) ... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Starting pkgProblemResolver with broken count: 0 117s Starting 2 pkgProblemResolver with broken count: 0 117s Done 118s Solving dependencies... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [11:11:43]: rebooting testbed after setup commands that affected boot 161s autopkgtest [11:12:24]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 186s autopkgtest [11:12:49]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 198s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (dsc) [2293 B] 198s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (tar) [1207 kB] 198s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (diff) [6736 B] 198s gpgv: Signature made Sun Mar 9 19:53:35 2025 UTC 198s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 198s gpgv: Can't check signature: No public key 198s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1ubuntu2.dsc: no acceptable signature found 198s autopkgtest [11:13:01]: testing package r-cran-vegan version 2.6-10+dfsg-1ubuntu2 200s autopkgtest [11:13:03]: build not needed 205s autopkgtest [11:13:08]: test run-unit-test: preparing testbed 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 208s The following NEW packages will be installed: 208s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 208s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 208s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 208s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 208s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 208s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 208s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 208s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 208s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 208s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 208s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 208s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 208s x11-common xdg-utils zip 208s 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 64.5 MB of archives. 208s After this operation, 148 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 209s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 209s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 210s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig-config armhf 2.15.0-2ubuntu1 [37.5 kB] 210s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libfontconfig1 armhf 2.15.0-2ubuntu1 [114 kB] 210s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf fontconfig armhf 2.15.0-2ubuntu1 [190 kB] 211s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 211s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 213s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 213s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 213s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 213s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 213s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 213s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libcairo2 armhf 1.18.2-2 [484 kB] 214s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 214s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 214s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 214s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 214s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 214s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 215s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf x11-common all 1:7.7+23ubuntu3 [21.7 kB] 215s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 215s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 215s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 215s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 215s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 215s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 216s Get:28 http://ftpmaster.internal/ubuntu plucky/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 216s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 218s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 218s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf libthai-data all 0.1.29-2build1 [158 kB] 218s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 218s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libpango-1.0-0 armhf 1.56.1-1 [216 kB] 219s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libpangoft2-1.0-0 armhf 1.56.1-1 [43.5 kB] 219s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libpangocairo-1.0-0 armhf 1.56.1-1 [25.1 kB] 219s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 219s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 219s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 219s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 219s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 220s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 220s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 220s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu4 [179 kB] 220s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 220s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 220s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 221s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 221s Get:48 http://ftpmaster.internal/ubuntu plucky/universe armhf node-normalize.css all 8.0.1-5 [10.8 kB] 221s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 222s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 222s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 222s Get:52 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 252s Get:53 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-cluster armhf 2.1.8-1 [563 kB] 252s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-commonmark armhf 1.9.2-2 [112 kB] 253s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-evaluate all 1.0.3-1 [114 kB] 253s Get:56 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-xfun armhf 0.51+dfsg-1 [573 kB] 253s Get:57 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 253s Get:58 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 253s Get:59 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 260s Get:60 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-knitr all 1.49+dfsg-1 [859 kB] 261s Get:61 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 263s Get:62 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-markdown all 1.13-1 [162 kB] 263s Get:63 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mass armhf 7.3-64-1 [1105 kB] 264s Get:64 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 268s Get:65 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-nlme armhf 3.1.167-1 [2306 kB] 271s Get:66 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 274s Get:67 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-permute all 0.9-7-1 [228 kB] 275s Get:68 http://ftpmaster.internal/ubuntu plucky/universe armhf r-cran-vegan armhf 2.6-10+dfsg-1ubuntu2 [3131 kB] 279s Preconfiguring packages ... 279s Fetched 64.5 MB in 1min 10s (920 kB/s) 279s Selecting previously unselected package libfreetype6:armhf. 279s (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 ... 64655 files and directories currently installed.) 279s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 279s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 279s Selecting previously unselected package fonts-dejavu-mono. 279s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 279s Unpacking fonts-dejavu-mono (2.37-8) ... 279s Selecting previously unselected package fonts-dejavu-core. 279s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 279s Unpacking fonts-dejavu-core (2.37-8) ... 279s Selecting previously unselected package fontconfig-config. 279s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_armhf.deb ... 279s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 279s Selecting previously unselected package libfontconfig1:armhf. 279s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_armhf.deb ... 279s Unpacking libfontconfig1:armhf (2.15.0-2ubuntu1) ... 279s Selecting previously unselected package fontconfig. 279s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_armhf.deb ... 279s Unpacking fontconfig (2.15.0-2ubuntu1) ... 279s Selecting previously unselected package fonts-glyphicons-halflings. 279s Preparing to unpack .../06-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 279s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 279s Selecting previously unselected package fonts-mathjax. 279s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 279s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 279s Selecting previously unselected package libblas3:armhf. 279s Preparing to unpack .../08-libblas3_3.12.1-2_armhf.deb ... 279s Unpacking libblas3:armhf (3.12.1-2) ... 279s Selecting previously unselected package libpixman-1-0:armhf. 279s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_armhf.deb ... 279s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 280s Selecting previously unselected package libxcb-render0:armhf. 280s Preparing to unpack .../10-libxcb-render0_1.17.0-2_armhf.deb ... 280s Unpacking libxcb-render0:armhf (1.17.0-2) ... 280s Selecting previously unselected package libxcb-shm0:armhf. 280s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_armhf.deb ... 280s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 280s Selecting previously unselected package libxrender1:armhf. 280s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 280s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 280s Selecting previously unselected package libcairo2:armhf. 280s Preparing to unpack .../13-libcairo2_1.18.2-2_armhf.deb ... 280s Unpacking libcairo2:armhf (1.18.2-2) ... 280s Selecting previously unselected package libdatrie1:armhf. 280s Preparing to unpack .../14-libdatrie1_0.2.13-3build1_armhf.deb ... 280s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 280s Selecting previously unselected package libdeflate0:armhf. 280s Preparing to unpack .../15-libdeflate0_1.23-1_armhf.deb ... 280s Unpacking libdeflate0:armhf (1.23-1) ... 280s Selecting previously unselected package libgfortran5:armhf. 280s Preparing to unpack .../16-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 280s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 280s Selecting previously unselected package libgomp1:armhf. 280s Preparing to unpack .../17-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 280s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 280s Selecting previously unselected package libgraphite2-3:armhf. 280s Preparing to unpack .../18-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 280s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 280s Selecting previously unselected package libharfbuzz0b:armhf. 280s Preparing to unpack .../19-libharfbuzz0b_10.2.0-1_armhf.deb ... 280s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 280s Selecting previously unselected package x11-common. 280s Preparing to unpack .../20-x11-common_1%3a7.7+23ubuntu3_all.deb ... 280s Unpacking x11-common (1:7.7+23ubuntu3) ... 280s Selecting previously unselected package libice6:armhf. 280s Preparing to unpack .../21-libice6_2%3a1.1.1-1_armhf.deb ... 280s Unpacking libice6:armhf (2:1.1.1-1) ... 280s Selecting previously unselected package libjpeg-turbo8:armhf. 280s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 280s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 280s Selecting previously unselected package libjpeg8:armhf. 280s Preparing to unpack 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(1.9-1-1) ... 286s Setting up r-cran-vegan (2.6-10+dfsg-1ubuntu2) ... 286s Processing triggers for libc-bin (2.41-1ubuntu2) ... 286s Processing triggers for man-db (2.13.0-1) ... 287s Processing triggers for install-info (7.1.1-1) ... 295s autopkgtest [11:14:38]: test run-unit-test: [----------------------- 297s 297s R version 4.4.3 (2025-02-28) -- "Trophy Case" 297s Copyright (C) 2025 The R Foundation for Statistical Computing 297s Platform: arm-unknown-linux-gnueabihf (32-bit) 297s 297s R is free software and comes with ABSOLUTELY NO WARRANTY. 297s You are welcome to redistribute it under certain conditions. 297s Type 'license()' or 'licence()' for distribution details. 297s 297s R is a collaborative project with many contributors. 297s Type 'contributors()' for more information and 297s 'citation()' on how to cite R or R packages in publications. 297s 297s Type 'demo()' for some demos, 'help()' for on-line help, or 297s 'help.start()' for an HTML browser interface to help. 297s Type 'q()' to quit R. 297s 297s > Stangle("decision-vegan.Rnw") 297s Writing to file decision-vegan.R 297s > source("decision-vegan.R", echo=TRUE) 297s 297s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 297s 297s > options(SweaveHooks = list(fig = figset)) 297s 297s > options(prompt = "> ", continue = " ") 297s 297s > options(width = 55) 297s 297s > require(vegan) 297s Loading required package: vegan 297s Loading required package: permute 297s Loading required package: lattice 298s 298s > data(sipoo) 298s 298s > mod <- nestedtemp(sipoo) 298s 298s > plot(mod, "i") 298s 298s > x <- mod$c["Falcsubb"] 298s 298s > y <- 1 - mod$r["Svartholm"] 298s 298s > points(x, y, pch = 16, cex = 1.5) 298s 298s > abline(x + y, -1, lty = 2) 298s 298s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 298s 298s > cross <- function(x, a, p) f(x, p) - a + x 298s 298s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 298s 298s > arrows(x, y, r, f(r, mod$p), lwd = 4) 298s 298s > library(vegan) 298s 298s > data(varespec) 298s 298s > data(varechem) 298s 298s > orig <- cca(varespec ~ Al + K, varechem) 298s 298s > plot(orig, dis = c("lc", "bp")) 298s 298s > plot(orig, dis = c("lc", "bp")) 298s 298s > i <- sample(nrow(varespec)) 298s 298s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 298s 298s > plot(shuff, dis = c("lc", "bp")) 298s 298s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 298s + dis = "lc"))) 298s 298s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 298s + dis = "lc"))) 298s 298s > tmp1 <- rda(varespec ~ Al + K, varechem) 298s 298s > i <- sample(nrow(varespec)) 298s 298s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 298s 298s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 298s + dis = "lc"))) 298s 298s > orig 298s Call: cca(formula = varespec ~ Al + K, data = 298s varechem) 298s 298s -- Model Summary -- 298s 298s Inertia Proportion Rank 298s Total 2.0832 1.0000 298s Constrained 0.4760 0.2285 2 298s Unconstrained 1.6072 0.7715 21 298s 298s Inertia is scaled Chi-square 298s 298s -- Eigenvalues -- 298s 298s Eigenvalues for constrained axes: 298s CCA1 CCA2 298s 0.3608 0.1152 298s 298s Eigenvalues for unconstrained axes: 298s CA1 CA2 CA3 CA4 CA5 CA6 CA7 298s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 298s CA8 298s 0.0757 298s (Showing 8 of 21 unconstrained eigenvalues) 298s 298s 298s > shuff 298s Call: cca(formula = varespec[i, ] ~ Al + K, data = 298s varechem) 298s 298s -- Model Summary -- 298s 298s Inertia Proportion Rank 298s Total 2.0832 1.0000 298s Constrained 0.2265 0.1087 2 298s Unconstrained 1.8567 0.8913 21 298s 298s Inertia is scaled Chi-square 298s 298s -- Eigenvalues -- 298s 298s Eigenvalues for constrained axes: 298s CCA1 CCA2 298s 0.18807 0.03847 298s 298s Eigenvalues for unconstrained axes: 298s CA1 CA2 CA3 CA4 CA5 CA6 CA7 298s 0.4350 0.3363 0.2029 0.1846 0.1755 0.1156 0.1039 298s CA8 298s 0.0834 298s (Showing 8 of 21 unconstrained eigenvalues) 298s 298s 298s > plot(procrustes(orig, shuff)) 298s 298s > tmp1 <- rda(varespec ~ ., varechem) 298s 298s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 298s 298s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 298s + scores(tmp2, dis = "lc", choi = 1:14)) 298s 298s > max(residuals(proc)) 298s [1] 3.066131e-14 298s 298s > data(dune) 298s 298s > data(dune.env) 298s 298s > orig <- cca(dune ~ Moisture, dune.env) 298s 298s > plot(orig, dis = "lc") 298s 298s > plot(orig, display = "wa", type = "points") 298s 298s > ordispider(orig, col = "red") 298s 298s > text(orig, dis = "cn", col = "blue") 298s 298s > plot(orig, display = "wa", type = "points") 298s 298s > ordispider(orig, col = "red") 298s 298s > text(orig, dis = "cn", col = "blue") 298s > 298s 298s R version 4.4.3 (2025-02-28) -- "Trophy Case" 298s Copyright (C) 2025 The R Foundation for Statistical Computing 298s Platform: arm-unknown-linux-gnueabihf (32-bit) 298s 298s R is free software and comes with ABSOLUTELY NO WARRANTY. 298s You are welcome to redistribute it under certain conditions. 298s Type 'license()' or 'licence()' for distribution details. 298s 298s R is a collaborative project with many contributors. 298s Type 'contributors()' for more information and 298s 'citation()' on how to cite R or R packages in publications. 298s 298s Type 'demo()' for some demos, 'help()' for on-line help, or 298s 'help.start()' for an HTML browser interface to help. 298s Type 'q()' to quit R. 298s 298s > Stangle("diversity-vegan.Rnw") 299s Writing to file diversity-vegan.R 299s > source("diversity-vegan.R", echo=TRUE) 299s 299s > par(mfrow = c(1, 1)) 299s 299s > options(width = 55) 299s 299s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 299s 299s > options(SweaveHooks = list(fig = figset)) 299s 299s > options(prompt = "> ", continue = " ") 299s 299s > library(vegan) 299s Loading required package: permute 299s Loading required package: lattice 300s 300s > data(BCI) 300s 300s > H <- diversity(BCI) 300s 300s > J <- H/log(specnumber(BCI)) 300s 300s > k <- sample(nrow(BCI), 6) 300s 300s > R <- renyi(BCI[k, ]) 300s 300s > print(plot(R)) 300s 300s > alpha <- fisher.alpha(BCI) 300s 300s > quantile(rowSums(BCI)) 300s 0% 25% 50% 75% 100% 300s 340.0 409.0 428.0 443.5 601.0 300s 300s > Srar <- rarefy(BCI, min(rowSums(BCI))) 300s 300s > S2 <- rarefy(BCI, 2) 300s 300s > all(rank(Srar) == rank(S2)) 300s [1] FALSE 300s 300s > range(diversity(BCI, "simp") - (S2 - 1)) 300s [1] -0.002868298 -0.001330663 300s 300s > data(dune) 300s 300s > data(dune.taxon) 300s 300s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 300s 300s > mod <- taxondive(dune, taxdis) 300s 300s > plot(mod) 300s forced matching of 'tree' labels and 'comm' names 300s 300s > tr <- hclust(taxdis, "aver") 300s 300s > mod <- treedive(dune, tr) 300s 300s > k <- sample(nrow(BCI), 1) 300s 300s > fish <- fisherfit(BCI[k, ]) 300s 300s > fish 300s 300s Fisher log series model 300s No. of species: 92 300s Fisher alpha: 35.88776 300s 300s 300s > plot(fish) 300s 300s > prestondistr(BCI[k, ]) 300s 300s Preston lognormal model 300s Method: maximized likelihood to log2 abundances 300s No. of species: 92 300s 300s mode width S0 300s 0.8352028 1.7913322 24.1844800 300s 300s Frequencies by Octave 300s 0 1 2 3 4 300s Observed 17.50000 27.00000 24.000 7.50000 10.000000 300s Fitted 21.69362 24.08235 19.576 11.65218 5.078656 300s 5 6 300s Observed 4.500000 1.5000000 300s Fitted 1.620871 0.3787968 300s 300s 300s > rad <- radfit(BCI[k, ]) 300s 300s > rad 300s 300s RAD models, family poisson 300s No. of species 92, total abundance 430 300s 300s par1 par2 par3 Deviance 300s Null 85.9601 300s Preemption 0.049495 70.0645 300s Lognormal 0.86697 1.1832 28.5832 300s Zipf 0.14615 -0.86285 37.0519 300s Mandelbrot 1.6203 -1.4888 5.7543 5.8926 300s AIC BIC 300s Null 348.6007 348.6007 300s Preemption 334.7051 337.2269 300s Lognormal 295.2238 300.2674 300s Zipf 303.6925 308.7361 300s Mandelbrot 274.5332 282.0986 300s 300s > print(radlattice(rad)) 300s 300s > sac <- specaccum(BCI) 300s 300s > plot(sac, ci.type = "polygon", ci.col = "yellow") 300s 300s > sac <- specaccum(BCI) 300s 300s > plot(sac, ci.type = "polygon", ci.col = "yellow") 300s 300s > ncol(BCI)/mean(specnumber(BCI)) - 1 300s [1] 1.478519 300s 300s > beta <- vegdist(BCI, binary = TRUE) 300s 300s > mean(beta) 300s [1] 0.3399075 300s 300s > betadiver(help = TRUE) 300s 1 "w" = (b+c)/(2*a+b+c) 300s 2 "-1" = (b+c)/(2*a+b+c) 300s 3 "c" = (b+c)/2 300s 4 "wb" = b+c 300s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 300s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 300s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 300s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 300s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 300s (2*a+b+c))-1 300s 8 "t" = (b+c)/(2*a+b+c) 300s 9 "me" = (b+c)/(2*a+b+c) 300s 10 "j" = a/(a+b+c) 300s 11 "sor" = 2*a/(2*a+b+c) 300s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 300s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 300s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 300s 15 "cc" = (b+c)/(a+b+c) 300s 16 "g" = (b+c)/(a+b+c) 300s 17 "-3" = pmin.int(b,c)/(a+b+c) 300s 18 "l" = (b+c)/2 300s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 300s 20 "hk" = (b+c)/(2*a+b+c) 300s 21 "rlb" = a/(a+c) 300s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 300s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 300s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 300s 300s > z <- betadiver(BCI, "z") 300s 300s > quantile(z) 300s 0% 25% 50% 75% 100% 300s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 300s 300s > data(dune) 300s 300s > data(dune.env) 300s 300s > z <- betadiver(dune, "z") 300s 300s > mod <- with(dune.env, betadisper(z, Management)) 300s 300s > mod 300s 300s Homogeneity of multivariate dispersions 300s 300s Call: betadisper(d = z, group = Management) 300s 300s No. of Positive Eigenvalues: 12 300s No. of Negative Eigenvalues: 7 300s 300s Average distance to median: 300s BF HF NM SF 300s 0.2532 0.2512 0.4406 0.3635 300s 300s Eigenvalues for PCoA axes: 300s (Showing 8 of 19 eigenvalues) 300s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 300s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 300s PCoA7 PCoA8 300s 0.16128 0.08099 300s 300s > boxplot(mod) 300s 300s > specpool(BCI) 300s Species chao chao.se jack1 jack1.se jack2 300s All 225 236.3732 6.54361 245.58 5.650522 247.8722 300s boot boot.se n 300s All 235.6862 3.468888 50 300s 300s > s <- sample(nrow(BCI), 25) 300s 300s > specpool(BCI[s, ]) 300s Species chao chao.se jack1 jack1.se jack2 300s All 205 222.6471 9.26244 229 7.959899 237.0117 300s boot boot.se n 300s All 216.7675 4.177153 25 300s 300s > estimateR(BCI[k, ]) 300s 36 300s S.obs 92.000000 300s S.chao1 121.750000 300s se.chao1 13.262409 300s S.ACE 136.318712 300s se.ACE 6.669613 300s 300s > veiledspec(prestondistr(BCI[k, ])) 300s Extrapolated Observed Veiled 300s 108.59325 92.00000 16.59325 300s 300s > veiledspec(BCI[k, ]) 300s Extrapolated Observed Veiled 300s 120.52468 92.00000 28.52468 300s 300s > smo <- beals(BCI) 300s 300s > j <- which(colnames(BCI) == "Ceiba.pentandra") 300s 300s > plot(beals(BCI, species = j, include = FALSE), BCI[, 300s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 300s 300s > j <- which(colnames(BCI) == "Ceiba.pentandra") 300s 300s > plot(beals(BCI, species = j, include = FALSE), BCI[, 300s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 300s Warning messages: 300s 1: In cor(x > 0) : the standard deviation is zero 300s 2: In cor(x > 0) : the standard deviation is zero 300s 3: In betadisper(z, Management) : 300s some squared distances are negative and changed to zero 300s > 301s 301s R version 4.4.3 (2025-02-28) -- "Trophy Case" 301s Copyright (C) 2025 The R Foundation for Statistical Computing 301s Platform: arm-unknown-linux-gnueabihf (32-bit) 301s 301s R is free software and comes with ABSOLUTELY NO WARRANTY. 301s You are welcome to redistribute it under certain conditions. 301s Type 'license()' or 'licence()' for distribution details. 301s 301s R is a collaborative project with many contributors. 301s Type 'contributors()' for more information and 301s 'citation()' on how to cite R or R packages in publications. 301s 301s Type 'demo()' for some demos, 'help()' for on-line help, or 301s 'help.start()' for an HTML browser interface to help. 301s Type 'q()' to quit R. 301s 301s > Stangle("intro-vegan.Rnw") 301s Writing to file intro-vegan.R 301s > source("intro-vegan.R", echo=TRUE) 301s 301s > par(mfrow = c(1, 1)) 301s 301s > options(width = 72) 301s 301s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 301s 301s > options(SweaveHooks = list(fig = figset)) 301s 301s > options(prompt = "> ", continue = " ") 301s 301s > library(vegan) 301s Loading required package: permute 301s Loading required package: lattice 302s 302s > data(dune) 302s 302s > ord <- decorana(dune) 302s 302s > ord 302s 302s Call: 302s decorana(veg = dune) 302s 302s Detrended correspondence analysis with 26 segments. 302s Rescaling of axes with 4 iterations. 302s Total inertia (scaled Chi-square): 2.1153 302s 302s DCA1 DCA2 DCA3 DCA4 302s Eigenvalues 0.5117 0.3036 0.12125 0.14267 302s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 302s Decorana values 0.5360 0.2869 0.08136 0.04814 302s Axis lengths 3.7004 3.1166 1.30055 1.47888 302s 302s 302s > ord <- metaMDS(dune, trace = FALSE) 302s 302s > ord 302s 302s Call: 302s metaMDS(comm = dune, trace = FALSE) 302s 302s global Multidimensional Scaling using monoMDS 302s 302s Data: dune 302s Distance: bray 302s 302s Dimensions: 2 302s Stress: 0.1183186 302s Stress type 1, weak ties 302s Best solution was repeated 3 times in 20 tries 302s The best solution was from try 6 (random start) 302s Scaling: centring, PC rotation, halfchange scaling 302s Species: expanded scores based on ‘dune’ 302s 302s 302s > plot(ord) 302s 302s > plot(ord) 302s 302s > plot(ord, type = "n") 302s 302s > points(ord, display = "sites", cex = 0.8, pch = 21, 302s + col = "red", bg = "yellow") 302s 302s > text(ord, display = "species", cex = 0.7, col = "blue") 302s 302s > plot(ord, type = "n") 302s 302s > points(ord, display = "sites", cex = 0.8, pch = 21, 302s + col = "red", bg = "yellow") 302s 302s > text(ord, display = "species", cex = 0.7, col = "blue") 302s 302s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 302s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 302s + col = "blue") 302s 302s > data(dune.env) 302s 302s > attach(dune.env) 302s 302s > plot(ord, disp = "sites", type = "n") 302s 302s > ordihull(ord, Management, col = 1:4, lwd = 3) 302s 302s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 302s + lwd = 3) 302s 302s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 302s 302s > ordispider(ord, Management, col = 1:4, label = TRUE) 302s 302s > points(ord, disp = "sites", pch = 21, col = "red", 302s + bg = "yellow", cex = 1.3) 302s 302s > plot(ord, disp = "sites", type = "n") 302s 302s > ordihull(ord, Management, col = 1:4, lwd = 3) 302s 302s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 302s + lwd = 3) 302s 302s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 302s 302s > ordispider(ord, Management, col = 1:4, label = TRUE) 302s 302s > points(ord, disp = "sites", pch = 21, col = "red", 302s + bg = "yellow", cex = 1.3) 302s 302s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 302s + perm = 999) 302s 302s > ord.fit 302s 302s ***VECTORS 302s 302s NMDS1 NMDS2 r2 Pr(>r) 302s A1 0.96473 0.26322 0.3649 0.013 * 302s --- 302s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 302s Permutation: free 302s Number of permutations: 999 302s 302s ***FACTORS: 302s 302s Centroids: 302s NMDS1 NMDS2 302s ManagementBF -0.4534 -0.0102 302s ManagementHF -0.2636 -0.1282 302s ManagementNM 0.2958 0.5790 302s ManagementSF 0.1506 -0.4670 302s 302s Goodness of fit: 302s r2 Pr(>r) 302s Management 0.4134 0.008 ** 302s --- 302s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 302s Permutation: free 302s Number of permutations: 999 302s 302s 302s 302s > plot(ord, dis = "site") 302s 302s > plot(ord.fit) 302s 302s > ordisurf(ord, A1, add = TRUE) 302s 302s Family: gaussian 302s Link function: identity 302s 302s Formula: 302s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 302s 302s Estimated degrees of freedom: 302s 1.59 total = 2.59 302s 302s REML score: 41.58728 302s 302s > plot(ord, dis = "site") 302s 302s > plot(ord.fit) 302s 302s > ordisurf(ord, A1, add = TRUE) 302s 302s Family: gaussian 302s Link function: identity 302s 302s Formula: 302s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 302s 302s Estimated degrees of freedom: 302s 1.59 total = 2.59 302s 302s REML score: 41.58728 302s 302s > ord <- cca(dune ~ A1 + Management, data = dune.env) 302s 302s > ord 302s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 302s 302s -- Model Summary -- 302s 302s Inertia Proportion Rank 302s Total 2.1153 1.0000 302s Constrained 0.7798 0.3686 4 302s Unconstrained 1.3355 0.6314 15 302s 302s Inertia is scaled Chi-square 302s 302s -- Eigenvalues -- 302s 302s Eigenvalues for constrained axes: 302s CCA1 CCA2 CCA3 CCA4 302s 0.3187 0.2372 0.1322 0.0917 302s 302s Eigenvalues for unconstrained axes: 302s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 302s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 302s CA11 CA12 CA13 CA14 CA15 302s 0.0317 0.0178 0.0116 0.0087 0.0047 302s 302s 302s > plot(ord) 302s 302s > plot(ord) 302s 302s > cca(dune ~ ., data = dune.env) 302s 302s Some constraints or conditions were aliased because they were 302s redundant. This can happen if terms are linearly dependent (collinear): 302s ‘Manure^4’ 302s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 302s Manure, data = dune.env) 302s 302s -- Model Summary -- 302s 302s Inertia Proportion Rank 302s Total 2.1153 1.0000 302s Constrained 1.5032 0.7106 12 302s Unconstrained 0.6121 0.2894 7 302s 302s Inertia is scaled Chi-square 302s 302s -- Note -- 302s 302s Some constraints or conditions were aliased because they were 302s redundant. This can happen if terms are linearly dependent 302s (collinear): ‘Manure^4’ 302s 302s -- Eigenvalues -- 302s 302s Eigenvalues for constrained axes: 302s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 302s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 302s CCA11 CCA12 302s 0.0228 0.0108 302s 302s Eigenvalues for unconstrained axes: 302s CA1 CA2 CA3 CA4 CA5 CA6 CA7 302s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 302s 302s 302s > anova(ord) 302s Permutation test for cca under reduced model 302s Permutation: free 302s Number of permutations: 999 302s 302s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 302s Df ChiSquare F Pr(>F) 302s Model 4 0.77978 2.1896 0.001 *** 302s Residual 15 1.33549 302s --- 302s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 302s 302s > anova(ord, by = "term", permutations = 199) 302s Permutation test for cca under reduced model 302s Terms added sequentially (first to last) 302s Permutation: free 302s Number of permutations: 199 302s 302s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 302s Df ChiSquare F Pr(>F) 302s A1 1 0.22476 2.5245 0.010 ** 302s Management 3 0.55502 2.0780 0.005 ** 302s Residual 15 1.33549 302s --- 302s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 302s 302s > anova(ord, by = "mar", permutations = 199) 302s Permutation test for cca under reduced model 302s Marginal effects of terms 302s Permutation: free 302s Number of permutations: 199 302s 302s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 302s Df ChiSquare F Pr(>F) 302s A1 1 0.17594 1.9761 0.040 * 302s Management 3 0.55502 2.0780 0.005 ** 302s Residual 15 1.33549 302s --- 302s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 302s 302s > anova(ord, by = "axis", permutations = 499) 303s Permutation test for cca under reduced model 303s Forward tests for axes 303s Permutation: free 303s Number of permutations: 499 303s 303s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 303s Df ChiSquare F Pr(>F) 303s CCA1 1 0.31875 3.5801 0.010 ** 303s CCA2 1 0.23718 2.6640 0.138 303s CCA3 1 0.13217 1.4845 0.844 303s CCA4 1 0.09168 1.0297 1.000 303s Residual 15 1.33549 303s --- 303s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 303s 303s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 303s + data = dune.env) 303s 303s > ord 303s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 303s data = dune.env) 303s 303s -- Model Summary -- 303s 303s Inertia Proportion Rank 303s Total 2.1153 1.0000 303s Conditional 0.6283 0.2970 3 303s Constrained 0.5109 0.2415 4 303s Unconstrained 0.9761 0.4615 12 303s 303s Inertia is scaled Chi-square 303s 303s -- Eigenvalues -- 303s 303s Eigenvalues for constrained axes: 303s CCA1 CCA2 CCA3 CCA4 303s 0.24932 0.12090 0.08160 0.05904 303s 303s Eigenvalues for unconstrained axes: 303s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 303s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 303s CA10 CA11 CA12 303s 0.02102 0.01254 0.00928 303s 303s 303s > anova(ord, by = "term", permutations = 499) 303s Permutation test for cca under reduced model 303s Terms added sequentially (first to last) 303s Permutation: free 303s Number of permutations: 499 303s 303s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 303s Df ChiSquare F Pr(>F) 303s A1 1 0.11543 1.4190 1.000 303s Management 3 0.39543 1.6205 0.002 ** 303s Residual 12 0.97610 303s --- 303s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 303s 303s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 303s 303s > anova(ord, by = "term", permutations = how) 303s Permutation test for cca under reduced model 303s Terms added sequentially (first to last) 303s Plots: dune.env$Moisture, plot permutation: none 303s Permutation: free 303s Number of permutations: 499 303s 303s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 303s Df ChiSquare F Pr(>F) 303s A1 1 0.11543 1.4190 1.000 303s Management 3 0.39543 1.6205 0.002 ** 303s Residual 12 0.97610 303s --- 303s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 303s 303s > detach(dune.env) 303s > 303s 303s R version 4.4.3 (2025-02-28) -- "Trophy Case" 303s Copyright (C) 2025 The R Foundation for Statistical Computing 303s Platform: arm-unknown-linux-gnueabihf (32-bit) 303s 303s R is free software and comes with ABSOLUTELY NO WARRANTY. 303s You are welcome to redistribute it under certain conditions. 303s Type 'license()' or 'licence()' for distribution details. 303s 303s R is a collaborative project with many contributors. 303s Type 'contributors()' for more information and 303s 'citation()' on how to cite R or R packages in publications. 303s 303s Type 'demo()' for some demos, 'help()' for on-line help, or 303s 'help.start()' for an HTML browser interface to help. 303s Type 'q()' to quit R. 303s 303s > Stangle("partitioning.Rnw") 303s Writing to file partitioning.R 303s > source("partitioning.R", echo=TRUE) 303s 303s > par(mfrow = c(1, 1)) 303s 303s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 303s 303s > options(SweaveHooks = list(fig = figset)) 303s 303s > library(vegan) 303s Loading required package: permute 303s Loading required package: lattice 304s 304s > labs <- paste("Table", 1:4) 304s 304s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 304s 304s > showvarparts(2, bg = cls, Xnames = labs) 304s 304s > showvarparts(3, bg = cls, Xnames = labs) 304s 304s > showvarparts(4, bg = cls, Xnames = labs) 304s > 312s Test cca-object-tests passed 313s Test oecosimu-tests passed 317s Test vegan-tests passed 317s autopkgtest [11:15:00]: test run-unit-test: -----------------------] 321s autopkgtest [11:15:04]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 321s run-unit-test PASS 325s autopkgtest [11:15:08]: test pkg-r-autopkgtest: preparing testbed 327s Reading package lists... 327s Building dependency tree... 327s Reading state information... 328s Starting pkgProblemResolver with broken count: 0 328s Starting 2 pkgProblemResolver with broken count: 0 328s Done 329s The following NEW packages will be installed: 329s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 329s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-14 g++-14-arm-linux-gnueabihf 329s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 329s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 329s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 329s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-14-dev 329s libgfortran-14-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 329s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 329s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 329s libreadline-dev libstdc++-14-dev libtirpc-dev libubsan1 linux-libc-dev 329s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 329s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 329s Need to get 78.1 MB of archives. 329s After this operation, 243 MB of additional disk space will be used. 329s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-dev-bin armhf 2.41-1ubuntu2 [23.0 kB] 329s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf linux-libc-dev armhf 6.14.0-10.10 [1683 kB] 331s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 331s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 331s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6-dev armhf 2.41-1ubuntu2 [1396 kB] 333s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libisl23 armhf 0.27-1 [546 kB] 334s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 334s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9220 kB] 344s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-14 armhf 14.2.0-17ubuntu3 [1030 B] 344s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 344s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 344s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libcc1-0 armhf 15-20250222-0ubuntu1 [38.9 kB] 344s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libasan8 armhf 15-20250222-0ubuntu1 [2955 kB] 347s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libubsan1 armhf 15-20250222-0ubuntu1 [1191 kB] 348s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-14-dev armhf 14.2.0-17ubuntu3 [897 kB] 350s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [18.0 MB] 368s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14 armhf 14.2.0-17ubuntu3 [506 kB] 369s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 369s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 369s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++-14-dev armhf 14.2.0-17ubuntu3 [2573 kB] 371s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [10.5 MB] 381s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf g++-14 armhf 14.2.0-17ubuntu3 [21.8 kB] 381s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 381s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 381s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf build-essential armhf 12.10ubuntu1 [4928 B] 381s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 381s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran-14-dev armhf 14.2.0-17ubuntu3 [370 kB] 382s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-17ubuntu3 [9763 kB] 390s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-14 armhf 14.2.0-17ubuntu3 [13.6 kB] 390s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 390s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 390s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 390s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 391s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 391s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 391s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 402s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 402s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 402s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 402s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 404s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 404s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 404s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 404s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 404s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 405s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 405s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 406s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf libpng-dev armhf 1.6.47-1 [251 kB] 406s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf libreadline-dev armhf 8.2-6 [153 kB] 406s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf liblzma-dev armhf 5.6.4-1 [166 kB] 406s Get:51 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 406s Get:52 http://ftpmaster.internal/ubuntu plucky/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 406s Get:53 http://ftpmaster.internal/ubuntu plucky/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 406s Get:54 http://ftpmaster.internal/ubuntu plucky/universe armhf r-base-dev all 4.4.3-1 [4176 B] 406s Get:55 http://ftpmaster.internal/ubuntu plucky/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 407s Fetched 78.1 MB in 1min 18s (1007 kB/s) 407s Selecting previously unselected package libc-dev-bin. 407s (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 ... 72634 files and directories currently installed.) 407s Preparing to unpack .../00-libc-dev-bin_2.41-1ubuntu2_armhf.deb ... 407s Unpacking libc-dev-bin (2.41-1ubuntu2) ... 407s Selecting previously unselected package linux-libc-dev:armhf. 407s Preparing to unpack .../01-linux-libc-dev_6.14.0-10.10_armhf.deb ... 407s Unpacking linux-libc-dev:armhf (6.14.0-10.10) ... 407s Selecting previously unselected package libcrypt-dev:armhf. 407s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 407s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 407s Selecting previously unselected package rpcsvc-proto. 407s Preparing to unpack .../03-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 407s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 407s Selecting previously unselected package libc6-dev:armhf. 407s Preparing to unpack .../04-libc6-dev_2.41-1ubuntu2_armhf.deb ... 407s Unpacking libc6-dev:armhf (2.41-1ubuntu2) ... 407s Selecting previously unselected package libisl23:armhf. 407s Preparing to unpack .../05-libisl23_0.27-1_armhf.deb ... 407s Unpacking libisl23:armhf (0.27-1) ... 407s Selecting previously unselected package libmpc3:armhf. 407s Preparing to unpack .../06-libmpc3_1.3.1-1build2_armhf.deb ... 407s Unpacking libmpc3:armhf (1.3.1-1build2) ... 407s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 408s Preparing to unpack .../07-cpp-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 408s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 408s Selecting previously unselected package cpp-14. 408s Preparing to unpack .../08-cpp-14_14.2.0-17ubuntu3_armhf.deb ... 408s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package cpp-arm-linux-gnueabihf. 409s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package cpp. 409s Preparing to unpack .../10-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking cpp (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package libcc1-0:armhf. 409s Preparing to unpack .../11-libcc1-0_15-20250222-0ubuntu1_armhf.deb ... 409s Unpacking libcc1-0:armhf (15-20250222-0ubuntu1) ... 409s Selecting previously unselected package libasan8:armhf. 409s Preparing to unpack .../12-libasan8_15-20250222-0ubuntu1_armhf.deb ... 409s Unpacking libasan8:armhf (15-20250222-0ubuntu1) ... 409s Selecting previously unselected package libubsan1:armhf. 409s Preparing to unpack .../13-libubsan1_15-20250222-0ubuntu1_armhf.deb ... 409s Unpacking libubsan1:armhf (15-20250222-0ubuntu1) ... 409s Selecting previously unselected package libgcc-14-dev:armhf. 409s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 409s Preparing to unpack .../15-gcc-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package gcc-14. 409s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package gcc-arm-linux-gnueabihf. 409s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package gcc. 409s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking gcc (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package libstdc++-14-dev:armhf. 409s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 409s Preparing to unpack .../20-g++-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package g++-14. 409s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking g++-14 (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package g++-arm-linux-gnueabihf. 409s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package g++. 409s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 409s Unpacking g++ (4:14.2.0-1ubuntu1) ... 409s Selecting previously unselected package build-essential. 409s Preparing to unpack .../24-build-essential_12.10ubuntu1_armhf.deb ... 409s Unpacking build-essential (12.10ubuntu1) ... 409s Selecting previously unselected package dctrl-tools. 409s Preparing to unpack .../25-dctrl-tools_2.24-3build3_armhf.deb ... 409s Unpacking dctrl-tools (2.24-3build3) ... 409s Selecting previously unselected package libgfortran-14-dev:armhf. 409s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 409s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 409s Preparing to unpack .../27-gfortran-14-arm-linux-gnueabihf_14.2.0-17ubuntu3_armhf.deb ... 409s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 410s Selecting previously unselected package gfortran-14. 410s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_armhf.deb ... 410s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 410s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 410s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 410s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 410s Selecting previously unselected package gfortran. 410s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 410s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 410s Selecting previously unselected package icu-devtools. 410s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_armhf.deb ... 410s Unpacking icu-devtools (76.1-1ubuntu2) ... 410s Selecting previously unselected package libblas-dev:armhf. 410s Preparing to unpack .../32-libblas-dev_3.12.1-2_armhf.deb ... 410s Unpacking libblas-dev:armhf (3.12.1-2) ... 410s Selecting previously unselected package libbz2-dev:armhf. 410s Preparing to unpack .../33-libbz2-dev_1.0.8-6_armhf.deb ... 410s Unpacking libbz2-dev:armhf (1.0.8-6) ... 410s Selecting previously unselected package libdeflate-dev:armhf. 410s Preparing to unpack .../34-libdeflate-dev_1.23-1_armhf.deb ... 410s Unpacking libdeflate-dev:armhf (1.23-1) ... 410s Selecting previously unselected package libicu-dev:armhf. 410s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_armhf.deb ... 410s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 410s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 410s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 410s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 410s Selecting previously unselected package libjpeg8-dev:armhf. 410s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 410s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 410s Selecting previously unselected package libjpeg-dev:armhf. 410s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 410s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 410s Selecting previously unselected package liblapack-dev:armhf. 410s Preparing to unpack .../39-liblapack-dev_3.12.1-2_armhf.deb ... 410s Unpacking liblapack-dev:armhf (3.12.1-2) ... 411s Selecting previously unselected package libncurses-dev:armhf. 411s Preparing to unpack .../40-libncurses-dev_6.5+20250216-2_armhf.deb ... 411s Unpacking libncurses-dev:armhf (6.5+20250216-2) ... 411s Selecting previously unselected package libpcre2-16-0:armhf. 411s Preparing to unpack .../41-libpcre2-16-0_10.45-1_armhf.deb ... 411s Unpacking libpcre2-16-0:armhf (10.45-1) ... 411s Selecting previously unselected package libpcre2-32-0:armhf. 411s Preparing to unpack .../42-libpcre2-32-0_10.45-1_armhf.deb ... 411s Unpacking libpcre2-32-0:armhf (10.45-1) ... 411s Selecting previously unselected package libpcre2-posix3:armhf. 411s Preparing to unpack .../43-libpcre2-posix3_10.45-1_armhf.deb ... 411s Unpacking libpcre2-posix3:armhf (10.45-1) ... 411s Selecting previously unselected package libpcre2-dev:armhf. 411s Preparing to unpack .../44-libpcre2-dev_10.45-1_armhf.deb ... 411s Unpacking libpcre2-dev:armhf (10.45-1) ... 411s Selecting previously unselected package libpkgconf3:armhf. 411s Preparing to unpack .../45-libpkgconf3_1.8.1-4_armhf.deb ... 411s Unpacking libpkgconf3:armhf (1.8.1-4) ... 411s Selecting previously unselected package zlib1g-dev:armhf. 411s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 411s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 411s Selecting previously unselected package libpng-dev:armhf. 411s Preparing to unpack .../47-libpng-dev_1.6.47-1_armhf.deb ... 411s Unpacking libpng-dev:armhf (1.6.47-1) ... 411s Selecting previously unselected package libreadline-dev:armhf. 411s Preparing to unpack .../48-libreadline-dev_8.2-6_armhf.deb ... 411s Unpacking libreadline-dev:armhf (8.2-6) ... 411s Selecting previously unselected package liblzma-dev:armhf. 411s Preparing to unpack .../49-liblzma-dev_5.6.4-1_armhf.deb ... 411s Unpacking liblzma-dev:armhf (5.6.4-1) ... 411s Selecting previously unselected package pkgconf-bin. 411s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_armhf.deb ... 411s Unpacking pkgconf-bin (1.8.1-4) ... 411s Selecting previously unselected package pkgconf:armhf. 411s Preparing to unpack .../51-pkgconf_1.8.1-4_armhf.deb ... 411s Unpacking pkgconf:armhf (1.8.1-4) ... 411s Selecting previously unselected package libtirpc-dev:armhf. 411s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 411s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 411s Selecting previously unselected package r-base-dev. 411s Preparing to unpack .../53-r-base-dev_4.4.3-1_all.deb ... 412s Unpacking r-base-dev (4.4.3-1) ... 412s Selecting previously unselected package pkg-r-autopkgtest. 412s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 412s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 412s Setting up linux-libc-dev:armhf (6.14.0-10.10) ... 412s Setting up libpcre2-16-0:armhf (10.45-1) ... 412s Setting up libpcre2-32-0:armhf (10.45-1) ... 412s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 412s Setting up libpkgconf3:armhf (1.8.1-4) ... 412s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 412s Setting up libmpc3:armhf (1.3.1-1build2) ... 412s Setting up icu-devtools (76.1-1ubuntu2) ... 412s Setting up pkgconf-bin (1.8.1-4) ... 412s Setting up liblzma-dev:armhf (5.6.4-1) ... 412s Setting up libubsan1:armhf (15-20250222-0ubuntu1) ... 412s Setting up libpcre2-posix3:armhf (10.45-1) ... 412s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 412s Setting up libasan8:armhf (15-20250222-0ubuntu1) ... 412s Setting up libgcc-14-dev:armhf (14.2.0-17ubuntu3) ... 412s Setting up libisl23:armhf (0.27-1) ... 412s Setting up libc-dev-bin (2.41-1ubuntu2) ... 412s Setting up libdeflate-dev:armhf (1.23-1) ... 412s Setting up libcc1-0:armhf (15-20250222-0ubuntu1) ... 412s Setting up libblas-dev:armhf (3.12.1-2) ... 412s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 412s Setting up dctrl-tools (2.24-3build3) ... 412s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 412s Setting up libgfortran-14-dev:armhf (14.2.0-17ubuntu3) ... 412s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-17ubuntu3) ... 412s Setting up pkgconf:armhf (1.8.1-4) ... 412s Setting up liblapack-dev:armhf (3.12.1-2) ... 412s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 412s Setting up cpp-14 (14.2.0-17ubuntu3) ... 412s Setting up libc6-dev:armhf (2.41-1ubuntu2) ... 412s Setting up libstdc++-14-dev:armhf (14.2.0-17ubuntu3) ... 412s 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pkg-r-autopkgtest (20231212ubuntu1) ... 412s Processing triggers for libc-bin (2.41-1ubuntu2) ... 412s Processing triggers for man-db (2.13.0-1) ... 413s Processing triggers for install-info (7.1.1-1) ... 421s autopkgtest [11:16:44]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 421s autopkgtest [11:16:44]: test pkg-r-autopkgtest: [----------------------- 423s Test: Try to load the R library vegan 423s 423s R version 4.4.3 (2025-02-28) -- "Trophy Case" 423s Copyright (C) 2025 The R Foundation for Statistical Computing 423s Platform: arm-unknown-linux-gnueabihf (32-bit) 423s 423s R is free software and comes with ABSOLUTELY NO WARRANTY. 423s You are welcome to redistribute it under certain conditions. 423s Type 'license()' or 'licence()' for distribution details. 423s 423s R is a collaborative project with many contributors. 423s Type 'contributors()' for more information and 423s 'citation()' on how to cite R or R packages in publications. 423s 423s Type 'demo()' for some demos, 'help()' for on-line help, or 423s 'help.start()' for an HTML browser interface to help. 423s Type 'q()' to quit R. 423s 423s > library('vegan') 423s Loading required package: permute 423s Loading required package: lattice 424s > 424s > 424s Other tests are currently unsupported! 424s They will be progressively added. 424s autopkgtest [11:16:47]: test pkg-r-autopkgtest: -----------------------] 428s pkg-r-autopkgtest PASS 428s autopkgtest [11:16:51]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 432s autopkgtest [11:16:55]: @@@@@@@@@@@@@@@@@@@@ summary 432s run-unit-test PASS 432s pkg-r-autopkgtest PASS