0s autopkgtest [04:17:19]: starting date and time: 2025-02-19 04:17:19+0000 0s autopkgtest [04:17:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [04:17:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kwju54bd/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-5.secgroup --name adt-plucky-arm64-r-cran-vegan-20250219-041719-juju-7f2275-prod-proposed-migration-environment-2-4e4e75ab-93ff-4545-9eea-9359f3d4649c --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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/ 167s autopkgtest [04:20:06]: testbed dpkg architecture: arm64 168s autopkgtest [04:20:07]: testbed apt version: 2.9.29 168s autopkgtest [04:20:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 168s autopkgtest [04:20:07]: testbed release detected to be: None 169s autopkgtest [04:20:08]: updating testbed package index (apt update) 170s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 170s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 170s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 170s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 170s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [79.1 kB] 170s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [788 kB] 170s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 170s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [97.6 kB] 170s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 170s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [698 kB] 170s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [12.1 kB] 170s Fetched 1811 kB in 1s (1966 kB/s) 171s Reading package lists... 172s Reading package lists... 172s Building dependency tree... 172s Reading state information... 173s Calculating upgrade... 173s The following packages will be upgraded: 173s dhcpcd-base 173s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 216 kB of archives. 173s After this operation, 0 B of additional disk space will be used. 173s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 dhcpcd-base arm64 1:10.1.0-7 [216 kB] 174s Fetched 216 kB in 0s (493 kB/s) 174s (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 ... 116620 files and directories currently installed.) 174s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_arm64.deb ... 174s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-6) ... 175s Setting up dhcpcd-base (1:10.1.0-7) ... 175s Processing triggers for man-db (2.13.0-1) ... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s autopkgtest [04:20:16]: upgrading testbed (apt dist-upgrade and autopurge) 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s Entering ResolveByKeep 179s 179s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 184s autopkgtest [04:20:23]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 184s autopkgtest [04:20:23]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (dsc) [2211 B] 186s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (tar) [1207 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (diff) [6328 B] 186s gpgv: Signature made Sun Feb 2 23:43:24 2025 UTC 186s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 186s gpgv: issuer "plessy@debian.org" 186s gpgv: Can't check signature: No public key 186s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1.dsc: no acceptable signature found 186s autopkgtest [04:20:25]: testing package r-cran-vegan version 2.6-10+dfsg-1 187s autopkgtest [04:20:26]: build not needed 192s autopkgtest [04:20:31]: test run-unit-test: preparing testbed 192s Reading package lists... 193s Building dependency tree... 193s Reading state information... 193s Starting pkgProblemResolver with broken count: 0 193s Starting 2 pkgProblemResolver with broken count: 0 193s Done 194s The following NEW packages will be installed: 194s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 194s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 194s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 194s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 194s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 194s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 194s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 194s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 194s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 194s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 194s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 194s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 194s x11-common xdg-utils zip 194s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 194s Need to get 65.4 MB of archives. 194s After this operation, 158 MB of additional disk space will be used. 194s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 194s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 194s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 194s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 194s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 195s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 195s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 195s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 195s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 195s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 195s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 195s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 195s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 195s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 195s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 195s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 195s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 195s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 195s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 195s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 195s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 195s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 195s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 195s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 195s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 195s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 195s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 195s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 195s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 195s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB] 195s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB] 195s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB] 195s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 195s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 195s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 195s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 195s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 195s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 195s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 195s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 195s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 195s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 195s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 195s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 195s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 195s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 195s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 195s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 195s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1build1 [28.4 MB] 196s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cluster arm64 2.1.8-1 [568 kB] 196s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.2-2 [129 kB] 196s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 196s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.50+dfsg-1 [567 kB] 196s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 196s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 196s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 197s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 197s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 197s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-markdown all 1.13-1 [162 kB] 197s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 197s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-2-1 [4153 kB] 197s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 197s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 197s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-permute all 0.9-7-1 [228 kB] 197s Get:67 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 r-cran-vegan arm64 2.6-10+dfsg-1 [3137 kB] 198s Preconfiguring packages ... 198s Fetched 65.4 MB in 3s (18.9 MB/s) 198s Selecting previously unselected package fonts-dejavu-mono. 198s (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 ... 116620 files and directories currently installed.) 198s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 198s Unpacking fonts-dejavu-mono (2.37-8) ... 198s Selecting previously unselected package fonts-dejavu-core. 198s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 198s Unpacking fonts-dejavu-core (2.37-8) ... 198s Selecting previously unselected package fontconfig-config. 198s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 198s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 198s Selecting previously unselected package libfontconfig1:arm64. 198s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 198s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 198s Selecting previously unselected package fontconfig. 198s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 198s Unpacking fontconfig (2.15.0-2ubuntu1) ... 198s Selecting previously unselected package fonts-glyphicons-halflings. 198s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 198s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 198s Selecting previously unselected package fonts-mathjax. 198s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 198s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 199s Selecting previously unselected package libblas3:arm64. 199s Preparing to unpack .../07-libblas3_3.12.1-2_arm64.deb ... 199s Unpacking libblas3:arm64 (3.12.1-2) ... 199s Selecting previously unselected package libpixman-1-0:arm64. 199s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_arm64.deb ... 199s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 199s Selecting previously unselected package libxcb-render0:arm64. 199s Preparing to unpack .../09-libxcb-render0_1.17.0-2_arm64.deb ... 199s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 199s Selecting previously unselected package libxcb-shm0:arm64. 199s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_arm64.deb ... 199s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 199s Selecting previously unselected package libxrender1:arm64. 199s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 199s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 199s Selecting previously unselected package libcairo2:arm64. 199s Preparing to unpack .../12-libcairo2_1.18.2-2_arm64.deb ... 199s Unpacking libcairo2:arm64 (1.18.2-2) ... 199s Selecting previously unselected package libdatrie1:arm64. 199s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_arm64.deb ... 199s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 199s Selecting previously unselected package libdeflate0:arm64. 199s Preparing to unpack .../14-libdeflate0_1.23-1_arm64.deb ... 199s Unpacking libdeflate0:arm64 (1.23-1) ... 199s Selecting previously unselected package libgfortran5:arm64. 199s Preparing to unpack .../15-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 199s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 199s Selecting previously unselected package libgomp1:arm64. 199s Preparing to unpack .../16-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 199s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 199s Selecting previously unselected package libgraphite2-3:arm64. 199s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 199s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 199s Selecting previously unselected package libharfbuzz0b:arm64. 199s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_arm64.deb ... 199s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 199s Selecting previously unselected package x11-common. 199s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 199s Unpacking x11-common (1:7.7+23ubuntu3) ... 199s Selecting previously unselected package libice6:arm64. 199s Preparing to unpack .../20-libice6_2%3a1.1.1-1_arm64.deb ... 199s Unpacking libice6:arm64 (2:1.1.1-1) ... 199s Selecting previously unselected package libjpeg-turbo8:arm64. 199s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 199s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 199s Selecting previously unselected package libjpeg8:arm64. 199s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ... 199s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 199s Selecting previously unselected package libjs-bootstrap. 199s Preparing to unpack .../23-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 199s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 199s Selecting previously unselected package libjs-highlight.js. 199s Preparing to unpack .../24-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 199s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 199s Selecting previously unselected package libjs-jquery. 199s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 199s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 200s Selecting previously unselected package libjs-jquery-datatables. 200s Preparing to unpack .../26-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 200s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 200s Selecting previously unselected package liblapack3:arm64. 200s Preparing to unpack .../27-liblapack3_3.12.1-2_arm64.deb ... 200s Unpacking liblapack3:arm64 (3.12.1-2) ... 200s Selecting previously unselected package liblerc4:arm64. 200s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 200s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 200s Selecting previously unselected package libthai-data. 200s Preparing to unpack .../29-libthai-data_0.1.29-2build1_all.deb ... 200s Unpacking libthai-data (0.1.29-2build1) ... 200s Selecting previously unselected package libthai0:arm64. 200s Preparing to unpack .../30-libthai0_0.1.29-2build1_arm64.deb ... 200s Unpacking libthai0:arm64 (0.1.29-2build1) ... 200s Selecting previously unselected package libpango-1.0-0:arm64. 200s Preparing to unpack .../31-libpango-1.0-0_1.56.1-1_arm64.deb ... 200s Unpacking libpango-1.0-0:arm64 (1.56.1-1) ... 200s Selecting previously unselected package libpangoft2-1.0-0:arm64. 200s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.1-1_arm64.deb ... 200s Unpacking libpangoft2-1.0-0:arm64 (1.56.1-1) ... 200s Selecting previously unselected package libpangocairo-1.0-0:arm64. 200s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.1-1_arm64.deb ... 200s 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run-unit-test: [----------------------- 209s 209s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 209s Copyright (C) 2024 The R Foundation for Statistical Computing 209s Platform: aarch64-unknown-linux-gnu 209s 209s R is free software and comes with ABSOLUTELY NO WARRANTY. 209s You are welcome to redistribute it under certain conditions. 209s Type 'license()' or 'licence()' for distribution details. 209s 209s R is a collaborative project with many contributors. 209s Type 'contributors()' for more information and 209s 'citation()' on how to cite R or R packages in publications. 209s 209s Type 'demo()' for some demos, 'help()' for on-line help, or 209s 'help.start()' for an HTML browser interface to help. 209s Type 'q()' to quit R. 209s 209s > Stangle("decision-vegan.Rnw") 209s Writing to file decision-vegan.R 209s > source("decision-vegan.R", echo=TRUE) 209s 209s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 209s 209s > options(SweaveHooks = list(fig = figset)) 209s 209s > options(prompt = "> ", continue = " ") 209s 209s > options(width = 55) 209s 209s > require(vegan) 209s Loading required package: vegan 209s Loading required package: permute 209s Loading required package: lattice 210s 210s > data(sipoo) 210s 210s > mod <- nestedtemp(sipoo) 210s 210s > plot(mod, "i") 210s 210s > x <- mod$c["Falcsubb"] 210s 210s > y <- 1 - mod$r["Svartholm"] 210s 210s > points(x, y, pch = 16, cex = 1.5) 210s 210s > abline(x + y, -1, lty = 2) 210s 210s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 210s 210s > cross <- function(x, a, p) f(x, p) - a + x 210s 210s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 210s 210s > arrows(x, y, r, f(r, mod$p), lwd = 4) 210s 210s > library(vegan) 210s 210s > data(varespec) 210s 210s > data(varechem) 210s 210s > orig <- cca(varespec ~ Al + K, varechem) 210s 210s > plot(orig, dis = c("lc", "bp")) 210s 210s > plot(orig, dis = c("lc", "bp")) 210s 210s > i <- sample(nrow(varespec)) 210s 210s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 210s 210s > plot(shuff, dis = c("lc", "bp")) 210s 210s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 210s + dis = "lc"))) 210s 210s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 210s + dis = "lc"))) 210s 210s > tmp1 <- rda(varespec ~ Al + K, varechem) 210s 210s > i <- sample(nrow(varespec)) 210s 210s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 210s 210s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 210s + dis = "lc"))) 210s 210s > orig 210s Call: cca(formula = varespec ~ Al + K, data = 210s varechem) 210s 210s -- Model Summary -- 210s 210s Inertia Proportion Rank 210s Total 2.0832 1.0000 210s Constrained 0.4760 0.2285 2 210s Unconstrained 1.6072 0.7715 21 210s 210s Inertia is scaled Chi-square 210s 210s -- Eigenvalues -- 210s 210s Eigenvalues for constrained axes: 210s CCA1 CCA2 210s 0.3608 0.1152 210s 210s Eigenvalues for unconstrained axes: 210s CA1 CA2 CA3 CA4 CA5 CA6 CA7 210s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 210s CA8 210s 0.0757 210s (Showing 8 of 21 unconstrained eigenvalues) 210s 210s 210s > shuff 210s Call: cca(formula = varespec[i, ] ~ Al + K, data = 210s varechem) 210s 210s -- Model Summary -- 210s 210s Inertia Proportion Rank 210s Total 2.0832 1.0000 210s Constrained 0.3583 0.1720 2 210s Unconstrained 1.7249 0.8280 21 210s 210s Inertia is scaled Chi-square 210s 210s -- Eigenvalues -- 210s 210s Eigenvalues for constrained axes: 210s CCA1 CCA2 210s 0.26511 0.09324 210s 210s Eigenvalues for unconstrained axes: 210s CA1 CA2 CA3 CA4 CA5 CA6 CA7 210s 0.3893 0.2850 0.2255 0.1916 0.1565 0.1111 0.0964 210s CA8 210s 0.0659 210s (Showing 8 of 21 unconstrained eigenvalues) 210s 210s 210s > plot(procrustes(orig, shuff)) 210s 210s > tmp1 <- rda(varespec ~ ., varechem) 210s 210s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 210s 210s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 210s + scores(tmp2, dis = "lc", choi = 1:14)) 210s 210s > max(residuals(proc)) 210s [1] 2.962934e-14 210s 210s > data(dune) 210s 210s > data(dune.env) 210s 210s > orig <- cca(dune ~ Moisture, dune.env) 210s 210s > plot(orig, dis = "lc") 210s 210s > plot(orig, display = "wa", type = "points") 210s 210s > ordispider(orig, col = "red") 210s 210s > text(orig, dis = "cn", col = "blue") 210s 210s > plot(orig, display = "wa", type = "points") 210s 210s > ordispider(orig, col = "red") 210s 210s > text(orig, dis = "cn", col = "blue") 210s > 210s 210s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 210s Copyright (C) 2024 The R Foundation for Statistical Computing 210s Platform: aarch64-unknown-linux-gnu 210s 210s R is free software and comes with ABSOLUTELY NO WARRANTY. 210s You are welcome to redistribute it under certain conditions. 210s Type 'license()' or 'licence()' for distribution details. 210s 210s R is a collaborative project with many contributors. 210s Type 'contributors()' for more information and 210s 'citation()' on how to cite R or R packages in publications. 210s 210s Type 'demo()' for some demos, 'help()' for on-line help, or 210s 'help.start()' for an HTML browser interface to help. 210s Type 'q()' to quit R. 210s 210s > Stangle("diversity-vegan.Rnw") 210s Writing to file diversity-vegan.R 210s > source("diversity-vegan.R", echo=TRUE) 210s 210s > par(mfrow = c(1, 1)) 210s 210s > options(width = 55) 210s 210s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 210s 210s > options(SweaveHooks = list(fig = figset)) 210s 210s > options(prompt = "> ", continue = " ") 210s 210s > library(vegan) 210s Loading required package: permute 210s Loading required package: lattice 211s 211s > data(BCI) 211s 211s > H <- diversity(BCI) 211s 211s > J <- H/log(specnumber(BCI)) 211s 211s > k <- sample(nrow(BCI), 6) 211s 211s > R <- renyi(BCI[k, ]) 211s 211s > print(plot(R)) 212s 212s > alpha <- fisher.alpha(BCI) 212s 212s > quantile(rowSums(BCI)) 212s 0% 25% 50% 75% 100% 212s 340.0 409.0 428.0 443.5 601.0 212s 212s > Srar <- rarefy(BCI, min(rowSums(BCI))) 212s 212s > S2 <- rarefy(BCI, 2) 212s 212s > all(rank(Srar) == rank(S2)) 212s [1] FALSE 212s 212s > range(diversity(BCI, "simp") - (S2 - 1)) 212s [1] -0.002868298 -0.001330663 212s 212s > data(dune) 212s 212s > data(dune.taxon) 212s 212s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 212s 212s > mod <- taxondive(dune, taxdis) 212s 212s > plot(mod) 212s 212s > tr <- hclust(taxdis, "aver") 212s 212s > mod <- treedive(dune, tr) 212s 212s > k <- sample(nrow(BCI), 1) 212s 212s > fish <- fisherfit(BCI[k, ]) 212s 212s > fish 212s 212s Fisher log series model 212s No. of species: 86 212s Fisher alpha: 35.54363 212s 212s 212s > plot(fish) 212s 212s > prestondistr(BCI[k, ]) 212s 212s Preston lognormal model 212s Method: maximized likelihood to log2 abundances 212s No. of species: 86 212s 212s mode width S0 212s 0.7090315 1.7052549 23.8984091 212s 212s Frequencies by Octave 212s 0 1 2 3 4 212s Observed 18.50000 26.00000 18.50000 14.500000 6.000000 212s Fitted 21.91936 23.55303 17.94385 9.692462 3.711953 212s 5 6 212s Observed 0.500000 2.0000000 212s Fitted 1.007908 0.1940389 212s 212s 212s > rad <- radfit(BCI[k, ]) 212s forced matching of 'tree' labels and 'comm' names 212s 212s > rad 212s 212s RAD models, family poisson 212s No. of species 86, total abundance 364 212s 212s par1 par2 par3 Deviance 212s Null 117.880 212s Preemption 0.052888 124.438 212s Lognormal 0.68438 1.2574 36.783 212s Zipf 0.173 -0.93219 15.446 212s Mandelbrot 0.24126 -1.0276 0.52084 13.861 212s AIC BIC 212s Null 355.738 355.738 212s Preemption 364.295 366.750 212s Lognormal 278.640 283.549 212s Zipf 257.303 262.212 212s Mandelbrot 257.718 265.081 212s 212s > print(radlattice(rad)) 212s 212s > sac <- specaccum(BCI) 212s 212s > plot(sac, ci.type = "polygon", ci.col = "yellow") 212s 212s > sac <- specaccum(BCI) 212s 212s > plot(sac, ci.type = "polygon", ci.col = "yellow") 212s 212s > ncol(BCI)/mean(specnumber(BCI)) - 1 212s [1] 1.478519 212s 212s > beta <- vegdist(BCI, binary = TRUE) 212s 212s > mean(beta) 212s [1] 0.3399075 212s 212s > betadiver(help = TRUE) 212s 1 "w" = (b+c)/(2*a+b+c) 212s 2 "-1" = (b+c)/(2*a+b+c) 212s 3 "c" = (b+c)/2 212s 4 "wb" = b+c 212s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 212s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 212s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 212s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 212s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 212s (2*a+b+c))-1 212s 8 "t" = (b+c)/(2*a+b+c) 212s 9 "me" = (b+c)/(2*a+b+c) 212s 10 "j" = a/(a+b+c) 212s 11 "sor" = 2*a/(2*a+b+c) 212s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 212s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 212s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 212s 15 "cc" = (b+c)/(a+b+c) 212s 16 "g" = (b+c)/(a+b+c) 212s 17 "-3" = pmin.int(b,c)/(a+b+c) 212s 18 "l" = (b+c)/2 212s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 212s 20 "hk" = (b+c)/(2*a+b+c) 212s 21 "rlb" = a/(a+c) 212s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 212s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 212s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 212s 212s > z <- betadiver(BCI, "z") 212s 212s > quantile(z) 212s 0% 25% 50% 75% 100% 212s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 212s 212s > data(dune) 212s 212s > data(dune.env) 212s 212s > z <- betadiver(dune, "z") 212s 212s > mod <- with(dune.env, betadisper(z, Management)) 212s 212s > mod 212s 212s Homogeneity of multivariate dispersions 212s 212s Call: betadisper(d = z, group = Management) 212s 212s No. of Positive Eigenvalues: 12 212s No. of Negative Eigenvalues: 7 212s 212s Average distance to median: 212s BF HF NM SF 212s 0.2532 0.2512 0.4406 0.3635 212s 212s Eigenvalues for PCoA axes: 212s (Showing 8 of 19 eigenvalues) 212s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 212s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 212s PCoA7 PCoA8 212s 0.16128 0.08099 212s 212s > boxplot(mod) 212s 212s > specpool(BCI) 212s Species chao chao.se jack1 jack1.se jack2 212s All 225 236.3732 6.54361 245.58 5.650522 247.8722 212s boot boot.se n 212s All 235.6862 3.468888 50 212s 212s > s <- sample(nrow(BCI), 25) 212s 212s > specpool(BCI[s, ]) 212s Species chao chao.se jack1 jack1.se jack2 212s All 205 235.752 14.69087 234.76 8.299976 250.055 212s boot boot.se n 212s All 218.447 4.380098 25 212s 212s > estimateR(BCI[k, ]) 212s 29 212s S.obs 86.00000 212s S.chao1 127.62500 212s se.chao1 18.31906 212s S.ACE 127.05647 212s se.ACE 5.85267 212s 212s > veiledspec(prestondistr(BCI[k, ])) 212s Extrapolated Observed Veiled 212s 102.15232 86.00000 16.15232 212s 212s > veiledspec(BCI[k, ]) 212s Extrapolated Observed Veiled 212s 108.8758 86.0000 22.8758 212s 212s > smo <- beals(BCI) 212s 212s > j <- which(colnames(BCI) == "Ceiba.pentandra") 212s 212s > plot(beals(BCI, species = j, include = FALSE), BCI[, 212s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 212s 212s > j <- which(colnames(BCI) == "Ceiba.pentandra") 212s 212s > plot(beals(BCI, species = j, include = FALSE), BCI[, 212s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 212s > 212s Warning messages: 212s 1: In cor(x > 0) : the standard deviation is zero 212s 2: In cor(x > 0) : the standard deviation is zero 212s 3: In betadisper(z, Management) : 212s some squared distances are negative and changed to zero 212s 212s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 212s Copyright (C) 2024 The R Foundation for Statistical Computing 212s Platform: aarch64-unknown-linux-gnu 212s 212s R is free software and comes with ABSOLUTELY NO WARRANTY. 212s You are welcome to redistribute it under certain conditions. 212s Type 'license()' or 'licence()' for distribution details. 212s 212s R is a collaborative project with many contributors. 212s Type 'contributors()' for more information and 212s 'citation()' on how to cite R or R packages in publications. 212s 212s Type 'demo()' for some demos, 'help()' for on-line help, or 212s 'help.start()' for an HTML browser interface to help. 212s Type 'q()' to quit R. 212s 212s > Stangle("intro-vegan.Rnw") 213s Writing to file intro-vegan.R 213s > source("intro-vegan.R", echo=TRUE) 213s 213s > par(mfrow = c(1, 1)) 213s 213s > options(width = 72) 213s 213s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 213s 213s > options(SweaveHooks = list(fig = figset)) 213s 213s > options(prompt = "> ", continue = " ") 213s 213s > library(vegan) 213s Loading required package: permute 213s Loading required package: lattice 214s 214s > data(dune) 214s 214s > ord <- decorana(dune) 214s 214s > ord 214s 214s Call: 214s decorana(veg = dune) 214s 214s Detrended correspondence analysis with 26 segments. 214s Rescaling of axes with 4 iterations. 214s Total inertia (scaled Chi-square): 2.1153 214s 214s DCA1 DCA2 DCA3 DCA4 214s Eigenvalues 0.5117 0.3036 0.12125 0.14267 214s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 214s Decorana values 0.5360 0.2869 0.08136 0.04814 214s Axis lengths 3.7004 3.1166 1.30055 1.47888 214s 214s 214s > ord <- metaMDS(dune, trace = FALSE) 214s 214s > ord 214s 214s Call: 214s metaMDS(comm = dune, trace = FALSE) 214s 214s global Multidimensional Scaling using monoMDS 214s 214s Data: dune 214s Distance: bray 214s 214s Dimensions: 2 214s Stress: 0.1183186 214s Stress type 1, weak ties 214s Best solution was repeated 4 times in 20 tries 214s The best solution was from try 15 (random start) 214s Scaling: centring, PC rotation, halfchange scaling 214s Species: expanded scores based on ‘dune’ 214s 214s 214s > plot(ord) 214s 214s > plot(ord) 214s 214s > plot(ord, type = "n") 214s 214s > points(ord, display = "sites", cex = 0.8, pch = 21, 214s + col = "red", bg = "yellow") 214s 214s > text(ord, display = "species", cex = 0.7, col = "blue") 214s 214s > plot(ord, type = "n") 214s 214s > points(ord, display = "sites", cex = 0.8, pch = 21, 214s + col = "red", bg = "yellow") 214s 214s > text(ord, display = "species", cex = 0.7, col = "blue") 214s 214s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 214s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 214s + col = "blue") 214s 214s > data(dune.env) 214s 214s > attach(dune.env) 214s 214s > plot(ord, disp = "sites", type = "n") 214s 214s > ordihull(ord, Management, col = 1:4, lwd = 3) 214s 214s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 214s + lwd = 3) 214s 214s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 214s 214s > ordispider(ord, Management, col = 1:4, label = TRUE) 214s 214s > points(ord, disp = "sites", pch = 21, col = "red", 214s + bg = "yellow", cex = 1.3) 214s 214s > plot(ord, disp = "sites", type = "n") 214s 214s > ordihull(ord, Management, col = 1:4, lwd = 3) 214s 214s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 214s + lwd = 3) 214s 214s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 214s 214s > ordispider(ord, Management, col = 1:4, label = TRUE) 214s 214s > points(ord, disp = "sites", pch = 21, col = "red", 214s + bg = "yellow", cex = 1.3) 214s 214s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 214s + perm = 999) 214s 214s > ord.fit 214s 214s ***VECTORS 214s 214s NMDS1 NMDS2 r2 Pr(>r) 214s A1 0.96474 0.26322 0.3649 0.021 * 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s Permutation: free 214s Number of permutations: 999 214s 214s ***FACTORS: 214s 214s Centroids: 214s NMDS1 NMDS2 214s ManagementBF -0.4534 -0.0102 214s ManagementHF -0.2636 -0.1282 214s ManagementNM 0.2958 0.5790 214s ManagementSF 0.1506 -0.4670 214s 214s Goodness of fit: 214s r2 Pr(>r) 214s Management 0.4134 0.008 ** 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s Permutation: free 214s Number of permutations: 999 214s 214s 214s 214s > plot(ord, dis = "site") 214s 214s > plot(ord.fit) 214s 214s > ordisurf(ord, A1, add = TRUE) 214s 214s Family: gaussian 214s Link function: identity 214s 214s Formula: 214s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 214s 214s Estimated degrees of freedom: 214s 1.59 total = 2.59 214s 214s REML score: 41.58728 214s 214s > plot(ord, dis = "site") 214s 214s > plot(ord.fit) 214s 214s > ordisurf(ord, A1, add = TRUE) 214s 214s Family: gaussian 214s Link function: identity 214s 214s Formula: 214s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 214s 214s Estimated degrees of freedom: 214s 1.59 total = 2.59 214s 214s REML score: 41.58728 214s 214s > ord <- cca(dune ~ A1 + Management, data = dune.env) 214s 214s > ord 214s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 214s 214s -- Model Summary -- 214s 214s Inertia Proportion Rank 214s Total 2.1153 1.0000 214s Constrained 0.7798 0.3686 4 214s Unconstrained 1.3355 0.6314 15 214s 214s Inertia is scaled Chi-square 214s 214s -- Eigenvalues -- 214s 214s Eigenvalues for constrained axes: 214s CCA1 CCA2 CCA3 CCA4 214s 0.3187 0.2372 0.1322 0.0917 214s 214s Eigenvalues for unconstrained axes: 214s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 214s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 214s CA11 CA12 CA13 CA14 CA15 214s 0.0317 0.0178 0.0116 0.0087 0.0047 214s 214s 214s > plot(ord) 214s 214s > plot(ord) 214s 214s > cca(dune ~ ., data = dune.env) 214s 214s Some constraints or conditions were aliased because they were 214s redundant. This can happen if terms are linearly dependent (collinear): 214s ‘Manure^4’ 214s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 214s Manure, data = dune.env) 214s 214s -- Model Summary -- 214s 214s Inertia Proportion Rank 214s Total 2.1153 1.0000 214s Constrained 1.5032 0.7106 12 214s Unconstrained 0.6121 0.2894 7 214s 214s Inertia is scaled Chi-square 214s 214s -- Note -- 214s 214s Some constraints or conditions were aliased because they were 214s redundant. This can happen if terms are linearly dependent 214s (collinear): ‘Manure^4’ 214s 214s -- Eigenvalues -- 214s 214s Eigenvalues for constrained axes: 214s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 214s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 214s CCA11 CCA12 214s 0.0228 0.0108 214s 214s Eigenvalues for unconstrained axes: 214s CA1 CA2 CA3 CA4 CA5 CA6 CA7 214s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 214s 214s 214s > anova(ord) 214s Permutation test for cca under reduced model 214s Permutation: free 214s Number of permutations: 999 214s 214s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 214s Df ChiSquare F Pr(>F) 214s Model 4 0.77978 2.1896 0.001 *** 214s Residual 15 1.33549 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > anova(ord, by = "term", permutations = 199) 214s Permutation test for cca under reduced model 214s Terms added sequentially (first to last) 214s Permutation: free 214s Number of permutations: 199 214s 214s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 214s Df ChiSquare F Pr(>F) 214s A1 1 0.22476 2.5245 0.020 * 214s Management 3 0.55502 2.0780 0.005 ** 214s Residual 15 1.33549 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > anova(ord, by = "mar", permutations = 199) 214s Permutation test for cca under reduced model 214s Marginal effects of terms 214s Permutation: free 214s Number of permutations: 199 214s 214s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 214s Df ChiSquare F Pr(>F) 214s A1 1 0.17594 1.9761 0.040 * 214s Management 3 0.55502 2.0780 0.005 ** 214s Residual 15 1.33549 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > anova(ord, by = "axis", permutations = 499) 214s Permutation test for cca under reduced model 214s Forward tests for axes 214s Permutation: free 214s Number of permutations: 499 214s 214s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 214s Df ChiSquare F Pr(>F) 214s CCA1 1 0.31875 3.5801 0.028 * 214s CCA2 1 0.23718 2.6640 0.144 214s CCA3 1 0.13217 1.4845 0.852 214s CCA4 1 0.09168 1.0297 1.000 214s Residual 15 1.33549 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 214s + data = dune.env) 214s 214s > ord 214s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 214s data = dune.env) 214s 214s -- Model Summary -- 214s 214s Inertia Proportion Rank 214s Total 2.1153 1.0000 214s Conditional 0.6283 0.2970 3 214s Constrained 0.5109 0.2415 4 214s Unconstrained 0.9761 0.4615 12 214s 214s Inertia is scaled Chi-square 214s 214s -- Eigenvalues -- 214s 214s Eigenvalues for constrained axes: 214s CCA1 CCA2 CCA3 CCA4 214s 0.24932 0.12090 0.08160 0.05904 214s 214s Eigenvalues for unconstrained axes: 214s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 214s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 214s CA10 CA11 CA12 214s 0.02102 0.01254 0.00928 214s 214s 214s > anova(ord, by = "term", permutations = 499) 214s Permutation test for cca under reduced model 214s Terms added sequentially (first to last) 214s Permutation: free 214s Number of permutations: 499 214s 214s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 214s Df ChiSquare F Pr(>F) 214s A1 1 0.11543 1.4190 1.000 214s Management 3 0.39543 1.6205 0.002 ** 214s Residual 12 0.97610 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 214s 214s > anova(ord, by = "term", permutations = how) 214s Permutation test for cca under reduced model 214s Terms added sequentially (first to last) 214s Plots: dune.env$Moisture, plot permutation: none 214s Permutation: free 214s Number of permutations: 499 214s 214s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 214s Df ChiSquare F Pr(>F) 214s A1 1 0.11543 1.4190 1.000 214s Management 3 0.39543 1.6205 0.002 ** 214s Residual 12 0.97610 214s --- 214s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 214s 214s > detach(dune.env) 214s > 214s 214s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 214s Copyright (C) 2024 The R Foundation for Statistical Computing 214s Platform: aarch64-unknown-linux-gnu 214s 214s R is free software and comes with ABSOLUTELY NO WARRANTY. 214s You are welcome to redistribute it under certain conditions. 214s Type 'license()' or 'licence()' for distribution details. 214s 214s R is a collaborative project with many contributors. 214s Type 'contributors()' for more information and 214s 'citation()' on how to cite R or R packages in publications. 214s 214s Type 'demo()' for some demos, 'help()' for on-line help, or 214s 'help.start()' for an HTML browser interface to help. 214s Type 'q()' to quit R. 214s 215s > Stangle("partitioning.Rnw") 215s Writing to file partitioning.R 215s > source("partitioning.R", echo=TRUE) 215s 215s > par(mfrow = c(1, 1)) 215s 215s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 215s 215s > options(SweaveHooks = list(fig = figset)) 215s 215s > library(vegan) 215s Loading required package: permute 215s Loading required package: lattice 216s 216s > labs <- paste("Table", 1:4) 216s 216s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 216s 216s > showvarparts(2, bg = cls, Xnames = labs) 216s 216s > showvarparts(3, bg = cls, Xnames = labs) 216s 216s > showvarparts(4, bg = cls, Xnames = labs) 216s > 223s --- cca-object-tests.Rout.save_ 2025-02-19 04:21:02.316828139 +0000 223s +++ cca-object-tests.Rout_ 2025-02-19 04:21:02.319828298 +0000 223s @@ -1,4 +1,4 @@ 223s - 223s + 223s 223s R is free software and comes with ABSOLUTELY NO WARRANTY. 223s You are welcome to redistribute it under certain conditions. 223s autopkgtest [04:21:02]: test run-unit-test: -----------------------] 224s autopkgtest [04:21:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 224s run-unit-test FAIL non-zero exit status 1 224s autopkgtest [04:21:03]: test pkg-r-autopkgtest: preparing testbed 224s Reading package lists... 225s Building dependency tree... 225s Reading state information... 225s Starting pkgProblemResolver with broken count: 0 225s Starting 2 pkgProblemResolver with broken count: 0 225s Done 226s The following NEW packages will be installed: 226s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 226s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 226s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 226s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 226s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 226s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 226s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 226s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 226s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 226s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 226s zlib1g-dev 226s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 226s Need to get 92.6 MB of archives. 226s After this operation, 334 MB of additional disk space will be used. 226s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [10.6 MB] 227s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu1 [1032 B] 227s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 227s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 227s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250213-1ubuntu1 [44.2 kB] 227s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250213-1ubuntu1 [28.0 kB] 227s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250213-1ubuntu1 [2928 kB] 228s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250213-1ubuntu1 [1319 kB] 228s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250213-1ubuntu1 [2695 kB] 228s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250213-1ubuntu1 [1178 kB] 228s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250213-1ubuntu1 [1642 kB] 228s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu1 [2593 kB] 228s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [20.9 MB] 229s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu1 [526 kB] 229s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 229s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 229s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu1 [2499 kB] 229s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [12.1 MB] 230s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu1 [21.8 kB] 230s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 230s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 230s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 230s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 230s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu1 [498 kB] 230s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu1 [11.4 MB] 230s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu1 [13.6 kB] 230s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 230s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 230s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 230s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 230s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 230s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 230s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 231s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 231s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 231s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 231s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 231s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250125-2 [388 kB] 231s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.42-4ubuntu3 [200 kB] 231s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.42-4ubuntu3 [187 kB] 231s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.42-4ubuntu3 [6704 B] 231s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.42-4ubuntu3 [694 kB] 231s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 231s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 231s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.46-4 [275 kB] 231s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 231s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.3-1 [180 kB] 231s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 231s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 231s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 231s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.2-1build1 [4342 B] 231s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 232s Fetched 92.6 MB in 5s (17.3 MB/s) 232s Selecting previously unselected package libisl23:arm64. 232s (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 ... 124593 files and directories currently installed.) 232s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 232s Unpacking libisl23:arm64 (0.27-1) ... 232s Selecting previously unselected package libmpc3:arm64. 232s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 232s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 232s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 232s Preparing to unpack .../02-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 232s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 232s Selecting previously unselected package cpp-14. 232s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu1_arm64.deb ... 232s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 232s Selecting previously unselected package cpp-aarch64-linux-gnu. 232s Preparing to unpack .../04-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 232s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Selecting previously unselected package cpp. 232s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 232s Unpacking cpp (4:14.2.0-1ubuntu1) ... 232s Selecting previously unselected package libcc1-0:arm64. 233s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libcc1-0:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libitm1:arm64. 233s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libitm1:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libasan8:arm64. 233s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libasan8:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package liblsan0:arm64. 233s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking liblsan0:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libtsan2:arm64. 233s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libtsan2:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libubsan1:arm64. 233s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libubsan1:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libhwasan0:arm64. 233s Preparing to unpack .../12-libhwasan0_15-20250213-1ubuntu1_arm64.deb ... 233s Unpacking libhwasan0:arm64 (15-20250213-1ubuntu1) ... 233s Selecting previously unselected package libgcc-14-dev:arm64. 233s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu1_arm64.deb ... 233s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 233s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 233s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 233s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package gcc-14. 234s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package gcc-aarch64-linux-gnu. 234s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 234s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 234s Selecting previously unselected package gcc. 234s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 234s Unpacking gcc (4:14.2.0-1ubuntu1) ... 234s Selecting previously unselected package libstdc++-14-dev:arm64. 234s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package g++-14-aarch64-linux-gnu. 234s Preparing to unpack .../19-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package g++-14. 234s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking g++-14 (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package g++-aarch64-linux-gnu. 234s Preparing to unpack .../21-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 234s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 234s Selecting previously unselected package g++. 234s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 234s Unpacking g++ (4:14.2.0-1ubuntu1) ... 234s Selecting previously unselected package build-essential. 234s Preparing to unpack .../23-build-essential_12.10ubuntu1_arm64.deb ... 234s Unpacking build-essential (12.10ubuntu1) ... 234s Selecting previously unselected package dctrl-tools. 234s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 234s Unpacking dctrl-tools (2.24-3build3) ... 234s Selecting previously unselected package libgfortran-14-dev:arm64. 234s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu1) ... 234s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 234s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu1_arm64.deb ... 234s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 235s Selecting previously unselected package gfortran-14. 235s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu1_arm64.deb ... 235s Unpacking gfortran-14 (14.2.0-17ubuntu1) ... 235s Selecting previously unselected package gfortran-aarch64-linux-gnu. 235s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 235s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 235s Selecting previously unselected package gfortran. 235s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 235s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 235s Selecting previously unselected package icu-devtools. 235s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 235s Unpacking icu-devtools (76.1-1ubuntu2) ... 235s Selecting previously unselected package libblas-dev:arm64. 235s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 235s Unpacking libblas-dev:arm64 (3.12.1-2) ... 235s Selecting previously unselected package libbz2-dev:arm64. 235s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 235s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 235s Selecting previously unselected package libdeflate-dev:arm64. 235s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 235s Unpacking libdeflate-dev:arm64 (1.23-1) ... 235s Selecting previously unselected package libicu-dev:arm64. 235s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 235s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 235s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 235s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 235s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 235s Selecting previously unselected package libjpeg8-dev:arm64. 235s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 235s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 235s Selecting previously unselected package libjpeg-dev:arm64. 235s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 235s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 235s Selecting previously unselected package liblapack-dev:arm64. 235s Preparing to unpack .../38-liblapack-dev_3.12.1-2_arm64.deb ... 235s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 236s Selecting previously unselected package libncurses-dev:arm64. 236s Preparing to unpack .../39-libncurses-dev_6.5+20250125-2_arm64.deb ... 236s Unpacking libncurses-dev:arm64 (6.5+20250125-2) ... 236s Selecting previously unselected package libpcre2-16-0:arm64. 236s Preparing to unpack .../40-libpcre2-16-0_10.42-4ubuntu3_arm64.deb ... 236s Unpacking libpcre2-16-0:arm64 (10.42-4ubuntu3) ... 236s Selecting previously unselected package libpcre2-32-0:arm64. 236s Preparing to unpack .../41-libpcre2-32-0_10.42-4ubuntu3_arm64.deb ... 236s Unpacking libpcre2-32-0:arm64 (10.42-4ubuntu3) ... 236s Selecting previously unselected package libpcre2-posix3:arm64. 236s Preparing to unpack .../42-libpcre2-posix3_10.42-4ubuntu3_arm64.deb ... 236s Unpacking libpcre2-posix3:arm64 (10.42-4ubuntu3) ... 236s Selecting previously unselected package libpcre2-dev:arm64. 236s Preparing to unpack .../43-libpcre2-dev_10.42-4ubuntu3_arm64.deb ... 236s Unpacking libpcre2-dev:arm64 (10.42-4ubuntu3) ... 236s Selecting previously unselected package libpkgconf3:arm64. 236s Preparing to unpack .../44-libpkgconf3_1.8.1-4_arm64.deb ... 236s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 236s Selecting previously unselected package zlib1g-dev:arm64. 236s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 236s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 236s Selecting previously unselected package libpng-dev:arm64. 236s Preparing to unpack .../46-libpng-dev_1.6.46-4_arm64.deb ... 236s Unpacking libpng-dev:arm64 (1.6.46-4) ... 236s Selecting previously unselected package libreadline-dev:arm64. 236s Preparing to unpack .../47-libreadline-dev_8.2-6_arm64.deb ... 236s Unpacking libreadline-dev:arm64 (8.2-6) ... 236s Selecting previously unselected package liblzma-dev:arm64. 236s Preparing to unpack .../48-liblzma-dev_5.6.3-1_arm64.deb ... 236s Unpacking liblzma-dev:arm64 (5.6.3-1) ... 236s Selecting previously unselected package pkgconf-bin. 236s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_arm64.deb ... 236s Unpacking pkgconf-bin (1.8.1-4) ... 236s Selecting previously unselected package pkgconf:arm64. 236s Preparing to unpack .../50-pkgconf_1.8.1-4_arm64.deb ... 236s Unpacking pkgconf:arm64 (1.8.1-4) ... 236s Selecting previously unselected package libtirpc-dev:arm64. 236s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 236s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 236s Selecting previously unselected package r-base-dev. 236s Preparing to unpack .../52-r-base-dev_4.4.2-1build1_all.deb ... 236s Unpacking r-base-dev (4.4.2-1build1) ... 236s Selecting previously unselected package pkg-r-autopkgtest. 236s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 236s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 236s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 236s Setting up libncurses-dev:arm64 (6.5+20250125-2) ... 236s Setting up libreadline-dev:arm64 (8.2-6) ... 236s Setting up libpcre2-16-0:arm64 (10.42-4ubuntu3) ... 236s Setting up libpcre2-32-0:arm64 (10.42-4ubuntu3) ... 236s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 236s Setting up libpkgconf3:arm64 (1.8.1-4) ... 236s Setting up libmpc3:arm64 (1.3.1-1build2) ... 236s Setting up icu-devtools (76.1-1ubuntu2) ... 236s Setting up pkgconf-bin (1.8.1-4) ... 236s Setting up liblzma-dev:arm64 (5.6.3-1) ... 236s Setting up libubsan1:arm64 (15-20250213-1ubuntu1) ... 236s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 236s Setting up libpcre2-posix3:arm64 (10.42-4ubuntu3) ... 236s Setting up libhwasan0:arm64 (15-20250213-1ubuntu1) ... 236s Setting up libasan8:arm64 (15-20250213-1ubuntu1) ... 236s Setting up libtsan2:arm64 (15-20250213-1ubuntu1) ... 236s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 236s Setting up libisl23:arm64 (0.27-1) ... 236s Setting up libdeflate-dev:arm64 (1.23-1) ... 236s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 236s Setting up libcc1-0:arm64 (15-20250213-1ubuntu1) ... 236s Setting up liblsan0:arm64 (15-20250213-1ubuntu1) ... 236s Setting up libblas-dev:arm64 (3.12.1-2) ... 236s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 236s Setting up dctrl-tools (2.24-3build3) ... 236s Setting up libitm1:arm64 (15-20250213-1ubuntu1) ... 236s Setting up libbz2-dev:arm64 (1.0.8-6) ... 236s Setting up libpcre2-dev:arm64 (10.42-4ubuntu3) ... 236s Setting up libpng-dev:arm64 (1.6.46-4) ... 236s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 236s Setting up pkgconf:arm64 (1.8.1-4) ... 236s Setting up liblapack-dev:arm64 (3.12.1-2) ... 236s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 236s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 236s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu1) ... 236s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu1) ... 236s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu1) ... 236s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 236s Setting up cpp-14 (14.2.0-17ubuntu1) ... 236s Setting up cpp (4:14.2.0-1ubuntu1) ... 236s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 236s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 236s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 236s Setting up gcc-14 (14.2.0-17ubuntu1) ... 236s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu1) ... 236s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 236s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 236s Setting up g++-14 (14.2.0-17ubuntu1) ... 236s Setting up gfortran-14 (14.2.0-17ubuntu1) ... 236s Setting up gcc (4:14.2.0-1ubuntu1) ... 236s Setting up g++ (4:14.2.0-1ubuntu1) ... 236s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 236s Setting up build-essential (12.10ubuntu1) ... 236s Setting up gfortran (4:14.2.0-1ubuntu1) ... 236s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 236s 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 236s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 236s 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 236s Setting up r-base-dev (4.4.2-1build1) ... 236s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 236s Processing triggers for libc-bin (2.40-4ubuntu1) ... 237s Processing triggers for man-db (2.13.0-1) ... 238s Processing triggers for install-info (7.1.1-1) ... 239s autopkgtest [04:21:18]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 239s autopkgtest [04:21:18]: test pkg-r-autopkgtest: [----------------------- 239s Test: Try to load the R library vegan 239s 239s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 239s Copyright (C) 2024 The R Foundation for Statistical Computing 239s Platform: aarch64-unknown-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > library('vegan') 239s Loading required package: permute 239s Loading required package: lattice 240s > 240s > 240s Other tests are currently unsupported! 240s They will be progressively added. 240s autopkgtest [04:21:19]: test pkg-r-autopkgtest: -----------------------] 241s pkg-r-autopkgtest PASS 241s autopkgtest [04:21:20]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 241s autopkgtest [04:21:20]: @@@@@@@@@@@@@@@@@@@@ summary 241s run-unit-test FAIL non-zero exit status 1 241s pkg-r-autopkgtest PASS 274s nova [W] Using flock in prodstack6-arm64 274s flock: timeout while waiting to get lock 274s Creating nova instance adt-plucky-arm64-r-cran-vegan-20250219-041719-juju-7f2275-prod-proposed-migration-environment-2-4e4e75ab-93ff-4545-9eea-9359f3d4649c from image adt/ubuntu-plucky-arm64-server-20250218.img (UUID db1e3557-ca0b-4978-8424-9ef955671030)... 274s nova [W] Timed out waiting for 8279d745-9136-433e-a01c-3c0087d6d460 to get deleted.