0s autopkgtest [23:05:06]: starting date and time: 2026-02-09 23:05:06+0000 0s autopkgtest [23:05:06]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [23:05:06]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gks9wkxp/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- lxd -r lxd-armhf-10.145.243.221 lxd-armhf-10.145.243.221:autopkgtest/ubuntu/resolute/armhf 26s autopkgtest [23:05:32]: testbed dpkg architecture: armhf 28s autopkgtest [23:05:34]: testbed apt version: 3.1.15 32s autopkgtest [23:05:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 34s autopkgtest [23:05:40]: testbed release detected to be: None 41s autopkgtest [23:05:47]: updating testbed package index (apt update) 43s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 43s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 44s Get:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease [124 kB] 44s Get:4 http://ftpmaster.internal/ubuntu resolute-security InRelease [124 kB] 44s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 44s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [246 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1405 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [7452 B] 50s Get:11 http://ftpmaster.internal/ubuntu resolute/main Sources [1398 kB] 52s Get:12 http://ftpmaster.internal/ubuntu resolute/restricted Sources [15.1 kB] 52s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.4 MB] 84s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 113s Fetched 43.5 MB in 1min 9s (626 kB/s) 114s Reading package lists... 120s autopkgtest [23:07:06]: upgrading testbed (apt dist-upgrade and autopurge) 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Calculating upgrade... 124s The following packages will be upgraded: 124s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 124s libip6tc2 libxtables12 wget 124s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Need to get 2407 kB of archives. 124s After this operation, 152 kB of additional disk space will be used. 124s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf iptables armhf 1.8.11-2ubuntu3 [345 kB] 125s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libip4tc2 armhf 1.8.11-2ubuntu3 [22.0 kB] 125s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libip6tc2 armhf 1.8.11-2ubuntu3 [22.3 kB] 125s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libxtables12 armhf 1.8.11-2ubuntu3 [33.5 kB] 125s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf iproute2 armhf 6.18.0-1ubuntu1 [1123 kB] 127s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libcryptsetup12 armhf 2:2.8.0-1ubuntu3 [254 kB] 127s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf wget armhf 1.25.0-2ubuntu4 [327 kB] 128s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cryptsetup-bin armhf 2:2.8.0-1ubuntu3 [232 kB] 128s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf dracut-install armhf 109-11ubuntu1 [47.9 kB] 129s Preconfiguring packages ... 129s Fetched 2407 kB in 4s (572 kB/s) 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 68683 files and directories currently installed.) 129s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_armhf.deb ... 129s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_armhf.deb ... 129s Unpacking libip4tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_armhf.deb ... 129s Unpacking libip6tc2:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_armhf.deb ... 129s Unpacking libxtables12:armhf (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 129s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_armhf.deb ... 129s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 130s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_armhf.deb ... 130s Unpacking libcryptsetup12:armhf (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 130s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_armhf.deb ... 130s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 130s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_armhf.deb ... 130s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 130s Preparing to unpack .../8-dracut-install_109-11ubuntu1_armhf.deb ... 130s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 130s Setting up libip4tc2:armhf (1.8.11-2ubuntu3) ... 130s Setting up wget (1.25.0-2ubuntu4) ... 130s Setting up libip6tc2:armhf (1.8.11-2ubuntu3) ... 130s Setting up libxtables12:armhf (1.8.11-2ubuntu3) ... 130s Setting up dracut-install (109-11ubuntu1) ... 130s Setting up libcryptsetup12:armhf (2:2.8.0-1ubuntu3) ... 130s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 130s Setting up iptables (1.8.11-2ubuntu3) ... 130s Setting up iproute2 (6.18.0-1ubuntu1) ... 130s Processing triggers for man-db (2.13.1-1build1) ... 131s Processing triggers for install-info (7.2-5) ... 132s Processing triggers for libc-bin (2.42-2ubuntu4) ... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Solving dependencies... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s autopkgtest [23:07:24]: rebooting testbed after setup commands that affected boot 180s autopkgtest [23:08:06]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 205s autopkgtest [23:08:31]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 217s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (dsc) [2211 B] 217s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (tar) [1207 kB] 217s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (diff) [6396 B] 218s gpgv: Signature made Sat Apr 19 05:22:19 2025 UTC 218s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 218s gpgv: issuer "tille@debian.org" 218s gpgv: Can't check signature: No public key 218s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-3.dsc: no acceptable signature found 218s autopkgtest [23:08:44]: testing package r-cran-vegan version 2.6-10+dfsg-3 220s autopkgtest [23:08:46]: build not needed 223s autopkgtest [23:08:49]: test run-unit-test: preparing testbed 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 226s Solving dependencies... 227s The following NEW packages will be installed: 227s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 227s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 227s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 227s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 227s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 227s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 227s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 227s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 227s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 227s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 227s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 227s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 227s x11-common xdg-utils zip 227s 0 upgraded, 68 newly installed, 0 to remove and 0 not upgraded. 227s Need to get 65.5 MB of archives. 227s After this operation, 149 MB of additional disk space will be used. 227s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libfreetype6 armhf 2.14.1+dfsg-2 [345 kB] 228s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-mono all 2.37-8build1 [502 kB] 229s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-dejavu-core all 2.37-8build1 [834 kB] 230s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig-config armhf 2.17.1-3ubuntu1 [38.5 kB] 230s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libfontconfig1 armhf 2.17.1-3ubuntu1 [117 kB] 230s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf fontconfig armhf 2.17.1-3ubuntu1 [180 kB] 230s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 230s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 233s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7ubuntu1 [133 kB] 234s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libpixman-1-0 armhf 0.46.4-1 [196 kB] 234s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-render0 armhf 1.17.0-2ubuntu1 [15.5 kB] 234s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libxcb-shm0 armhf 1.17.0-2ubuntu1 [5956 B] 234s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libxrender1 armhf 1:0.9.12-1 [16.6 kB] 234s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libcairo2 armhf 1.18.4-3 [489 kB] 235s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libdatrie1 armhf 0.2.14-1 [16.4 kB] 235s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2build1 [38.8 kB] 235s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-12ubuntu1 [334 kB] 235s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 235s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libgraphite2-3 armhf 1.3.14-11ubuntu1 [65.2 kB] 235s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libharfbuzz0b armhf 12.3.2-1 [501 kB] 236s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf x11-common all 1:7.7+24ubuntu1 [22.4 kB] 236s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libice6 armhf 2:1.1.1-1build1 [37.5 kB] 236s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8 armhf 2.1.5-4ubuntu3 [129 kB] 237s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 237s Get:25 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 237s Get:26 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 237s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 237s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 238s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7ubuntu1 [2090 kB] 240s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu2 [162 kB] 241s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libthai-data all 0.1.30-1 [155 kB] 241s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libthai0 armhf 0.1.30-1 [15.4 kB] 241s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libpango-1.0-0 armhf 1.57.0-1 [218 kB] 241s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libpangoft2-1.0-0 armhf 1.57.0-1 [45.2 kB] 241s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libpangocairo-1.0-0 armhf 1.57.0-1 [25.3 kB] 241s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper2 armhf 2.2.5-0.3build1 [16.3 kB] 241s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libpaper-utils armhf 2.2.5-0.3build1 [14.2 kB] 241s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libsharpyuv0 armhf 1.5.0-0.1build1 [16.3 kB] 241s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libsm6 armhf 2:1.2.6-1build1 [15.3 kB] 241s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf libtcl8.6 armhf 8.6.17+dfsg-1build1 [918 kB] 243s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libjbig0 armhf 2.1-6.1ubuntu3 [25.3 kB] 243s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libwebp7 armhf 1.5.0-0.1build1 [189 kB] 243s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libtiff6 armhf 4.7.0-3ubuntu3 [188 kB] 243s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libxft2 armhf 2.3.6-1build2 [37.2 kB] 244s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libxss1 armhf 1:1.2.3-1build4 [6328 B] 244s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libtk8.6 armhf 8.6.17-1 [694 kB] 245s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf libxt6t64 armhf 1:1.2.1-1.3 [145 kB] 245s Get:48 http://ftpmaster.internal/ubuntu resolute/universe armhf node-normalize.css all 8.0.1-5.1 [10.4 kB] 245s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf zip armhf 3.0-15ubuntu3 [164 kB] 245s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf unzip armhf 6.0-29ubuntu1 [167 kB] 245s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 246s Get:52 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-core armhf 4.5.2-1ubuntu2 [28.5 MB] 289s Get:53 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-cluster armhf 2.1.8.2-1 [564 kB] 290s Get:54 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-commonmark armhf 1.9.5-1 [112 kB] 290s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-evaluate all 1.0.5-1 [117 kB] 290s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-xfun armhf 0.55+dfsg-1 [589 kB] 291s Get:57 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-highr all 0.11+dfsg-1 [38.5 kB] 291s Get:58 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-yaml armhf 2.3.10-1 [101 kB] 291s Get:59 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 299s Get:60 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-knitr all 1.51+dfsg-1 [847 kB] 300s Get:61 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf r-cran-lattice armhf 0.22-9-1 [1399 kB] 302s Get:62 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-markdown all 1.13-1 [162 kB] 302s Get:63 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mass armhf 7.3-65-1 [1108 kB] 304s Get:64 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-matrix armhf 1.7-4-1 [4139 kB] 310s Get:65 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 313s Get:66 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-mgcv armhf 1.9-4-1 [3515 kB] 320s Get:67 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-permute all 0.9-8-1 [237 kB] 320s Get:68 http://ftpmaster.internal/ubuntu resolute/universe armhf r-cran-vegan armhf 2.6-10+dfsg-3 [3130 kB] 325s Preconfiguring packages ... 325s Fetched 65.5 MB in 1min 38s (671 kB/s) 325s Selecting previously unselected package libfreetype6:armhf. 325s (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 ... 68686 files and directories currently installed.) 325s Preparing to unpack .../00-libfreetype6_2.14.1+dfsg-2_armhf.deb ... 325s Unpacking libfreetype6:armhf (2.14.1+dfsg-2) ... 325s Selecting previously unselected package fonts-dejavu-mono. 325s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8build1_all.deb ... 325s Unpacking fonts-dejavu-mono (2.37-8build1) ... 325s Selecting previously unselected package fonts-dejavu-core. 325s Preparing to unpack .../02-fonts-dejavu-core_2.37-8build1_all.deb ... 326s Unpacking fonts-dejavu-core (2.37-8build1) ... 326s Selecting previously unselected package fontconfig-config. 326s Preparing to unpack .../03-fontconfig-config_2.17.1-3ubuntu1_armhf.deb ... 326s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 326s Selecting previously unselected package libfontconfig1:armhf. 326s Preparing to unpack .../04-libfontconfig1_2.17.1-3ubuntu1_armhf.deb ... 326s Unpacking libfontconfig1:armhf (2.17.1-3ubuntu1) ... 326s Selecting previously unselected package fontconfig. 326s Preparing to unpack .../05-fontconfig_2.17.1-3ubuntu1_armhf.deb ... 326s Unpacking fontconfig (2.17.1-3ubuntu1) ... 326s Selecting previously unselected package fonts-glyphicons-halflings. 326s Preparing to unpack .../06-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 326s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 326s Selecting previously unselected package fonts-mathjax. 326s Preparing to unpack .../07-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 326s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 326s Selecting previously unselected package libblas3:armhf. 326s Preparing to unpack .../08-libblas3_3.12.1-7ubuntu1_armhf.deb ... 326s Unpacking libblas3:armhf (3.12.1-7ubuntu1) ... 326s Selecting previously unselected package libpixman-1-0:armhf. 326s Preparing to unpack .../09-libpixman-1-0_0.46.4-1_armhf.deb ... 326s Unpacking libpixman-1-0:armhf (0.46.4-1) ... 326s Selecting previously unselected package libxcb-render0:armhf. 326s Preparing to unpack .../10-libxcb-render0_1.17.0-2ubuntu1_armhf.deb ... 326s Unpacking libxcb-render0:armhf (1.17.0-2ubuntu1) ... 327s Selecting previously unselected package libxcb-shm0:armhf. 327s Preparing to unpack .../11-libxcb-shm0_1.17.0-2ubuntu1_armhf.deb ... 327s Unpacking libxcb-shm0:armhf (1.17.0-2ubuntu1) ... 327s Selecting previously unselected package libxrender1:armhf. 327s Preparing to unpack .../12-libxrender1_1%3a0.9.12-1_armhf.deb ... 327s Unpacking libxrender1:armhf (1:0.9.12-1) ... 327s Selecting previously unselected package libcairo2:armhf. 327s Preparing to unpack .../13-libcairo2_1.18.4-3_armhf.deb ... 327s Unpacking libcairo2:armhf (1.18.4-3) ... 327s Selecting previously unselected package libdatrie1:armhf. 327s Preparing to unpack .../14-libdatrie1_0.2.14-1_armhf.deb ... 327s Unpacking libdatrie1:armhf (0.2.14-1) ... 327s Selecting previously unselected package libdeflate0:armhf. 327s Preparing to unpack .../15-libdeflate0_1.23-2build1_armhf.deb ... 327s Unpacking libdeflate0:armhf (1.23-2build1) ... 327s Selecting previously unselected package libgfortran5:armhf. 327s Preparing to unpack .../16-libgfortran5_15.2.0-12ubuntu1_armhf.deb ... 327s Unpacking libgfortran5:armhf (15.2.0-12ubuntu1) ... 327s Selecting previously unselected package libgomp1:armhf. 327s Preparing to unpack .../17-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 327s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 327s Selecting previously 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335s Setting up r-cran-matrix (1.7-4-1) ... 335s Setting up r-cran-knitr (1.51+dfsg-1) ... 335s Setting up r-cran-mgcv (1.9-4-1) ... 335s Setting up r-cran-vegan (2.6-10+dfsg-3) ... 335s Processing triggers for libc-bin (2.42-2ubuntu4) ... 335s Processing triggers for man-db (2.13.1-1build1) ... 336s Processing triggers for install-info (7.2-5) ... 344s autopkgtest [23:10:50]: test run-unit-test: [----------------------- 347s 347s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 347s Copyright (C) 2025 The R Foundation for Statistical Computing 347s Platform: arm-unknown-linux-gnueabihf (32-bit) 347s 347s R is free software and comes with ABSOLUTELY NO WARRANTY. 347s You are welcome to redistribute it under certain conditions. 347s Type 'license()' or 'licence()' for distribution details. 347s 347s R is a collaborative project with many contributors. 347s Type 'contributors()' for more information and 347s 'citation()' on how to cite R or R packages in publications. 347s 347s Type 'demo()' for some demos, 'help()' for on-line help, or 347s 'help.start()' for an HTML browser interface to help. 347s Type 'q()' to quit R. 347s 347s > Stangle("decision-vegan.Rnw") 347s Writing to file decision-vegan.R 347s > source("decision-vegan.R", echo=TRUE) 347s Loading required package: vegan 347s 347s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 347s 347s > options(SweaveHooks = list(fig = figset)) 347s 347s > options(prompt = "> ", continue = " ") 347s 347s > options(width = 55) 347s 347s > require(vegan) 347s Loading required package: permute 347s Loading required package: lattice 348s 348s > data(sipoo) 348s 348s > mod <- nestedtemp(sipoo) 348s 348s > plot(mod, "i") 348s 348s > x <- mod$c["Falcsubb"] 348s 348s > y <- 1 - mod$r["Svartholm"] 348s 348s > points(x, y, pch = 16, cex = 1.5) 348s 348s > abline(x + y, -1, lty = 2) 348s 348s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 348s 348s > cross <- function(x, a, p) f(x, p) - a + x 348s 348s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 348s 348s > arrows(x, y, r, f(r, mod$p), lwd = 4) 348s 348s > library(vegan) 348s 348s > data(varespec) 348s 348s > data(varechem) 348s 348s > orig <- cca(varespec ~ Al + K, varechem) 348s 348s > plot(orig, dis = c("lc", "bp")) 348s 348s > plot(orig, dis = c("lc", "bp")) 348s 348s > i <- sample(nrow(varespec)) 348s 348s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 348s 348s > plot(shuff, dis = c("lc", "bp")) 348s 348s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 348s + dis = "lc"))) 348s 348s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 348s + dis = "lc"))) 348s 348s > tmp1 <- rda(varespec ~ Al + K, varechem) 348s 348s > i <- sample(nrow(varespec)) 348s 348s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 348s 348s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 348s + dis = "lc"))) 348s 348s > orig 348s Call: cca(formula = varespec ~ Al + K, data = 348s varechem) 348s 348s -- Model Summary -- 348s 348s Inertia Proportion Rank 348s Total 2.0832 1.0000 348s Constrained 0.4760 0.2285 2 348s Unconstrained 1.6072 0.7715 21 348s 348s Inertia is scaled Chi-square 348s 348s -- Eigenvalues -- 348s 348s Eigenvalues for constrained axes: 348s CCA1 CCA2 348s 0.3608 0.1152 348s 348s Eigenvalues for unconstrained axes: 348s CA1 CA2 CA3 CA4 CA5 CA6 CA7 348s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 348s CA8 348s 0.0757 348s (Showing 8 of 21 unconstrained eigenvalues) 348s 348s 348s > shuff 348s Call: cca(formula = varespec[i, ] ~ Al + K, data = 348s varechem) 348s 348s -- Model Summary -- 348s 348s Inertia Proportion Rank 348s Total 2.08320 1.00000 348s Constrained 0.18597 0.08927 2 348s Unconstrained 1.89723 0.91073 21 348s 348s Inertia is scaled Chi-square 348s 348s -- Eigenvalues -- 348s 348s Eigenvalues for constrained axes: 348s CCA1 CCA2 348s 0.13956 0.04641 348s 348s Eigenvalues for unconstrained axes: 348s CA1 CA2 CA3 CA4 CA5 CA6 CA7 348s 0.5219 0.3511 0.2128 0.1807 0.1403 0.1157 0.1107 348s CA8 348s 0.0755 348s (Showing 8 of 21 unconstrained eigenvalues) 348s 348s 348s > plot(procrustes(orig, shuff)) 348s 348s > tmp1 <- rda(varespec ~ ., varechem) 348s 348s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 348s 348s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 348s + scores(tmp2, dis = "lc", choi = 1:14)) 348s 348s > max(residuals(proc)) 348s [1] 3.24768e-14 348s 348s > data(dune) 348s 348s > data(dune.env) 348s 348s > orig <- cca(dune ~ Moisture, dune.env) 348s 348s > plot(orig, dis = "lc") 348s 348s > plot(orig, display = "wa", type = "points") 348s 348s > ordispider(orig, col = "red") 348s 348s > text(orig, dis = "cn", col = "blue") 348s 348s > plot(orig, display = "wa", type = "points") 348s 348s > ordispider(orig, col = "red") 348s 348s > text(orig, dis = "cn", col = "blue") 348s > 349s 349s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 349s Copyright (C) 2025 The R Foundation for Statistical Computing 349s Platform: arm-unknown-linux-gnueabihf (32-bit) 349s 349s R is free software and comes with ABSOLUTELY NO WARRANTY. 349s You are welcome to redistribute it under certain conditions. 349s Type 'license()' or 'licence()' for distribution details. 349s 349s R is a collaborative project with many contributors. 349s Type 'contributors()' for more information and 349s 'citation()' on how to cite R or R packages in publications. 349s 349s Type 'demo()' for some demos, 'help()' for on-line help, or 349s 'help.start()' for an HTML browser interface to help. 349s Type 'q()' to quit R. 349s 349s > Stangle("diversity-vegan.Rnw") 349s Writing to file diversity-vegan.R 349s > source("diversity-vegan.R", echo=TRUE) 349s 349s > par(mfrow = c(1, 1)) 349s 349s > options(width = 55) 349s 349s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 349s 349s > options(SweaveHooks = list(fig = figset)) 349s 349s > options(prompt = "> ", continue = " ") 349s 349s > library(vegan) 349s Loading required package: permute 349s Loading required package: lattice 350s 350s > data(BCI) 350s 350s > H <- diversity(BCI) 350s 350s > J <- H/log(specnumber(BCI)) 350s 350s > k <- sample(nrow(BCI), 6) 350s 350s > R <- renyi(BCI[k, ]) 350s 350s > print(plot(R)) 351s 351s > alpha <- fisher.alpha(BCI) 351s 351s > quantile(rowSums(BCI)) 351s 0% 25% 50% 75% 100% 351s 340.0 409.0 428.0 443.5 601.0 351s 351s > Srar <- rarefy(BCI, min(rowSums(BCI))) 351s 351s > S2 <- rarefy(BCI, 2) 351s 351s > all(rank(Srar) == rank(S2)) 351s [1] FALSE 351s 351s > range(diversity(BCI, "simp") - (S2 - 1)) 351s [1] -0.002868298 -0.001330663 351s 351s > data(dune) 351s 351s > data(dune.taxon) 351s 351s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 351s 351s > mod <- taxondive(dune, taxdis) 351s forced matching of 'tree' labels and 'comm' names 351s 351s > plot(mod) 351s 351s > tr <- hclust(taxdis, "aver") 351s 351s > mod <- treedive(dune, tr) 351s 351s > k <- sample(nrow(BCI), 1) 351s 351s > fish <- fisherfit(BCI[k, ]) 351s 351s > fish 351s 351s Fisher log series model 351s No. of species: 92 351s Fisher alpha: 35.88776 351s 351s 351s > plot(fish) 351s 351s > prestondistr(BCI[k, ]) 351s 351s Preston lognormal model 351s Method: maximized likelihood to log2 abundances 351s No. of species: 92 351s 351s mode width S0 351s 0.8352028 1.7913322 24.1844800 351s 351s Frequencies by Octave 351s 0 1 2 3 4 351s Observed 17.50000 27.00000 24.000 7.50000 10.000000 351s Fitted 21.69362 24.08235 19.576 11.65218 5.078656 351s 5 6 351s Observed 4.500000 1.5000000 351s Fitted 1.620871 0.3787968 351s 351s 351s > rad <- radfit(BCI[k, ]) 351s 351s > rad 351s 351s RAD models, family poisson 351s No. of species 92, total abundance 430 351s 351s par1 par2 par3 Deviance 351s Null 85.9601 351s Preemption 0.049495 70.0645 351s Lognormal 0.86697 1.1832 28.5832 351s Zipf 0.14615 -0.86285 37.0519 351s Mandelbrot 1.6203 -1.4888 5.7543 5.8926 351s AIC BIC 351s Null 348.6007 348.6007 351s Preemption 334.7051 337.2269 351s Lognormal 295.2238 300.2674 351s Zipf 303.6925 308.7361 351s Mandelbrot 274.5332 282.0986 351s 351s > print(radlattice(rad)) 351s 351s > sac <- specaccum(BCI) 351s 351s > plot(sac, ci.type = "polygon", ci.col = "yellow") 351s 351s > sac <- specaccum(BCI) 351s 351s > plot(sac, ci.type = "polygon", ci.col = "yellow") 351s 351s > ncol(BCI)/mean(specnumber(BCI)) - 1 351s [1] 1.478519 351s 351s > beta <- vegdist(BCI, binary = TRUE) 351s 351s > mean(beta) 351s [1] 0.3399075 351s 351s > betadiver(help = TRUE) 351s 1 "w" = (b+c)/(2*a+b+c) 351s 2 "-1" = (b+c)/(2*a+b+c) 351s 3 "c" = (b+c)/2 351s 4 "wb" = b+c 351s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 351s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 351s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 351s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 351s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 351s (2*a+b+c))-1 351s 8 "t" = (b+c)/(2*a+b+c) 351s 9 "me" = (b+c)/(2*a+b+c) 351s 10 "j" = a/(a+b+c) 351s 11 "sor" = 2*a/(2*a+b+c) 351s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 351s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 351s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 351s 15 "cc" = (b+c)/(a+b+c) 351s 16 "g" = (b+c)/(a+b+c) 351s 17 "-3" = pmin.int(b,c)/(a+b+c) 351s 18 "l" = (b+c)/2 351s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 351s 20 "hk" = (b+c)/(2*a+b+c) 351s 21 "rlb" = a/(a+c) 351s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 351s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 351s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 351s 351s > z <- betadiver(BCI, "z") 351s 351s > quantile(z) 351s 0% 25% 50% 75% 100% 351s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 351s 351s > data(dune) 351s 351s > data(dune.env) 351s 351s > z <- betadiver(dune, "z") 351s 351s > mod <- with(dune.env, betadisper(z, Management)) 351s 351s > mod 351s 351s Homogeneity of multivariate dispersions 351s 351s Call: betadisper(d = z, group = Management) 351s 351s No. of Positive Eigenvalues: 12 351s No. of Negative Eigenvalues: 7 351s 351s Average distance to median: 351s BF HF NM SF 351s 0.2532 0.2512 0.4406 0.3635 351s 351s Eigenvalues for PCoA axes: 351s (Showing 8 of 19 eigenvalues) 351s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 351s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 351s PCoA7 PCoA8 351s 0.16128 0.08099 351s 351s > boxplot(mod) 351s 351s > specpool(BCI) 351s Species chao chao.se jack1 jack1.se jack2 351s All 225 236.3732 6.54361 245.58 5.650522 247.8722 351s boot boot.se n 351s All 235.6862 3.468888 50 351s 351s > s <- sample(nrow(BCI), 25) 351s 351s > specpool(BCI[s, ]) 351s Species chao chao.se jack1 jack1.se jack2 351s All 209 234.088 12.52852 235.88 8.364496 248.415 351s boot boot.se n 351s All 221.5592 4.57264 25 351s 351s > estimateR(BCI[k, ]) 351s 36 351s S.obs 92.000000 351s S.chao1 121.750000 351s se.chao1 13.262409 351s S.ACE 136.318712 351s se.ACE 6.669613 351s 351s > veiledspec(prestondistr(BCI[k, ])) 351s Extrapolated Observed Veiled 351s 108.59325 92.00000 16.59325 351s 351s > veiledspec(BCI[k, ]) 351s Extrapolated Observed Veiled 351s 120.52468 92.00000 28.52468 351s 351s > smo <- beals(BCI) 351s 351s > j <- which(colnames(BCI) == "Ceiba.pentandra") 351s 351s > plot(beals(BCI, species = j, include = FALSE), BCI[, 351s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 351s 351s > j <- which(colnames(BCI) == "Ceiba.pentandra") 351s 351s > plot(beals(BCI, species = j, include = FALSE), BCI[, 351s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 351s > 351s Warning messages: 351s 1: In cor(x > 0) : the standard deviation is zero 351s 2: In cor(x > 0) : the standard deviation is zero 351s 3: In betadisper(z, Management) : 351s some squared distances are negative and changed to zero 351s 351s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 351s Copyright (C) 2025 The R Foundation for Statistical Computing 351s Platform: arm-unknown-linux-gnueabihf (32-bit) 351s 351s R is free software and comes with ABSOLUTELY NO WARRANTY. 351s You are welcome to redistribute it under certain conditions. 351s Type 'license()' or 'licence()' for distribution details. 351s 351s R is a collaborative project with many contributors. 351s Type 'contributors()' for more information and 351s 'citation()' on how to cite R or R packages in publications. 351s 351s Type 'demo()' for some demos, 'help()' for on-line help, or 351s 'help.start()' for an HTML browser interface to help. 351s Type 'q()' to quit R. 351s 352s > Stangle("intro-vegan.Rnw") 352s Writing to file intro-vegan.R 352s > source("intro-vegan.R", echo=TRUE) 352s 352s > par(mfrow = c(1, 1)) 352s 352s > options(width = 72) 352s 352s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 352s 352s > options(SweaveHooks = list(fig = figset)) 352s 352s > options(prompt = "> ", continue = " ") 352s 352s > library(vegan) 352s Loading required package: permute 352s Loading required package: lattice 353s 353s > data(dune) 353s 353s > ord <- decorana(dune) 353s 353s > ord 353s 353s Call: 353s decorana(veg = dune) 353s 353s Detrended correspondence analysis with 26 segments. 353s Rescaling of axes with 4 iterations. 353s Total inertia (scaled Chi-square): 2.1153 353s 353s DCA1 DCA2 DCA3 DCA4 353s Eigenvalues 0.5117 0.3036 0.12125 0.14267 353s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 353s Decorana values 0.5360 0.2869 0.08136 0.04814 353s Axis lengths 3.7004 3.1166 1.30055 1.47888 353s 353s 353s > ord <- metaMDS(dune, trace = FALSE) 353s 353s > ord 353s 353s Call: 353s metaMDS(comm = dune, trace = FALSE) 353s 353s global Multidimensional Scaling using monoMDS 353s 353s Data: dune 353s Distance: bray 353s 353s Dimensions: 2 353s Stress: 0.1183186 353s Stress type 1, weak ties 353s Best solution was repeated 2 times in 20 tries 353s The best solution was from try 10 (random start) 353s Scaling: centring, PC rotation, halfchange scaling 353s Species: expanded scores based on ‘dune’ 353s 353s 353s > plot(ord) 353s 353s > plot(ord) 353s 353s > plot(ord, type = "n") 353s 353s > points(ord, display = "sites", cex = 0.8, pch = 21, 353s + col = "red", bg = "yellow") 353s 353s > text(ord, display = "species", cex = 0.7, col = "blue") 353s 353s > plot(ord, type = "n") 353s 353s > points(ord, display = "sites", cex = 0.8, pch = 21, 353s + col = "red", bg = "yellow") 353s 353s > text(ord, display = "species", cex = 0.7, col = "blue") 353s 353s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 353s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 353s + col = "blue") 353s 353s > data(dune.env) 353s 353s > attach(dune.env) 353s 353s > plot(ord, disp = "sites", type = "n") 353s 353s > ordihull(ord, Management, col = 1:4, lwd = 3) 353s 353s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 353s + lwd = 3) 353s 353s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 353s 353s > ordispider(ord, Management, col = 1:4, label = TRUE) 353s 353s > points(ord, disp = "sites", pch = 21, col = "red", 353s + bg = "yellow", cex = 1.3) 353s 353s > plot(ord, disp = "sites", type = "n") 353s 353s > ordihull(ord, Management, col = 1:4, lwd = 3) 353s 353s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 353s + lwd = 3) 353s 353s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 353s 353s > ordispider(ord, Management, col = 1:4, label = TRUE) 353s 353s > points(ord, disp = "sites", pch = 21, col = "red", 353s + bg = "yellow", cex = 1.3) 353s 353s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 353s + perm = 999) 353s 353s > ord.fit 353s 353s ***VECTORS 353s 354s NMDS1 NMDS2 r2 Pr(>r) 354s A1 0.96474 0.26321 0.3649 0.019 * 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s Permutation: free 354s Number of permutations: 999 354s 354s ***FACTORS: 354s 354s Centroids: 354s NMDS1 NMDS2 354s ManagementBF -0.4534 -0.0102 354s ManagementHF -0.2636 -0.1282 354s ManagementNM 0.2958 0.5790 354s ManagementSF 0.1506 -0.4670 354s 354s Goodness of fit: 354s r2 Pr(>r) 354s Management 0.4134 0.006 ** 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s Permutation: free 354s Number of permutations: 999 354s 354s 354s 354s > plot(ord, dis = "site") 354s 354s > plot(ord.fit) 354s 354s > ordisurf(ord, A1, add = TRUE) 354s 354s Family: gaussian 354s Link function: identity 354s 354s Formula: 354s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 354s 354s Estimated degrees of freedom: 354s 1.59 total = 2.59 354s 354s REML score: 41.58727 354s 354s > plot(ord, dis = "site") 354s 354s > plot(ord.fit) 354s 354s > ordisurf(ord, A1, add = TRUE) 354s 354s Family: gaussian 354s Link function: identity 354s 354s Formula: 354s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 354s 354s Estimated degrees of freedom: 354s 1.59 total = 2.59 354s 354s REML score: 41.58727 354s 354s > ord <- cca(dune ~ A1 + Management, data = dune.env) 354s 354s > ord 354s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 354s 354s -- Model Summary -- 354s 354s Inertia Proportion Rank 354s Total 2.1153 1.0000 354s Constrained 0.7798 0.3686 4 354s Unconstrained 1.3355 0.6314 15 354s 354s Inertia is scaled Chi-square 354s 354s -- Eigenvalues -- 354s 354s Eigenvalues for constrained axes: 354s CCA1 CCA2 CCA3 CCA4 354s 0.3187 0.2372 0.1322 0.0917 354s 354s Eigenvalues for unconstrained axes: 354s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 354s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 354s CA11 CA12 CA13 CA14 CA15 354s 0.0317 0.0178 0.0116 0.0087 0.0047 354s 354s 354s > plot(ord) 354s 354s > plot(ord) 354s 354s > cca(dune ~ ., data = dune.env) 354s 354s Some constraints or conditions were aliased because they were 354s redundant. This can happen if terms are linearly dependent (collinear): 354s ‘Manure^4’ 354s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 354s Manure, data = dune.env) 354s 354s -- Model Summary -- 354s 354s Inertia Proportion Rank 354s Total 2.1153 1.0000 354s Constrained 1.5032 0.7106 12 354s Unconstrained 0.6121 0.2894 7 354s 354s Inertia is scaled Chi-square 354s 354s -- Note -- 354s 354s Some constraints or conditions were aliased because they were 354s redundant. This can happen if terms are linearly dependent 354s (collinear): ‘Manure^4’ 354s 354s -- Eigenvalues -- 354s 354s Eigenvalues for constrained axes: 354s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 354s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 354s CCA11 CCA12 354s 0.0228 0.0108 354s 354s Eigenvalues for unconstrained axes: 354s CA1 CA2 CA3 CA4 CA5 CA6 CA7 354s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 354s 354s 354s > anova(ord) 354s Permutation test for cca under reduced model 354s Permutation: free 354s Number of permutations: 999 354s 354s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 354s Df ChiSquare F Pr(>F) 354s Model 4 0.77978 2.1896 0.001 *** 354s Residual 15 1.33549 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > anova(ord, by = "term", permutations = 199) 354s Permutation test for cca under reduced model 354s Terms added sequentially (first to last) 354s Permutation: free 354s Number of permutations: 199 354s 354s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 354s Df ChiSquare F Pr(>F) 354s A1 1 0.22476 2.5245 0.015 * 354s Management 3 0.55502 2.0780 0.005 ** 354s Residual 15 1.33549 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > anova(ord, by = "mar", permutations = 199) 354s Permutation test for cca under reduced model 354s Marginal effects of terms 354s Permutation: free 354s Number of permutations: 199 354s 354s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 354s Df ChiSquare F Pr(>F) 354s A1 1 0.17594 1.9761 0.020 * 354s Management 3 0.55502 2.0780 0.005 ** 354s Residual 15 1.33549 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > anova(ord, by = "axis", permutations = 499) 354s Permutation test for cca under reduced model 354s Forward tests for axes 354s Permutation: free 354s Number of permutations: 499 354s 354s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 354s Df ChiSquare F Pr(>F) 354s CCA1 1 0.31875 3.5801 0.012 * 354s CCA2 1 0.23718 2.6640 0.150 354s CCA3 1 0.13217 1.4845 0.838 354s CCA4 1 0.09168 1.0297 1.000 354s Residual 15 1.33549 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 354s + data = dune.env) 354s 354s > ord 354s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 354s data = dune.env) 354s 354s -- Model Summary -- 354s 354s Inertia Proportion Rank 354s Total 2.1153 1.0000 354s Conditional 0.6283 0.2970 3 354s Constrained 0.5109 0.2415 4 354s Unconstrained 0.9761 0.4615 12 354s 354s Inertia is scaled Chi-square 354s 354s -- Eigenvalues -- 354s 354s Eigenvalues for constrained axes: 354s CCA1 CCA2 CCA3 CCA4 354s 0.24932 0.12090 0.08160 0.05904 354s 354s Eigenvalues for unconstrained axes: 354s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 354s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 354s CA10 CA11 CA12 354s 0.02102 0.01254 0.00928 354s 354s 354s > anova(ord, by = "term", permutations = 499) 354s Permutation test for cca under reduced model 354s Terms added sequentially (first to last) 354s Permutation: free 354s Number of permutations: 499 354s 354s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 354s Df ChiSquare F Pr(>F) 354s A1 1 0.11543 1.4190 1.000 354s Management 3 0.39543 1.6205 0.002 ** 354s Residual 12 0.97610 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 354s 354s > anova(ord, by = "term", permutations = how) 354s Permutation test for cca under reduced model 354s Terms added sequentially (first to last) 354s Plots: dune.env$Moisture, plot permutation: none 354s Permutation: free 354s Number of permutations: 499 354s 354s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 354s Df ChiSquare F Pr(>F) 354s A1 1 0.11543 1.4190 1.000 354s Management 3 0.39543 1.6205 0.002 ** 354s Residual 12 0.97610 354s --- 354s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 354s 354s > detach(dune.env) 354s > 354s 354s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 354s Copyright (C) 2025 The R Foundation for Statistical Computing 354s Platform: arm-unknown-linux-gnueabihf (32-bit) 354s 354s R is free software and comes with ABSOLUTELY NO WARRANTY. 354s You are welcome to redistribute it under certain conditions. 354s Type 'license()' or 'licence()' for distribution details. 354s 354s R is a collaborative project with many contributors. 354s Type 'contributors()' for more information and 354s 'citation()' on how to cite R or R packages in publications. 354s 354s Type 'demo()' for some demos, 'help()' for on-line help, or 354s 'help.start()' for an HTML browser interface to help. 354s Type 'q()' to quit R. 354s 355s > Stangle("partitioning.Rnw") 355s Writing to file partitioning.R 355s > source("partitioning.R", echo=TRUE) 355s 355s > par(mfrow = c(1, 1)) 355s 355s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 355s 355s > options(SweaveHooks = list(fig = figset)) 355s 355s > library(vegan) 355s Loading required package: permute 355s Loading required package: lattice 356s 356s > labs <- paste("Table", 1:4) 356s 356s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 356s 356s > showvarparts(2, bg = cls, Xnames = labs) 356s 356s > showvarparts(3, bg = cls, Xnames = labs) 356s 356s > showvarparts(4, bg = cls, Xnames = labs) 356s > 365s Test cca-object-tests passed 367s Test oecosimu-tests passed 372s Test vegan-tests passed 373s autopkgtest [23:11:19]: test run-unit-test: -----------------------] 377s autopkgtest [23:11:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 377s run-unit-test PASS 381s autopkgtest [23:11:27]: test pkg-r-autopkgtest: preparing testbed 382s Reading package lists... 383s Building dependency tree... 383s Reading state information... 383s Solving dependencies... 384s The following NEW packages will be installed: 384s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 384s cpp-arm-linux-gnueabihf dctrl-tools g++ g++-15 g++-15-arm-linux-gnueabihf 384s g++-arm-linux-gnueabihf gcc gcc-15 gcc-15-arm-linux-gnueabihf 384s gcc-arm-linux-gnueabihf gfortran gfortran-15 gfortran-15-arm-linux-gnueabihf 384s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libbz2-dev 384s libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libdeflate-dev libgcc-15-dev 384s libgfortran-15-dev libicu-dev libisl23 libjpeg-dev libjpeg-turbo8-dev 384s libjpeg8-dev liblapack-dev liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 384s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 384s libreadline-dev libstdc++-15-dev libtirpc-dev libubsan1 libzstd-dev 384s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto 384s zlib1g-dev 385s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 385s Need to get 83.1 MB of archives. 385s After this operation, 253 MB of additional disk space will be used. 385s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf libc-dev-bin armhf 2.42-2ubuntu4 [21.8 kB] 385s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.19.0-3.3 [1804 kB] 387s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 387s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 387s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libc6-dev armhf 2.42-2ubuntu4 [1416 kB] 389s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 390s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 390s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 403s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 403s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 403s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 403s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 403s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 407s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 408s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 409s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 435s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 436s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 436s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 436s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 440s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 457s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 457s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 457s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 457s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 457s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf dctrl-tools armhf 2.24-3build4 [95.0 kB] 457s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran-15-dev armhf 15.2.0-12ubuntu1 [380 kB] 458s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.7 MB] 470s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-15 armhf 15.2.0-12ubuntu1 [18.1 kB] 470s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1020 B] 470s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf gfortran armhf 4:15.2.0-4ubuntu1 [1162 B] 470s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf icu-devtools armhf 78.2-1ubuntu1 [203 kB] 470s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf libblas-dev armhf 3.12.1-7ubuntu1 [141 kB] 470s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libbz2-dev armhf 1.0.8-6build2 [31.2 kB] 470s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate-dev armhf 1.23-2build1 [45.1 kB] 470s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf libicu-dev armhf 78.2-1ubuntu1 [12.2 MB] 484s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-turbo8-dev armhf 2.1.5-4ubuntu3 [265 kB] 485s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 485s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 485s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack-dev armhf 3.12.1-7ubuntu1 [2207 kB] 487s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf libncurses-dev armhf 6.6+20251231-1 [348 kB] 488s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-16-0 armhf 10.46-1 [206 kB] 488s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-32-0 armhf 10.46-1 [197 kB] 488s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-posix3 armhf 10.46-1 [6286 B] 488s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf libpcre2-dev armhf 10.46-1 [744 kB] 489s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf libpkgconf3 armhf 1.8.1-4build1 [26.6 kB] 489s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu2 [881 kB] 490s Get:48 http://ftpmaster.internal/ubuntu resolute/main armhf libpng-dev armhf 1.6.54-1 [252 kB] 490s Get:49 http://ftpmaster.internal/ubuntu resolute/main armhf libreadline-dev armhf 8.3-3 [165 kB] 491s Get:50 http://ftpmaster.internal/ubuntu resolute/main armhf libzstd-dev armhf 1.5.7+dfsg-3 [342 kB] 491s Get:51 http://ftpmaster.internal/ubuntu resolute/main armhf liblzma-dev armhf 5.8.2-2 [167 kB] 491s Get:52 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf-bin armhf 1.8.1-4build1 [21.4 kB] 491s Get:53 http://ftpmaster.internal/ubuntu resolute/main armhf pkgconf armhf 1.8.1-4build1 [16.8 kB] 491s Get:54 http://ftpmaster.internal/ubuntu resolute/main armhf libtirpc-dev armhf 1.3.6+ds-1 [184 kB] 491s Get:55 http://ftpmaster.internal/ubuntu resolute/universe armhf r-base-dev all 4.5.2-1ubuntu2 [1880 B] 491s Get:56 http://ftpmaster.internal/ubuntu resolute/universe armhf pkg-r-autopkgtest all 20250812 [6158 B] 492s Fetched 83.1 MB in 1min 47s (776 kB/s) 492s Selecting previously unselected package libc-dev-bin. 492s (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 ... 76679 files and directories currently installed.) 492s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_armhf.deb ... 492s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 492s Selecting previously unselected package linux-libc-dev:armhf. 492s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_armhf.deb ... 492s Unpacking linux-libc-dev:armhf (6.19.0-3.3) ... 493s Selecting previously unselected package libcrypt-dev:armhf. 493s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 493s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 493s Selecting previously unselected package rpcsvc-proto. 493s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 493s Unpacking rpcsvc-proto (1.4.3-1build1) ... 493s Selecting previously unselected package libc6-dev:armhf. 493s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_armhf.deb ... 493s Unpacking libc6-dev:armhf (2.42-2ubuntu4) ... 493s Selecting previously unselected package libisl23:armhf. 493s Preparing to unpack .../05-libisl23_0.27-1build1_armhf.deb ... 493s Unpacking libisl23:armhf (0.27-1build1) ... 493s Selecting previously unselected package libmpc3:armhf. 493s Preparing to unpack .../06-libmpc3_1.3.1-2_armhf.deb ... 493s Unpacking libmpc3:armhf (1.3.1-2) ... 493s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 493s Preparing to unpack .../07-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 493s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package cpp-15. 494s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package cpp-arm-linux-gnueabihf. 494s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 494s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 494s Selecting previously unselected package cpp. 494s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 494s Unpacking cpp (4:15.2.0-4ubuntu1) ... 494s Selecting previously unselected package libcc1-0:armhf. 494s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package libasan8:armhf. 494s Preparing to unpack .../12-libasan8_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package libubsan1:armhf. 494s Preparing to unpack .../13-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package libgcc-15-dev:armhf. 494s Preparing to unpack .../14-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 494s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 494s Preparing to unpack .../15-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 494s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 495s Selecting previously unselected package gcc-15. 495s Preparing to unpack .../16-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 495s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 495s Selecting previously unselected package gcc-arm-linux-gnueabihf. 495s Preparing to unpack .../17-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 495s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 495s Selecting previously unselected package gcc. 495s Preparing to unpack .../18-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 495s Unpacking gcc (4:15.2.0-4ubuntu1) ... 495s Selecting previously unselected package libstdc++-15-dev:armhf. 495s Preparing to unpack .../19-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 495s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 495s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 495s Preparing to unpack .../20-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 495s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package g++-15. 496s Preparing to unpack .../21-g++-15_15.2.0-12ubuntu1_armhf.deb ... 496s Unpacking g++-15 (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package g++-arm-linux-gnueabihf. 496s Preparing to unpack .../22-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 496s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 496s Selecting previously unselected package g++. 496s Preparing to unpack .../23-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 496s Unpacking g++ (4:15.2.0-4ubuntu1) ... 496s Selecting previously unselected package build-essential. 496s Preparing to unpack .../24-build-essential_12.12ubuntu2_armhf.deb ... 496s Unpacking build-essential (12.12ubuntu2) ... 496s Selecting previously unselected package dctrl-tools. 496s Preparing to unpack .../25-dctrl-tools_2.24-3build4_armhf.deb ... 496s Unpacking dctrl-tools (2.24-3build4) ... 496s Selecting previously unselected package libgfortran-15-dev:armhf. 496s Preparing to unpack .../26-libgfortran-15-dev_15.2.0-12ubuntu1_armhf.deb ... 496s Unpacking libgfortran-15-dev:armhf (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package gfortran-15-arm-linux-gnueabihf. 496s Preparing to unpack .../27-gfortran-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 496s Unpacking gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package gfortran-15. 496s Preparing to unpack .../28-gfortran-15_15.2.0-12ubuntu1_armhf.deb ... 496s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 496s Preparing to unpack .../29-gfortran-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 496s Unpacking gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 496s Selecting previously unselected package gfortran. 496s Preparing to unpack .../30-gfortran_4%3a15.2.0-4ubuntu1_armhf.deb ... 496s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 496s Selecting previously unselected package icu-devtools. 496s Preparing to unpack .../31-icu-devtools_78.2-1ubuntu1_armhf.deb ... 496s Unpacking icu-devtools (78.2-1ubuntu1) ... 497s Selecting previously unselected package libblas-dev:armhf. 497s Preparing to unpack .../32-libblas-dev_3.12.1-7ubuntu1_armhf.deb ... 497s Unpacking libblas-dev:armhf (3.12.1-7ubuntu1) ... 497s Selecting previously unselected package libbz2-dev:armhf. 497s Preparing to unpack .../33-libbz2-dev_1.0.8-6build2_armhf.deb ... 497s Unpacking libbz2-dev:armhf (1.0.8-6build2) ... 497s Selecting previously unselected package libdeflate-dev:armhf. 497s Preparing to unpack .../34-libdeflate-dev_1.23-2build1_armhf.deb ... 497s Unpacking libdeflate-dev:armhf (1.23-2build1) ... 497s Selecting previously unselected package libicu-dev:armhf. 497s Preparing to unpack .../35-libicu-dev_78.2-1ubuntu1_armhf.deb ... 497s Unpacking libicu-dev:armhf (78.2-1ubuntu1) ... 497s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 497s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-4ubuntu3_armhf.deb ... 497s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 497s Selecting previously unselected package libjpeg8-dev:armhf. 497s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 497s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 497s Selecting previously unselected package libjpeg-dev:armhf. 497s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 497s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 497s Selecting previously unselected package liblapack-dev:armhf. 497s Preparing to unpack .../39-liblapack-dev_3.12.1-7ubuntu1_armhf.deb ... 497s Unpacking liblapack-dev:armhf (3.12.1-7ubuntu1) ... 498s Selecting previously unselected package libncurses-dev:armhf. 498s Preparing to unpack .../40-libncurses-dev_6.6+20251231-1_armhf.deb ... 498s Unpacking libncurses-dev:armhf (6.6+20251231-1) ... 498s Selecting previously unselected package libpcre2-16-0:armhf. 498s Preparing to unpack .../41-libpcre2-16-0_10.46-1_armhf.deb ... 498s Unpacking libpcre2-16-0:armhf (10.46-1) ... 498s Selecting previously unselected package libpcre2-32-0:armhf. 498s Preparing to unpack .../42-libpcre2-32-0_10.46-1_armhf.deb ... 498s Unpacking libpcre2-32-0:armhf (10.46-1) ... 498s Selecting previously unselected package libpcre2-posix3:armhf. 498s Preparing to unpack .../43-libpcre2-posix3_10.46-1_armhf.deb ... 498s Unpacking libpcre2-posix3:armhf (10.46-1) ... 498s Selecting previously unselected package libpcre2-dev:armhf. 498s Preparing to unpack .../44-libpcre2-dev_10.46-1_armhf.deb ... 498s Unpacking libpcre2-dev:armhf (10.46-1) ... 498s Selecting previously unselected package libpkgconf3:armhf. 498s Preparing to unpack .../45-libpkgconf3_1.8.1-4build1_armhf.deb ... 498s Unpacking libpkgconf3:armhf (1.8.1-4build1) ... 498s Selecting previously unselected package zlib1g-dev:armhf. 498s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_armhf.deb ... 498s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 498s Selecting previously unselected package libpng-dev:armhf. 498s Preparing to unpack .../47-libpng-dev_1.6.54-1_armhf.deb ... 498s Unpacking libpng-dev:armhf (1.6.54-1) ... 498s Selecting previously unselected package libreadline-dev:armhf. 498s Preparing to unpack .../48-libreadline-dev_8.3-3_armhf.deb ... 498s Unpacking libreadline-dev:armhf (8.3-3) ... 498s Selecting previously unselected package libzstd-dev:armhf. 498s Preparing to unpack .../49-libzstd-dev_1.5.7+dfsg-3_armhf.deb ... 498s Unpacking libzstd-dev:armhf (1.5.7+dfsg-3) ... 498s Selecting previously unselected package liblzma-dev:armhf. 498s Preparing to unpack .../50-liblzma-dev_5.8.2-2_armhf.deb ... 498s Unpacking liblzma-dev:armhf (5.8.2-2) ... 498s Selecting previously unselected package pkgconf-bin. 498s Preparing to unpack .../51-pkgconf-bin_1.8.1-4build1_armhf.deb ... 498s Unpacking pkgconf-bin (1.8.1-4build1) ... 498s Selecting previously unselected package pkgconf:armhf. 498s Preparing to unpack .../52-pkgconf_1.8.1-4build1_armhf.deb ... 498s Unpacking pkgconf:armhf (1.8.1-4build1) ... 498s Selecting previously unselected package libtirpc-dev:armhf. 498s Preparing to unpack .../53-libtirpc-dev_1.3.6+ds-1_armhf.deb ... 498s Unpacking libtirpc-dev:armhf (1.3.6+ds-1) ... 498s Selecting previously unselected package r-base-dev. 498s Preparing to unpack .../54-r-base-dev_4.5.2-1ubuntu2_all.deb ... 498s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 499s Selecting previously unselected package pkg-r-autopkgtest. 499s Preparing to unpack .../55-pkg-r-autopkgtest_20250812_all.deb ... 499s Unpacking pkg-r-autopkgtest (20250812) ... 499s Setting up libzstd-dev:armhf (1.5.7+dfsg-3) ... 499s Setting up linux-libc-dev:armhf (6.19.0-3.3) ... 499s Setting up libpcre2-16-0:armhf (10.46-1) ... 499s Setting up libpcre2-32-0:armhf (10.46-1) ... 499s Setting up libtirpc-dev:armhf (1.3.6+ds-1) ... 499s Setting up libpkgconf3:armhf (1.8.1-4build1) ... 499s Setting up rpcsvc-proto (1.4.3-1build1) ... 499s Setting up libmpc3:armhf (1.3.1-2) ... 499s Setting up icu-devtools (78.2-1ubuntu1) ... 499s Setting up pkgconf-bin (1.8.1-4build1) ... 499s Setting up liblzma-dev:armhf (5.8.2-2) ... 499s Setting up libubsan1:armhf (15.2.0-12ubuntu1) ... 499s Setting up libpcre2-posix3:armhf (10.46-1) ... 499s Setting up 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... 499s 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 499s Setting up cpp-15 (15.2.0-12ubuntu1) ... 499s Setting up cpp (4:15.2.0-4ubuntu1) ... 499s Setting up libc6-dev:armhf (2.42-2ubuntu4) ... 499s Setting up libicu-dev:armhf (78.2-1ubuntu1) ... 499s Setting up libbz2-dev:armhf (1.0.8-6build2) ... 499s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 499s Setting up libjpeg-turbo8-dev:armhf (2.1.5-4ubuntu3) ... 499s Setting up libncurses-dev:armhf (6.6+20251231-1) ... 499s Setting up gfortran-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 499s Setting up libpcre2-dev:armhf (10.46-1) ... 499s Setting up libreadline-dev:armhf (8.3-3) ... 499s Setting up gfortran-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 499s Setting up gcc-15 (15.2.0-12ubuntu1) ... 499s Setting up libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 499s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 499s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 499s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 499s Setting up libpng-dev:armhf (1.6.54-1) ... 499s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 499s Setting up g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 499s Setting up gcc (4:15.2.0-4ubuntu1) ... 499s Setting up g++-15 (15.2.0-12ubuntu1) ... 499s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 499s Setting up gfortran (4:15.2.0-4ubuntu1) ... 499s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 499s 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 499s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 499s 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 499s Setting up g++ (4:15.2.0-4ubuntu1) ... 499s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 499s Setting up build-essential (12.12ubuntu2) ... 499s Setting up r-base-dev (4.5.2-1ubuntu2) ... 499s Setting up pkg-r-autopkgtest (20250812) ... 499s Processing triggers for libc-bin (2.42-2ubuntu4) ... 499s Processing triggers for man-db (2.13.1-1build1) ... 500s Processing triggers for install-info (7.2-5) ... 508s autopkgtest [23:13:34]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 508s autopkgtest [23:13:34]: test pkg-r-autopkgtest: [----------------------- 510s Test: Try to load the R library vegan 510s 510s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 510s Copyright (C) 2025 The R Foundation for Statistical Computing 510s Platform: arm-unknown-linux-gnueabihf (32-bit) 510s 510s R is free software and comes with ABSOLUTELY NO WARRANTY. 510s You are welcome to redistribute it under certain conditions. 510s Type 'license()' or 'licence()' for distribution details. 510s 510s R is a collaborative project with many contributors. 510s Type 'contributors()' for more information and 510s 'citation()' on how to cite R or R packages in publications. 510s 510s Type 'demo()' for some demos, 'help()' for on-line help, or 510s 'help.start()' for an HTML browser interface to help. 510s Type 'q()' to quit R. 510s 510s > library('vegan') 510s Loading required package: permute 510s Loading required package: lattice 512s > 512s autopkgtest [23:13:38]: test pkg-r-autopkgtest: -----------------------] 516s autopkgtest [23:13:42]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 516s pkg-r-autopkgtest PASS 520s autopkgtest [23:13:46]: @@@@@@@@@@@@@@@@@@@@ summary 520s run-unit-test PASS 520s pkg-r-autopkgtest PASS