0s autopkgtest [22:52:22]: starting date and time: 2026-02-09 22:52:22+0000 0s autopkgtest [22:52:22]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [22:52:22]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fir65n5y/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-ppc64el-4.secgroup --name adt-resolute-ppc64el-r-cran-vegan-20260209-225222-juju-7f2275-prod-proposed-migration-environment-15-54f74d94-5df0-4a57-b017-b1ab6874fcb5 --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-r-cran-vegan-20260209-225222-juju-7f2275-prod-proposed-migration-environment-15-54f74d94-5df0-4a57-b017-b1ab6874fcb5 from image adt/ubuntu-resolute-ppc64el-server-20260209.img (UUID f7f31435-4cd1-4090-aa55-59cfefa097ca)... 110s autopkgtest [22:54:12]: testbed dpkg architecture: ppc64el 110s autopkgtest [22:54:12]: testbed apt version: 3.1.15 110s autopkgtest [22:54:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 110s autopkgtest [22:54:12]: testbed release detected to be: None 111s autopkgtest [22:54:13]: updating testbed package index (apt update) 111s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 111s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 112s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 112s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 112s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 114s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 114s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [246 kB] 114s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [1534 kB] 116s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [19.4 kB] 117s Fetched 3774 kB in 5s (730 kB/s) 118s Reading package lists... 118s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 118s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 118s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 118s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 119s Reading package lists... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 119s The following packages will be upgraded: 119s cryptsetup-bin dracut-install iproute2 iptables libcryptsetup12 libip4tc2 119s libip6tc2 libxtables12 wget 119s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Need to get 3125 kB of archives. 119s After this operation, 78.8 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el iptables ppc64el 1.8.11-2ubuntu3 [464 kB] 119s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip4tc2 ppc64el 1.8.11-2ubuntu3 [27.8 kB] 119s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libip6tc2 ppc64el 1.8.11-2ubuntu3 [28.2 kB] 119s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxtables12 ppc64el 1.8.11-2ubuntu3 [41.2 kB] 119s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el iproute2 ppc64el 6.18.0-1ubuntu1 [1458 kB] 122s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcryptsetup12 ppc64el 2:2.8.0-1ubuntu3 [404 kB] 122s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el wget ppc64el 1.25.0-2ubuntu4 [401 kB] 122s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cryptsetup-bin ppc64el 2:2.8.0-1ubuntu3 [250 kB] 122s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 109-11ubuntu1 [51.3 kB] 122s dpkg-preconfigure: unable to re-open stdin: No such file or directory 122s Fetched 3125 kB in 2s (1260 kB/s) 122s (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 ... 122003 files and directories currently installed.) 122s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_ppc64el.deb ... 123s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 123s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_ppc64el.deb ... 123s Unpacking libip4tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 123s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_ppc64el.deb ... 123s Unpacking libip6tc2:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 123s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_ppc64el.deb ... 123s Unpacking libxtables12:ppc64el (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 123s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_ppc64el.deb ... 123s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 123s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 123s Unpacking libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 123s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_ppc64el.deb ... 123s Unpacking wget (1.25.0-2ubuntu4) over (1.25.0-2ubuntu3) ... 123s Preparing to unpack .../7-cryptsetup-bin_2%3a2.8.0-1ubuntu3_ppc64el.deb ... 124s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 124s Preparing to unpack .../8-dracut-install_109-11ubuntu1_ppc64el.deb ... 124s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 124s Setting up libip4tc2:ppc64el (1.8.11-2ubuntu3) ... 124s Setting up wget (1.25.0-2ubuntu4) ... 124s Setting up libip6tc2:ppc64el (1.8.11-2ubuntu3) ... 124s Setting up libxtables12:ppc64el (1.8.11-2ubuntu3) ... 124s Setting up dracut-install (109-11ubuntu1) ... 124s Setting up libcryptsetup12:ppc64el (2:2.8.0-1ubuntu3) ... 124s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 124s Setting up iptables (1.8.11-2ubuntu3) ... 124s Setting up iproute2 (6.18.0-1ubuntu1) ... 124s Processing triggers for man-db (2.13.1-1build1) ... 125s Processing triggers for install-info (7.2-5) ... 125s Processing triggers for libc-bin (2.42-2ubuntu4) ... 126s autopkgtest [22:54:28]: upgrading testbed (apt dist-upgrade and autopurge) 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Solving dependencies... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 129s autopkgtest [22:54:31]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:13:51 UTC 2026 129s autopkgtest [22:54:31]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 133s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (dsc) [2211 B] 133s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (tar) [1207 kB] 133s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (diff) [6396 B] 134s gpgv: Signature made Sat Apr 19 05:22:19 2025 UTC 134s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 134s gpgv: issuer "tille@debian.org" 134s gpgv: Can't check signature: No public key 134s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-3.dsc: no acceptable signature found 134s autopkgtest [22:54:36]: testing package r-cran-vegan version 2.6-10+dfsg-3 134s autopkgtest [22:54:36]: build not needed 135s autopkgtest [22:54:37]: test run-unit-test: preparing testbed 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Solving dependencies... 136s The following NEW packages will be installed: 136s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 136s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 136s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 136s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 136s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 136s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 136s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 136s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 136s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 136s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 136s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 136s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 136s x11-common xdg-utils zip 136s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 136s Need to get 70.2 MB of archives. 136s After this operation, 171 MB of additional disk space will be used. 136s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-mono all 2.37-8build1 [502 kB] 136s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-dejavu-core all 2.37-8build1 [834 kB] 137s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig-config ppc64el 2.17.1-3ubuntu1 [38.5 kB] 137s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libfontconfig1 ppc64el 2.17.1-3ubuntu1 [193 kB] 137s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el fontconfig ppc64el 2.17.1-3ubuntu1 [182 kB] 137s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 137s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 140s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-7ubuntu1 [291 kB] 140s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpixman-1-0 ppc64el 0.46.4-1 [347 kB] 140s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-render0 ppc64el 1.17.0-2ubuntu1 [17.4 kB] 140s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxcb-shm0 ppc64el 1.17.0-2ubuntu1 [6072 B] 140s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxrender1 ppc64el 1:0.9.12-1 [23.0 kB] 140s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcairo2 ppc64el 1.18.4-3 [759 kB] 142s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdatrie1 ppc64el 0.2.14-1 [22.7 kB] 142s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate0 ppc64el 1.23-2build1 [64.1 kB] 142s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-12ubuntu1 [620 kB] 143s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgomp1 ppc64el 15.2.0-12ubuntu1 [169 kB] 143s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgraphite2-3 ppc64el 1.3.14-11ubuntu1 [85.3 kB] 143s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libharfbuzz0b ppc64el 12.3.2-1 [663 kB] 144s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el x11-common all 1:7.7+24ubuntu1 [22.4 kB] 144s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el libice6 ppc64el 2:1.1.1-1build1 [51.9 kB] 144s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-4ubuntu3 [214 kB] 144s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 144s Get:24 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 144s Get:25 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 144s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 144s Get:27 http://ftpmaster.internal/ubuntu resolute/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 144s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-7ubuntu1 [2960 kB] 148s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu2 [315 kB] 148s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai-data all 0.1.30-1 [155 kB] 148s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libthai0 ppc64el 0.1.30-1 [22.5 kB] 148s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpango-1.0-0 ppc64el 1.57.0-1 [283 kB] 148s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangoft2-1.0-0 ppc64el 1.57.0-1 [61.2 kB] 148s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpangocairo-1.0-0 ppc64el 1.57.0-1 [31.0 kB] 148s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper2 ppc64el 2.2.5-0.3build1 [18.1 kB] 148s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpaper-utils ppc64el 2.2.5-0.3build1 [15.7 kB] 148s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1build1 [24.7 kB] 148s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libsm6 ppc64el 2:1.2.6-1build1 [18.6 kB] 148s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtcl8.6 ppc64el 8.6.17+dfsg-1build1 [1239 kB] 150s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu3 [37.1 kB] 150s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libwebp7 ppc64el 1.5.0-0.1build1 [330 kB] 150s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtiff6 ppc64el 4.7.0-3ubuntu3 [307 kB] 150s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxft2 ppc64el 2.3.6-1build2 [61.6 kB] 150s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxss1 ppc64el 1:1.2.3-1build4 [7470 B] 150s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtk8.6 ppc64el 8.6.17-1 [968 kB] 151s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.3 [203 kB] 151s Get:47 http://ftpmaster.internal/ubuntu resolute/universe ppc64el node-normalize.css all 8.0.1-5.1 [10.4 kB] 151s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el zip ppc64el 3.0-15ubuntu3 [198 kB] 151s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el unzip ppc64el 6.0-29ubuntu1 [200 kB] 151s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 151s Get:51 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-core ppc64el 4.5.2-1ubuntu2 [29.3 MB] 195s Get:52 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-cluster ppc64el 2.1.8.2-1 [588 kB] 196s Get:53 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-commonmark ppc64el 1.9.5-1 [142 kB] 196s Get:54 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-evaluate all 1.0.5-1 [117 kB] 196s Get:55 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-xfun ppc64el 0.55+dfsg-1 [589 kB] 197s Get:56 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 197s Get:57 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 197s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 206s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-knitr all 1.51+dfsg-1 [847 kB] 207s Get:60 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el r-cran-lattice ppc64el 0.22-9-1 [1399 kB] 210s Get:61 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-markdown all 1.13-1 [162 kB] 210s Get:62 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mass ppc64el 7.3-65-1 [1116 kB] 212s Get:63 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-matrix ppc64el 1.7-4-1 [4584 kB] 219s Get:64 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-nlme ppc64el 3.1.168-1 [2327 kB] 222s Get:65 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-mgcv ppc64el 1.9-4-1 [3694 kB] 227s Get:66 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-permute all 0.9-8-1 [237 kB] 228s Get:67 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-cran-vegan ppc64el 2.6-10+dfsg-3 [3151 kB] 232s Preconfiguring packages ... 233s Fetched 70.2 MB in 1min 37s (727 kB/s) 233s Selecting previously unselected package fonts-dejavu-mono. 233s (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 ... 122006 files and directories currently installed.) 233s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 233s Unpacking fonts-dejavu-mono (2.37-8build1) ... 233s Selecting previously unselected package fonts-dejavu-core. 233s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 233s Unpacking fonts-dejavu-core (2.37-8build1) ... 233s Selecting previously unselected package fontconfig-config. 233s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_ppc64el.deb ... 233s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 233s Selecting previously unselected package libfontconfig1:ppc64el. 233s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_ppc64el.deb ... 233s Unpacking libfontconfig1:ppc64el (2.17.1-3ubuntu1) ... 233s Selecting previously unselected package fontconfig. 233s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_ppc64el.deb ... 233s Unpacking fontconfig (2.17.1-3ubuntu1) ... 233s Selecting previously unselected package fonts-glyphicons-halflings. 233s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 233s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 233s Selecting previously unselected package fonts-mathjax. 233s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 233s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 233s Selecting previously unselected package libblas3:ppc64el. 233s Preparing to unpack .../07-libblas3_3.12.1-7ubuntu1_ppc64el.deb ... 233s Unpacking libblas3:ppc64el (3.12.1-7ubuntu1) ... 233s Selecting previously unselected package libpixman-1-0:ppc64el. 233s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_ppc64el.deb ... 233s Unpacking libpixman-1-0:ppc64el (0.46.4-1) ... 233s Selecting previously unselected package libxcb-render0:ppc64el. 233s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_ppc64el.deb ... 233s Unpacking libxcb-render0:ppc64el (1.17.0-2ubuntu1) ... 233s Selecting previously unselected package libxcb-shm0:ppc64el. 233s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_ppc64el.deb ... 233s Unpacking libxcb-shm0:ppc64el (1.17.0-2ubuntu1) ... 233s Selecting previously unselected package libxrender1:ppc64el. 233s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_ppc64el.deb ... 233s Unpacking libxrender1:ppc64el (1:0.9.12-1) ... 233s Selecting previously unselected package libcairo2:ppc64el. 233s Preparing to unpack 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libsm6:ppc64el (2:1.2.6-1build1) ... 236s Setting up fontconfig (2.17.1-3ubuntu1) ... 238s Regenerating fonts cache... done. 238s Setting up libxft2:ppc64el (2.3.6-1build2) ... 238s Setting up libtk8.6:ppc64el (8.6.17-1) ... 238s Setting up libpango-1.0-0:ppc64el (1.57.0-1) ... 238s Setting up libcairo2:ppc64el (1.18.4-3) ... 238s Setting up libxt6t64:ppc64el (1:1.2.1-1.3) ... 238s Setting up libpangoft2-1.0-0:ppc64el (1.57.0-1) ... 238s Setting up libpangocairo-1.0-0:ppc64el (1.57.0-1) ... 238s Setting up r-base-core (4.5.2-1ubuntu2) ... 238s Creating config file /etc/R/Renviron with new version 238s Setting up r-cran-lattice (0.22-9-1) ... 238s Setting up r-cran-nlme (3.1.168-1) ... 238s Setting up r-cran-cluster (2.1.8.2-1) ... 238s Setting up r-cran-commonmark (1.9.5-1) ... 238s Setting up r-cran-permute (0.9-8-1) ... 238s Setting up r-cran-xfun (0.55+dfsg-1) ... 238s Setting up r-cran-yaml (2.3.10-1) ... 238s Setting up r-cran-evaluate (1.0.5-1) ... 238s Setting up r-cran-highr (0.11+dfsg-1) ... 238s Setting up r-cran-mass (7.3-65-1) ... 238s Setting up r-cran-markdown (1.13-1) ... 238s Setting up r-cran-matrix (1.7-4-1) ... 238s Setting up r-cran-knitr (1.51+dfsg-1) ... 238s Setting up r-cran-mgcv (1.9-4-1) ... 238s Setting up r-cran-vegan (2.6-10+dfsg-3) ... 238s Processing triggers for libc-bin (2.42-2ubuntu4) ... 238s Processing triggers for man-db (2.13.1-1build1) ... 239s Processing triggers for install-info (7.2-5) ... 240s autopkgtest [22:56:22]: test run-unit-test: [----------------------- 240s 240s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 240s Copyright (C) 2025 The R Foundation for Statistical Computing 240s Platform: powerpc64le-unknown-linux-gnu 240s 240s R is free software and comes with ABSOLUTELY NO WARRANTY. 240s You are welcome to redistribute it under certain conditions. 240s Type 'license()' or 'licence()' for distribution details. 240s 240s R is a collaborative project with many contributors. 240s Type 'contributors()' for more information and 240s 'citation()' on how to cite R or R packages in publications. 240s 240s Type 'demo()' for some demos, 'help()' for on-line help, or 240s 'help.start()' for an HTML browser interface to help. 240s Type 'q()' to quit R. 240s 240s > Stangle("decision-vegan.Rnw") 240s Writing to file decision-vegan.R 240s > source("decision-vegan.R", echo=TRUE) 240s 240s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 240s 240s > options(SweaveHooks = list(fig = figset)) 240s 240s > options(prompt = "> ", continue = " ") 240s 240s > options(width = 55) 240s 240s > require(vegan) 240s Loading required package: vegan 240s Loading required package: permute 240s Loading required package: lattice 241s 241s > data(sipoo) 241s 241s > mod <- nestedtemp(sipoo) 241s 241s > plot(mod, "i") 241s 241s > x <- mod$c["Falcsubb"] 241s 241s > y <- 1 - mod$r["Svartholm"] 241s 241s > points(x, y, pch = 16, cex = 1.5) 241s 241s > abline(x + y, -1, lty = 2) 241s 241s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 241s 241s > cross <- function(x, a, p) f(x, p) - a + x 241s 241s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 241s 241s > arrows(x, y, r, f(r, mod$p), lwd = 4) 241s 241s > library(vegan) 241s 241s > data(varespec) 241s 241s > data(varechem) 241s 241s > orig <- cca(varespec ~ Al + K, varechem) 241s 241s > plot(orig, dis = c("lc", "bp")) 241s 241s > plot(orig, dis = c("lc", "bp")) 241s 241s > i <- sample(nrow(varespec)) 241s 241s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 241s 241s > plot(shuff, dis = c("lc", "bp")) 241s 241s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 241s + dis = "lc"))) 241s 241s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 241s + dis = "lc"))) 241s 241s > tmp1 <- rda(varespec ~ Al + K, varechem) 241s 241s > i <- sample(nrow(varespec)) 241s 241s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 241s 241s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 241s + dis = "lc"))) 241s 241s > orig 241s Call: cca(formula = varespec ~ Al + K, data = 241s varechem) 241s 241s -- Model Summary -- 241s 241s Inertia Proportion Rank 241s Total 2.0832 1.0000 241s Constrained 0.4760 0.2285 2 241s Unconstrained 1.6072 0.7715 21 241s 241s Inertia is scaled Chi-square 241s 241s -- Eigenvalues -- 241s 241s Eigenvalues for constrained axes: 241s CCA1 CCA2 241s 0.3608 0.1152 241s 241s Eigenvalues for unconstrained axes: 241s CA1 CA2 CA3 CA4 CA5 CA6 CA7 241s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 241s CA8 241s 0.0757 241s (Showing 8 of 21 unconstrained eigenvalues) 241s 241s 241s > shuff 241s Call: cca(formula = varespec[i, ] ~ Al + K, data = 241s varechem) 241s 241s -- Model Summary -- 241s 241s Inertia Proportion Rank 241s Total 2.08320 1.00000 241s Constrained 0.10590 0.05084 2 241s Unconstrained 1.97730 0.94916 21 241s 241s Inertia is scaled Chi-square 241s 241s -- Eigenvalues -- 241s 241s Eigenvalues for constrained axes: 241s CCA1 CCA2 241s 0.06222 0.04368 241s 241s Eigenvalues for unconstrained axes: 241s CA1 CA2 CA3 CA4 CA5 CA6 CA7 241s 0.5230 0.3299 0.2252 0.1840 0.1665 0.1172 0.1096 241s CA8 241s 0.0880 241s (Showing 8 of 21 unconstrained eigenvalues) 241s 241s 241s > plot(procrustes(orig, shuff)) 241s 241s > tmp1 <- rda(varespec ~ ., varechem) 241s 241s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 241s 241s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 241s + scores(tmp2, dis = "lc", choi = 1:14)) 241s 241s > max(residuals(proc)) 241s [1] 2.966836e-14 241s 241s > data(dune) 241s 241s > data(dune.env) 241s 241s > orig <- cca(dune ~ Moisture, dune.env) 241s 241s > plot(orig, dis = "lc") 241s 241s > plot(orig, display = "wa", type = "points") 241s 241s > ordispider(orig, col = "red") 241s 241s > text(orig, dis = "cn", col = "blue") 241s 241s > plot(orig, display = "wa", type = "points") 241s 241s > ordispider(orig, col = "red") 241s 241s > text(orig, dis = "cn", col = "blue") 241s > 241s 241s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 241s Copyright (C) 2025 The R Foundation for Statistical Computing 241s Platform: powerpc64le-unknown-linux-gnu 241s 241s R is free software and comes with ABSOLUTELY NO WARRANTY. 241s You are welcome to redistribute it under certain conditions. 241s Type 'license()' or 'licence()' for distribution details. 241s 241s R is a collaborative project with many contributors. 241s Type 'contributors()' for more information and 241s 'citation()' on how to cite R or R packages in publications. 241s 241s Type 'demo()' for some demos, 'help()' for on-line help, or 241s 'help.start()' for an HTML browser interface to help. 241s Type 'q()' to quit R. 241s 242s > Stangle("diversity-vegan.Rnw") 242s Writing to file diversity-vegan.R 242s > source("diversity-vegan.R", echo=TRUE) 242s 242s > par(mfrow = c(1, 1)) 242s 242s > options(width = 55) 242s 242s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 242s 242s > options(SweaveHooks = list(fig = figset)) 242s 242s > options(prompt = "> ", continue = " ") 242s 242s > library(vegan) 242s Loading required package: permute 242s Loading required package: lattice 243s 243s > data(BCI) 243s 243s > H <- diversity(BCI) 243s 243s > J <- H/log(specnumber(BCI)) 243s 243s > k <- sample(nrow(BCI), 6) 243s 243s > R <- renyi(BCI[k, ]) 243s 243s > print(plot(R)) 243s 243s > alpha <- fisher.alpha(BCI) 243s 243s > quantile(rowSums(BCI)) 243s 0% 25% 50% 75% 100% 243s 340.0 409.0 428.0 443.5 601.0 243s 243s > Srar <- rarefy(BCI, min(rowSums(BCI))) 243s 243s > S2 <- rarefy(BCI, 2) 243s 243s > all(rank(Srar) == rank(S2)) 243s [1] FALSE 243s 243s > range(diversity(BCI, "simp") - (S2 - 1)) 243s [1] -0.002868298 -0.001330663 243s 243s > data(dune) 243s 243s > data(dune.taxon) 243s 243s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 243s 243s > mod <- taxondive(dune, taxdis) 243s 243s > plot(mod) 243s 243s > tr <- hclust(taxdis, "aver") 243s 243s > mod <- treedive(dune, tr) 243s forced matching of 'tree' labels and 'comm' names 243s 243s > k <- sample(nrow(BCI), 1) 243s 243s > fish <- fisherfit(BCI[k, ]) 243s 243s > fish 243s 243s Fisher log series model 243s No. of species: 90 243s Fisher alpha: 33.32033 243s 243s 243s > plot(fish) 243s 243s > prestondistr(BCI[k, ]) 243s 243s Preston lognormal model 243s Method: maximized likelihood to log2 abundances 243s No. of species: 90 243s 243s mode width S0 243s 0.7976925 1.9441100 22.4558697 243s 243s Frequencies by Octave 243s 0 1 2 3 4 243s Observed 18.50000 24.50000 18.50000 14.00000 8.000000 243s Fitted 20.64295 22.33461 18.54723 11.82153 5.783124 243s 5 6 243s Observed 4.500000 2.0000000 243s Fitted 2.171427 0.6257803 243s 243s 243s > rad <- radfit(BCI[k, ]) 243s 243s > rad 243s 243s RAD models, family poisson 243s No. of species 90, total abundance 463 243s 243s par1 par2 par3 Deviance 243s Null 86.1127 243s Preemption 0.052303 58.9295 243s Lognormal 0.94937 1.1957 29.2719 243s Zipf 0.14769 -0.86485 50.1262 243s Mandelbrot 3.9471 -1.705 8.1741 5.7342 243s AIC BIC 243s Null 347.8863 347.8863 243s Preemption 322.7031 325.2029 243s Lognormal 295.0455 300.0451 243s Zipf 315.8997 320.8994 243s Mandelbrot 273.5077 281.0072 243s 243s > print(radlattice(rad)) 243s 243s > sac <- specaccum(BCI) 243s 243s > plot(sac, ci.type = "polygon", ci.col = "yellow") 243s 243s > sac <- specaccum(BCI) 243s 243s > plot(sac, ci.type = "polygon", ci.col = "yellow") 243s 243s > ncol(BCI)/mean(specnumber(BCI)) - 1 243s [1] 1.478519 243s 243s > beta <- vegdist(BCI, binary = TRUE) 243s 243s > mean(beta) 243s [1] 0.3399075 243s 243s > betadiver(help = TRUE) 243s 1 "w" = (b+c)/(2*a+b+c) 243s 2 "-1" = (b+c)/(2*a+b+c) 243s 3 "c" = (b+c)/2 243s 4 "wb" = b+c 243s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 243s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 243s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 243s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 243s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 243s (2*a+b+c))-1 243s 8 "t" = (b+c)/(2*a+b+c) 243s 9 "me" = (b+c)/(2*a+b+c) 243s 10 "j" = a/(a+b+c) 243s 11 "sor" = 2*a/(2*a+b+c) 243s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 243s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 243s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 243s 15 "cc" = (b+c)/(a+b+c) 243s 16 "g" = (b+c)/(a+b+c) 243s 17 "-3" = pmin.int(b,c)/(a+b+c) 243s 18 "l" = (b+c)/2 243s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 243s 20 "hk" = (b+c)/(2*a+b+c) 243s 21 "rlb" = a/(a+c) 243s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 243s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 243s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 243s 243s > z <- betadiver(BCI, "z") 243s 243s > quantile(z) 243s 0% 25% 50% 75% 100% 243s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 243s 243s > data(dune) 243s 243s > data(dune.env) 243s 243s > z <- betadiver(dune, "z") 243s 243s > mod <- with(dune.env, betadisper(z, Management)) 243s 243s > mod 243s 243s Homogeneity of multivariate dispersions 243s 243s Call: betadisper(d = z, group = Management) 243s 243s No. of Positive Eigenvalues: 12 243s No. of Negative Eigenvalues: 7 243s 243s Average distance to median: 243s BF HF NM SF 243s 0.2532 0.2512 0.4406 0.3635 243s 243s Eigenvalues for PCoA axes: 243s (Showing 8 of 19 eigenvalues) 243s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 243s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 243s PCoA7 PCoA8 243s 0.16128 0.08099 243s 243s > boxplot(mod) 243s 243s > specpool(BCI) 243s Species chao chao.se jack1 jack1.se jack2 243s All 225 236.3732 6.54361 245.58 5.650522 247.8722 243s boot boot.se n 243s All 235.6862 3.468888 50 243s 243s > s <- sample(nrow(BCI), 25) 243s 243s > specpool(BCI[s, ]) 243s Species chao chao.se jack1 jack1.se jack2 243s All 208 238.752 14.69087 237.76 8.414844 253.055 243s boot boot.se n 243s All 221.5454 4.550633 25 243s 243s > estimateR(BCI[k, ]) 243s 3 243s S.obs 90.000000 243s S.chao1 141.230769 243s se.chao1 23.001405 243s S.ACE 134.669844 243s se.ACE 6.191618 243s 243s > veiledspec(prestondistr(BCI[k, ])) 243s Extrapolated Observed Veiled 243s 109.43107 90.00000 19.43107 243s 243s > veiledspec(BCI[k, ]) 243s Extrapolated Observed Veiled 243s 122.83052 90.00000 32.83052 243s 243s > smo <- beals(BCI) 243s 243s > j <- which(colnames(BCI) == "Ceiba.pentandra") 243s 243s > plot(beals(BCI, species = j, include = FALSE), BCI[, 243s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 243s 243s > j <- which(colnames(BCI) == "Ceiba.pentandra") 243s 243s > plot(beals(BCI, species = j, include = FALSE), BCI[, 243s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 243s Warning messages: 243s 1: In cor(x > 0) : the standard deviation is zero 243s 2: In cor(x > 0) : the standard deviation is zero 243s 3: In betadisper(z, Management) : 243s some squared distances are negative and changed to zero 243s > 243s 243s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 243s Copyright (C) 2025 The R Foundation for Statistical Computing 243s Platform: powerpc64le-unknown-linux-gnu 243s 243s R is free software and comes with ABSOLUTELY NO WARRANTY. 243s You are welcome to redistribute it under certain conditions. 243s Type 'license()' or 'licence()' for distribution details. 243s 243s R is a collaborative project with many contributors. 243s Type 'contributors()' for more information and 243s 'citation()' on how to cite R or R packages in publications. 243s 243s Type 'demo()' for some demos, 'help()' for on-line help, or 243s 'help.start()' for an HTML browser interface to help. 243s Type 'q()' to quit R. 243s 243s > Stangle("intro-vegan.Rnw") 243s Writing to file intro-vegan.R 243s > source("intro-vegan.R", echo=TRUE) 243s 243s > par(mfrow = c(1, 1)) 243s 243s > options(width = 72) 243s 243s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 243s 243s > options(SweaveHooks = list(fig = figset)) 243s 243s > options(prompt = "> ", continue = " ") 243s 243s > library(vegan) 243s Loading required package: permute 243s Loading required package: lattice 244s 244s > data(dune) 244s 244s > ord <- decorana(dune) 244s 244s > ord 244s 244s Call: 244s decorana(veg = dune) 244s 244s Detrended correspondence analysis with 26 segments. 244s Rescaling of axes with 4 iterations. 244s Total inertia (scaled Chi-square): 2.1153 244s 244s DCA1 DCA2 DCA3 DCA4 244s Eigenvalues 0.5117 0.3036 0.12125 0.14267 244s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 244s Decorana values 0.5360 0.2869 0.08136 0.04814 244s Axis lengths 3.7004 3.1166 1.30055 1.47888 244s 244s 244s > ord <- metaMDS(dune, trace = FALSE) 244s 244s > ord 244s 244s Call: 244s metaMDS(comm = dune, trace = FALSE) 244s 244s global Multidimensional Scaling using monoMDS 244s 244s Data: dune 244s Distance: bray 244s 244s Dimensions: 2 244s Stress: 0.1183186 244s Stress type 1, weak ties 244s Best solution was repeated 1 time in 20 tries 244s The best solution was from try 19 (random start) 244s Scaling: centring, PC rotation, halfchange scaling 244s Species: expanded scores based on ‘dune’ 244s 244s 244s > plot(ord) 244s 244s > plot(ord) 244s 244s > plot(ord, type = "n") 244s 244s > points(ord, display = "sites", cex = 0.8, pch = 21, 244s + col = "red", bg = "yellow") 244s 244s > text(ord, display = "species", cex = 0.7, col = "blue") 244s 244s > plot(ord, type = "n") 244s 244s > points(ord, display = "sites", cex = 0.8, pch = 21, 244s + col = "red", bg = "yellow") 244s 244s > text(ord, display = "species", cex = 0.7, col = "blue") 244s 244s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 244s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 244s + col = "blue") 244s 244s > data(dune.env) 244s 244s > attach(dune.env) 244s 244s > plot(ord, disp = "sites", type = "n") 244s 244s > ordihull(ord, Management, col = 1:4, lwd = 3) 244s 244s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 244s + lwd = 3) 244s 244s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 244s 244s > ordispider(ord, Management, col = 1:4, label = TRUE) 244s 244s > points(ord, disp = "sites", pch = 21, col = "red", 244s + bg = "yellow", cex = 1.3) 244s 244s > plot(ord, disp = "sites", type = "n") 244s 244s > ordihull(ord, Management, col = 1:4, lwd = 3) 244s 244s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 244s + lwd = 3) 244s 244s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 244s 244s > ordispider(ord, Management, col = 1:4, label = TRUE) 244s 244s > points(ord, disp = "sites", pch = 21, col = "red", 244s + bg = "yellow", cex = 1.3) 244s 244s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 244s + perm = 999) 245s 245s > ord.fit 245s 245s ***VECTORS 245s 245s NMDS1 NMDS2 r2 Pr(>r) 245s A1 0.96474 0.26322 0.3649 0.015 * 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s Permutation: free 245s Number of permutations: 999 245s 245s ***FACTORS: 245s 245s Centroids: 245s NMDS1 NMDS2 245s ManagementBF -0.4534 -0.0102 245s ManagementHF -0.2636 -0.1282 245s ManagementNM 0.2958 0.5790 245s ManagementSF 0.1506 -0.4670 245s 245s Goodness of fit: 245s r2 Pr(>r) 245s Management 0.4134 0.005 ** 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s Permutation: free 245s Number of permutations: 999 245s 245s 245s 245s > plot(ord, dis = "site") 245s 245s > plot(ord.fit) 245s 245s > ordisurf(ord, A1, add = TRUE) 245s 245s Family: gaussian 245s Link function: identity 245s 245s Formula: 245s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 245s 245s Estimated degrees of freedom: 245s 1.59 total = 2.59 245s 245s REML score: 41.58728 245s 245s > plot(ord, dis = "site") 245s 245s > plot(ord.fit) 245s 245s > ordisurf(ord, A1, add = TRUE) 245s 245s Family: gaussian 245s Link function: identity 245s 245s Formula: 245s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 245s 245s Estimated degrees of freedom: 245s 1.59 total = 2.59 245s 245s REML score: 41.58728 245s 245s > ord <- cca(dune ~ A1 + Management, data = dune.env) 245s 245s > ord 245s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 245s 245s -- Model Summary -- 245s 245s Inertia Proportion Rank 245s Total 2.1153 1.0000 245s Constrained 0.7798 0.3686 4 245s Unconstrained 1.3355 0.6314 15 245s 245s Inertia is scaled Chi-square 245s 245s -- Eigenvalues -- 245s 245s Eigenvalues for constrained axes: 245s CCA1 CCA2 CCA3 CCA4 245s 0.3187 0.2372 0.1322 0.0917 245s 245s Eigenvalues for unconstrained axes: 245s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 245s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 245s CA11 CA12 CA13 CA14 CA15 245s 0.0317 0.0178 0.0116 0.0087 0.0047 245s 245s 245s > plot(ord) 245s 245s > plot(ord) 245s 245s > cca(dune ~ ., data = dune.env) 245s 245s Some constraints or conditions were aliased because they were 245s redundant. This can happen if terms are linearly dependent (collinear): 245s ‘Manure^4’ 245s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 245s Manure, data = dune.env) 245s 245s -- Model Summary -- 245s 245s Inertia Proportion Rank 245s Total 2.1153 1.0000 245s Constrained 1.5032 0.7106 12 245s Unconstrained 0.6121 0.2894 7 245s 245s Inertia is scaled Chi-square 245s 245s -- Note -- 245s 245s Some constraints or conditions were aliased because they were 245s redundant. This can happen if terms are linearly dependent 245s (collinear): ‘Manure^4’ 245s 245s -- Eigenvalues -- 245s 245s Eigenvalues for constrained axes: 245s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 245s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 245s CCA11 CCA12 245s 0.0228 0.0108 245s 245s Eigenvalues for unconstrained axes: 245s CA1 CA2 CA3 CA4 CA5 CA6 CA7 245s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 245s 245s 245s > anova(ord) 245s Permutation test for cca under reduced model 245s Permutation: free 245s Number of permutations: 999 245s 245s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 245s Df ChiSquare F Pr(>F) 245s Model 4 0.77978 2.1896 0.001 *** 245s Residual 15 1.33549 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > anova(ord, by = "term", permutations = 199) 245s Permutation test for cca under reduced model 245s Terms added sequentially (first to last) 245s Permutation: free 245s Number of permutations: 199 245s 245s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 245s Df ChiSquare F Pr(>F) 245s A1 1 0.22476 2.5245 0.015 * 245s Management 3 0.55502 2.0780 0.005 ** 245s Residual 15 1.33549 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > anova(ord, by = "mar", permutations = 199) 245s Permutation test for cca under reduced model 245s Marginal effects of terms 245s Permutation: free 245s Number of permutations: 199 245s 245s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 245s Df ChiSquare F Pr(>F) 245s A1 1 0.17594 1.9761 0.030 * 245s Management 3 0.55502 2.0780 0.005 ** 245s Residual 15 1.33549 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > anova(ord, by = "axis", permutations = 499) 245s Permutation test for cca under reduced model 245s Forward tests for axes 245s Permutation: free 245s Number of permutations: 499 245s 245s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 245s Df ChiSquare F Pr(>F) 245s CCA1 1 0.31875 3.5801 0.014 * 245s CCA2 1 0.23718 2.6640 0.158 245s CCA3 1 0.13217 1.4845 0.868 245s CCA4 1 0.09168 1.0297 1.000 245s Residual 15 1.33549 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 245s + data = dune.env) 245s 245s > ord 245s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 245s data = dune.env) 245s 245s -- Model Summary -- 245s 245s Inertia Proportion Rank 245s Total 2.1153 1.0000 245s Conditional 0.6283 0.2970 3 245s Constrained 0.5109 0.2415 4 245s Unconstrained 0.9761 0.4615 12 245s 245s Inertia is scaled Chi-square 245s 245s -- Eigenvalues -- 245s 245s Eigenvalues for constrained axes: 245s CCA1 CCA2 CCA3 CCA4 245s 0.24932 0.12090 0.08160 0.05904 245s 245s Eigenvalues for unconstrained axes: 245s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 245s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 245s CA10 CA11 CA12 245s 0.02102 0.01254 0.00928 245s 245s 245s > anova(ord, by = "term", permutations = 499) 245s Permutation test for cca under reduced model 245s Terms added sequentially (first to last) 245s Permutation: free 245s Number of permutations: 499 245s 245s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 245s Df ChiSquare F Pr(>F) 245s A1 1 0.11543 1.4190 1.000 245s Management 3 0.39543 1.6205 0.002 ** 245s Residual 12 0.97610 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 245s 245s > anova(ord, by = "term", permutations = how) 245s Permutation test for cca under reduced model 245s Terms added sequentially (first to last) 245s Plots: dune.env$Moisture, plot permutation: none 245s Permutation: free 245s Number of permutations: 499 245s 245s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 245s Df ChiSquare F Pr(>F) 245s A1 1 0.11543 1.4190 1.000 245s Management 3 0.39543 1.6205 0.002 ** 245s Residual 12 0.97610 245s --- 245s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 245s 245s > detach(dune.env) 245s > 245s 245s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 245s Copyright (C) 2025 The R Foundation for Statistical Computing 245s Platform: powerpc64le-unknown-linux-gnu 245s 245s R is free software and comes with ABSOLUTELY NO WARRANTY. 245s You are welcome to redistribute it under certain conditions. 245s Type 'license()' or 'licence()' for distribution details. 245s 245s R is a collaborative project with many contributors. 245s Type 'contributors()' for more information and 245s 'citation()' on how to cite R or R packages in publications. 245s 245s Type 'demo()' for some demos, 'help()' for on-line help, or 245s 'help.start()' for an HTML browser interface to help. 245s Type 'q()' to quit R. 245s 245s > Stangle("partitioning.Rnw") 245s Writing to file partitioning.R 245s > source("partitioning.R", echo=TRUE) 245s 245s > par(mfrow = c(1, 1)) 245s 245s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 245s 245s > options(SweaveHooks = list(fig = figset)) 245s 245s > library(vegan) 245s Loading required package: permute 245s Loading required package: lattice 246s 246s > labs <- paste("Table", 1:4) 246s 246s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 246s 246s > showvarparts(2, bg = cls, Xnames = labs) 246s 246s > showvarparts(3, bg = cls, Xnames = labs) 246s 246s > showvarparts(4, bg = cls, Xnames = labs) 246s > 252s Test cca-object-tests passed 254s Test oecosimu-tests passed 257s Test vegan-tests passed 258s autopkgtest [22:56:40]: test run-unit-test: -----------------------] 258s autopkgtest [22:56:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 258s run-unit-test PASS 258s autopkgtest [22:56:40]: test pkg-r-autopkgtest: preparing testbed 259s Reading package lists... 259s Building dependency tree... 259s Reading state information... 259s Solving dependencies... 259s The following NEW packages will be installed: 259s build-essential cpp cpp-15 cpp-15-powerpc64le-linux-gnu 259s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-15 259s g++-15-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-15 259s gcc-15-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-15 259s gfortran-15-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 259s icu-devtools libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 259s libcrypt-dev libdeflate-dev libgcc-15-dev libgfortran-15-dev libicu-dev 259s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 259s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 259s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 259s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 259s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto 259s zlib1g-dev 259s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 259s Need to get 104 MB of archives. 259s After this operation, 388 MB of additional disk space will be used. 259s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc-dev-bin ppc64el 2.42-2ubuntu4 [23.9 kB] 259s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el linux-libc-dev ppc64el 6.19.0-3.3 [1832 kB] 262s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcrypt-dev ppc64el 1:4.5.1-1 [162 kB] 262s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el rpcsvc-proto ppc64el 1.4.3-1build1 [84.2 kB] 262s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libc6-dev ppc64el 2.42-2ubuntu4 [2080 kB] 265s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el libisl23 ppc64el 0.27-1build1 [893 kB] 266s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el libmpc3 ppc64el 1.3.1-2 [62.5 kB] 266s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [11.4 MB] 283s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-15 ppc64el 15.2.0-12ubuntu1 [1038 B] 283s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [5746 B] 283s Get:11 http://ftpmaster.internal/ubuntu resolute/main ppc64el cpp ppc64el 4:15.2.0-4ubuntu1 [22.4 kB] 283s Get:12 http://ftpmaster.internal/ubuntu resolute/main ppc64el libcc1-0 ppc64el 15.2.0-12ubuntu1 [49.0 kB] 283s Get:13 http://ftpmaster.internal/ubuntu resolute/main ppc64el libitm1 ppc64el 15.2.0-12ubuntu1 [32.2 kB] 283s Get:14 http://ftpmaster.internal/ubuntu resolute/main ppc64el libasan8 ppc64el 15.2.0-12ubuntu1 [3006 kB] 288s Get:15 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblsan0 ppc64el 15.2.0-12ubuntu1 [1374 kB] 291s Get:16 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtsan2 ppc64el 15.2.0-12ubuntu1 [2729 kB] 296s Get:17 http://ftpmaster.internal/ubuntu resolute/main ppc64el libubsan1 ppc64el 15.2.0-12ubuntu1 [1231 kB] 298s Get:18 http://ftpmaster.internal/ubuntu resolute/main ppc64el libquadmath0 ppc64el 15.2.0-12ubuntu1 [160 kB] 298s Get:19 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgcc-15-dev ppc64el 15.2.0-12ubuntu1 [1670 kB] 302s Get:20 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [22.4 MB] 350s Get:21 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-15 ppc64el 15.2.0-12ubuntu1 [530 kB] 350s Get:22 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1220 B] 350s Get:23 http://ftpmaster.internal/ubuntu resolute/main ppc64el gcc ppc64el 4:15.2.0-4ubuntu1 [5032 B] 350s Get:24 http://ftpmaster.internal/ubuntu resolute/main ppc64el libstdc++-15-dev ppc64el 15.2.0-12ubuntu1 [2747 kB] 354s Get:25 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [13.0 MB] 374s Get:26 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-15 ppc64el 15.2.0-12ubuntu1 [25.3 kB] 374s Get:27 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [970 B] 374s Get:28 http://ftpmaster.internal/ubuntu resolute/main ppc64el g++ ppc64el 4:15.2.0-4ubuntu1 [1092 B] 374s Get:29 http://ftpmaster.internal/ubuntu resolute/main ppc64el build-essential ppc64el 12.12ubuntu2 [5256 B] 374s Get:30 http://ftpmaster.internal/ubuntu resolute/main ppc64el dctrl-tools ppc64el 2.24-3build4 [108 kB] 374s Get:31 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran-15-dev ppc64el 15.2.0-12ubuntu1 [651 kB] 375s Get:32 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15-powerpc64le-linux-gnu ppc64el 15.2.0-12ubuntu1 [12.3 MB] 393s Get:33 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-15 ppc64el 15.2.0-12ubuntu1 [18.1 kB] 393s Get:34 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:15.2.0-4ubuntu1 [1020 B] 393s Get:35 http://ftpmaster.internal/ubuntu resolute/main ppc64el gfortran ppc64el 4:15.2.0-4ubuntu1 [1166 B] 393s Get:36 http://ftpmaster.internal/ubuntu resolute/main ppc64el icu-devtools ppc64el 78.2-1ubuntu1 [246 kB] 393s Get:37 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas-dev ppc64el 3.12.1-7ubuntu1 [306 kB] 393s Get:38 http://ftpmaster.internal/ubuntu resolute/main ppc64el libbz2-dev ppc64el 1.0.8-6build2 [50.0 kB] 393s Get:39 http://ftpmaster.internal/ubuntu resolute/main ppc64el libdeflate-dev ppc64el 1.23-2build1 [71.8 kB] 393s Get:40 http://ftpmaster.internal/ubuntu resolute/main ppc64el libicu-dev ppc64el 78.2-1ubuntu1 [13.3 MB] 416s Get:41 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-4ubuntu3 [358 kB] 416s Get:42 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 416s Get:43 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 416s Get:44 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack-dev ppc64el 3.12.1-7ubuntu1 [6357 kB] 426s Get:45 http://ftpmaster.internal/ubuntu resolute/main ppc64el libncurses-dev ppc64el 6.6+20251231-1 [505 kB] 426s Get:46 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-16-0 ppc64el 10.46-1 [292 kB] 426s Get:47 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-32-0 ppc64el 10.46-1 [275 kB] 426s Get:48 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-posix3 ppc64el 10.46-1 [7334 B] 426s Get:49 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpcre2-dev ppc64el 10.46-1 [937 kB] 427s Get:50 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpkgconf3 ppc64el 1.8.1-4build1 [37.9 kB] 427s Get:51 http://ftpmaster.internal/ubuntu resolute/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu2 [903 kB] 429s Get:52 http://ftpmaster.internal/ubuntu resolute/main ppc64el libpng-dev ppc64el 1.6.54-1 [326 kB] 429s Get:53 http://ftpmaster.internal/ubuntu resolute/main ppc64el libreadline-dev ppc64el 8.3-3 [252 kB] 429s Get:54 http://ftpmaster.internal/ubuntu resolute/main ppc64el libzstd-dev ppc64el 1.5.7+dfsg-3 [528 kB] 430s Get:55 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblzma-dev ppc64el 5.8.2-2 [210 kB] 430s Get:56 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf-bin ppc64el 1.8.1-4build1 [22.7 kB] 430s Get:57 http://ftpmaster.internal/ubuntu resolute/main ppc64el pkgconf ppc64el 1.8.1-4build1 [16.8 kB] 430s Get:58 http://ftpmaster.internal/ubuntu resolute/main ppc64el libtirpc-dev ppc64el 1.3.6+ds-1 [223 kB] 430s Get:59 http://ftpmaster.internal/ubuntu resolute/universe ppc64el r-base-dev all 4.5.2-1ubuntu2 [1880 B] 430s Get:60 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pkg-r-autopkgtest all 20250812 [6158 B] 430s Fetched 104 MB in 2min 51s (607 kB/s) 430s Selecting previously unselected package libc-dev-bin. 430s (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 ... 129993 files and directories currently installed.) 430s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_ppc64el.deb ... 430s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 430s Selecting previously unselected package linux-libc-dev:ppc64el. 430s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_ppc64el.deb ... 430s Unpacking linux-libc-dev:ppc64el (6.19.0-3.3) ... 430s Selecting previously unselected package libcrypt-dev:ppc64el. 430s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_ppc64el.deb ... 430s Unpacking libcrypt-dev:ppc64el (1:4.5.1-1) ... 430s Selecting previously unselected package rpcsvc-proto. 430s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_ppc64el.deb ... 430s Unpacking rpcsvc-proto (1.4.3-1build1) ... 430s Selecting previously unselected package libc6-dev:ppc64el. 430s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_ppc64el.deb ... 430s Unpacking libc6-dev:ppc64el (2.42-2ubuntu4) ... 430s Selecting previously unselected package libisl23:ppc64el. 430s Preparing to unpack .../05-libisl23_0.27-1build1_ppc64el.deb ... 430s Unpacking libisl23:ppc64el (0.27-1build1) ... 431s Selecting previously unselected package libmpc3:ppc64el. 431s Preparing to unpack .../06-libmpc3_1.3.1-2_ppc64el.deb ... 431s Unpacking libmpc3:ppc64el (1.3.1-2) ... 431s Selecting previously unselected package cpp-15-powerpc64le-linux-gnu. 431s Preparing to unpack .../07-cpp-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package cpp-15. 431s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 431s Preparing to unpack .../09-cpp-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package cpp. 431s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking cpp (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package libcc1-0:ppc64el. 431s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libitm1:ppc64el. 431s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libitm1:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libasan8:ppc64el. 431s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libasan8:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package liblsan0:ppc64el. 431s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking liblsan0:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libtsan2:ppc64el. 431s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libtsan2:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libubsan1:ppc64el. 431s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libubsan1:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libquadmath0:ppc64el. 431s Preparing to unpack .../17-libquadmath0_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package libgcc-15-dev:ppc64el. 431s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package gcc-15-powerpc64le-linux-gnu. 431s Preparing to unpack .../19-gcc-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package gcc-15. 431s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 431s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 431s Preparing to unpack .../21-gcc-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package gcc. 431s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 431s Unpacking gcc (4:15.2.0-4ubuntu1) ... 431s Selecting previously unselected package libstdc++-15-dev:ppc64el. 431s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 431s Unpacking libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-15-powerpc64le-linux-gnu. 432s Preparing to unpack .../24-g++-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-15. 432s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking g++-15 (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package g++-powerpc64le-linux-gnu. 432s Preparing to unpack .../26-g++-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package g++. 432s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking g++ (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package build-essential. 432s Preparing to unpack .../28-build-essential_12.12ubuntu2_ppc64el.deb ... 432s Unpacking build-essential (12.12ubuntu2) ... 432s Selecting previously unselected package dctrl-tools. 432s Preparing to unpack .../29-dctrl-tools_2.24-3build4_ppc64el.deb ... 432s Unpacking dctrl-tools (2.24-3build4) ... 432s Selecting previously unselected package libgfortran-15-dev:ppc64el. 432s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gfortran-15-powerpc64le-linux-gnu. 432s Preparing to unpack .../31-gfortran-15-powerpc64le-linux-gnu_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gfortran-15. 432s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_ppc64el.deb ... 432s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 432s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 432s Preparing to unpack .../33-gfortran-powerpc64le-linux-gnu_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package gfortran. 432s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_ppc64el.deb ... 432s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 432s Selecting previously unselected package icu-devtools. 432s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_ppc64el.deb ... 432s Unpacking icu-devtools (78.2-1ubuntu1) ... 432s Selecting previously unselected package libblas-dev:ppc64el. 432s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_ppc64el.deb ... 432s Unpacking libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 432s Selecting previously unselected package libbz2-dev:ppc64el. 432s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_ppc64el.deb ... 432s Unpacking libbz2-dev:ppc64el (1.0.8-6build2) ... 432s Selecting previously unselected package libdeflate-dev:ppc64el. 432s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_ppc64el.deb ... 432s Unpacking libdeflate-dev:ppc64el (1.23-2build1) ... 432s Selecting previously unselected package libicu-dev:ppc64el. 432s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_ppc64el.deb ... 432s Unpacking libicu-dev:ppc64el (78.2-1ubuntu1) ... 432s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 432s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_ppc64el.deb ... 432s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 432s Selecting previously unselected package libjpeg8-dev:ppc64el. 432s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 432s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 432s Selecting previously unselected package libjpeg-dev:ppc64el. 432s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 432s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 432s Selecting previously unselected package liblapack-dev:ppc64el. 432s Preparing to unpack .../43-liblapack-dev_3.12.1-7ubuntu1_ppc64el.deb ... 432s Unpacking liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 433s Selecting previously unselected package libncurses-dev:ppc64el. 433s Preparing to unpack .../44-libncurses-dev_6.6+20251231-1_ppc64el.deb ... 433s Unpacking libncurses-dev:ppc64el (6.6+20251231-1) ... 433s Selecting previously unselected package libpcre2-16-0:ppc64el. 433s Preparing to unpack .../45-libpcre2-16-0_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-16-0:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpcre2-32-0:ppc64el. 433s Preparing to unpack .../46-libpcre2-32-0_10.46-1_ppc64el.deb ... 433s Unpacking libpcre2-32-0:ppc64el (10.46-1) ... 433s Selecting previously unselected package libpcre2-posix3:ppc64el. 433s Preparing to unpack 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.../52-libreadline-dev_8.3-3_ppc64el.deb ... 433s Unpacking libreadline-dev:ppc64el (8.3-3) ... 433s Selecting previously unselected package libzstd-dev:ppc64el. 433s Preparing to unpack .../53-libzstd-dev_1.5.7+dfsg-3_ppc64el.deb ... 433s Unpacking libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 433s Selecting previously unselected package liblzma-dev:ppc64el. 433s Preparing to unpack .../54-liblzma-dev_5.8.2-2_ppc64el.deb ... 433s Unpacking liblzma-dev:ppc64el (5.8.2-2) ... 433s Selecting previously unselected package pkgconf-bin. 433s Preparing to unpack .../55-pkgconf-bin_1.8.1-4build1_ppc64el.deb ... 433s Unpacking pkgconf-bin (1.8.1-4build1) ... 433s Selecting previously unselected package pkgconf:ppc64el. 433s Preparing to unpack .../56-pkgconf_1.8.1-4build1_ppc64el.deb ... 433s Unpacking pkgconf:ppc64el (1.8.1-4build1) ... 433s Selecting previously unselected package libtirpc-dev:ppc64el. 433s Preparing to unpack .../57-libtirpc-dev_1.3.6+ds-1_ppc64el.deb ... 433s Unpacking libtirpc-dev:ppc64el (1.3.6+ds-1) ... 433s Selecting previously unselected package r-base-dev. 433s Preparing to unpack .../58-r-base-dev_4.5.2-1ubuntu2_all.deb ... 433s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 433s Selecting previously unselected package pkg-r-autopkgtest. 433s Preparing to unpack .../59-pkg-r-autopkgtest_20250812_all.deb ... 433s Unpacking pkg-r-autopkgtest (20250812) ... 433s Setting up libzstd-dev:ppc64el (1.5.7+dfsg-3) ... 433s Setting up linux-libc-dev:ppc64el (6.19.0-3.3) ... 433s Setting up libpcre2-16-0:ppc64el (10.46-1) ... 433s Setting up libpcre2-32-0:ppc64el (10.46-1) ... 433s Setting up libtirpc-dev:ppc64el (1.3.6+ds-1) ... 433s Setting up libpkgconf3:ppc64el (1.8.1-4build1) ... 433s Setting up rpcsvc-proto (1.4.3-1build1) ... 433s Setting up libquadmath0:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libmpc3:ppc64el (1.3.1-2) ... 433s Setting up icu-devtools (78.2-1ubuntu1) ... 433s Setting up pkgconf-bin (1.8.1-4build1) ... 433s Setting up liblzma-dev:ppc64el (5.8.2-2) ... 433s Setting up libubsan1:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libpcre2-posix3:ppc64el (10.46-1) ... 433s Setting up libcrypt-dev:ppc64el (1:4.5.1-1) ... 433s Setting up libasan8:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libtsan2:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libisl23:ppc64el (0.27-1build1) ... 433s Setting up libc-dev-bin (2.42-2ubuntu4) ... 433s Setting up libdeflate-dev:ppc64el (1.23-2build1) ... 433s Setting up libcc1-0:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up liblsan0:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libblas-dev:ppc64el (3.12.1-7ubuntu1) ... 433s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 433s Setting up dctrl-tools (2.24-3build4) ... 433s Setting up libitm1:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libgcc-15-dev:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up libgfortran-15-dev:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up pkgconf:ppc64el (1.8.1-4build1) ... 433s Setting up cpp-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 433s Setting up liblapack-dev:ppc64el (3.12.1-7ubuntu1) ... 433s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 433s Setting up cpp-15 (15.2.0-12ubuntu1) ... 433s Setting up libc6-dev:ppc64el (2.42-2ubuntu4) ... 433s Setting up libicu-dev:ppc64el (78.2-1ubuntu1) ... 433s Setting up cpp-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 433s Setting up libbz2-dev:ppc64el (1.0.8-6build2) ... 433s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-4ubuntu3) ... 433s Setting up libncurses-dev:ppc64el (6.6+20251231-1) ... 433s Setting up libpcre2-dev:ppc64el (10.46-1) ... 433s Setting up gcc-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 433s Setting up libreadline-dev:ppc64el (8.3-3) ... 433s Setting up gcc-15 (15.2.0-12ubuntu1) ... 433s Setting up libstdc++-15-dev:ppc64el (15.2.0-12ubuntu1) ... 433s Setting up gcc-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 433s Setting up gfortran-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 433s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 433s Setting up cpp (4:15.2.0-4ubuntu1) ... 433s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 433s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 433s Setting up g++-15-powerpc64le-linux-gnu (15.2.0-12ubuntu1) ... 433s Setting up libpng-dev:ppc64el (1.6.54-1) ... 433s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 433s Setting up gcc (4:15.2.0-4ubuntu1) ... 433s Setting up gfortran-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 433s Setting up g++-15 (15.2.0-12ubuntu1) ... 433s Setting up g++-powerpc64le-linux-gnu (4:15.2.0-4ubuntu1) ... 433s Setting up gfortran (4:15.2.0-4ubuntu1) ... 433s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 433s 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 433s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 433s 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 433s Setting up g++ (4:15.2.0-4ubuntu1) ... 433s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 433s Setting up build-essential (12.12ubuntu2) ... 433s Setting up r-base-dev (4.5.2-1ubuntu2) ... 433s Setting up pkg-r-autopkgtest (20250812) ... 433s Processing triggers for libc-bin (2.42-2ubuntu4) ... 433s Processing triggers for man-db (2.13.1-1build1) ... 434s Processing triggers for install-info (7.2-5) ... 435s autopkgtest [22:59:37]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 435s autopkgtest [22:59:37]: test pkg-r-autopkgtest: [----------------------- 435s Test: Try to load the R library vegan 435s 435s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 435s Copyright (C) 2025 The R Foundation for Statistical Computing 435s Platform: powerpc64le-unknown-linux-gnu 435s 435s R is free software and comes with ABSOLUTELY NO WARRANTY. 435s You are welcome to redistribute it under certain conditions. 435s Type 'license()' or 'licence()' for distribution details. 435s 435s R is a collaborative project with many contributors. 435s Type 'contributors()' for more information and 435s 'citation()' on how to cite R or R packages in publications. 435s 435s Type 'demo()' for some demos, 'help()' for on-line help, or 435s 'help.start()' for an HTML browser interface to help. 435s Type 'q()' to quit R. 435s 436s > library('vegan') 436s Loading required package: permute 436s Loading required package: lattice 436s > 437s autopkgtest [22:59:39]: test pkg-r-autopkgtest: -----------------------] 437s pkg-r-autopkgtest PASS 437s autopkgtest [22:59:39]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 437s autopkgtest [22:59:39]: @@@@@@@@@@@@@@@@@@@@ summary 437s run-unit-test PASS 437s pkg-r-autopkgtest PASS