0s autopkgtest [23:11:39]: starting date and time: 2026-02-09 23:11:39+0000 0s autopkgtest [23:11:39]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [23:11:39]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o1zyu835/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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-arm64-11.secgroup --name adt-resolute-arm64-r-cran-vegan-20260209-231138-juju-7f2275-prod-proposed-migration-environment-15-397becbe-ed20-4c91-8dad-e96e9e03dad8 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-r-cran-vegan-20260209-231138-juju-7f2275-prod-proposed-migration-environment-15-397becbe-ed20-4c91-8dad-e96e9e03dad8 from image adt/ubuntu-resolute-arm64-server-20260209.img (UUID 793037ca-75af-461b-82de-f8081300b2e3)... 108s autopkgtest [23:13:27]: testbed dpkg architecture: arm64 109s autopkgtest [23:13:28]: testbed apt version: 3.1.15 109s autopkgtest [23:13:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 109s autopkgtest [23:13:28]: testbed release detected to be: None 110s autopkgtest [23:13:29]: updating testbed package index (apt update) 110s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 110s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 110s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 110s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1645 kB] 112s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [176 kB] 112s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 112s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [246 kB] 112s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [6216 B] 113s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 113s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1580 kB] 115s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [32.0 kB] 115s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [21.7 kB] 115s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [688 B] 116s Fetched 3862 kB in 5s (816 kB/s) 117s 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 118s 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 2534 kB of archives. 119s After this operation, 18.4 kB of additional disk space will be used. 119s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 iptables arm64 1.8.11-2ubuntu3 [386 kB] 119s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libip4tc2 arm64 1.8.11-2ubuntu3 [24.3 kB] 119s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libip6tc2 arm64 1.8.11-2ubuntu3 [24.7 kB] 119s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libxtables12 arm64 1.8.11-2ubuntu3 [36.7 kB] 119s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 iproute2 arm64 6.18.0-1ubuntu1 [1171 kB] 121s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libcryptsetup12 arm64 2:2.8.0-1ubuntu3 [274 kB] 121s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 wget arm64 1.25.0-2ubuntu4 [344 kB] 121s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cryptsetup-bin arm64 2:2.8.0-1ubuntu3 [227 kB] 121s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 dracut-install arm64 109-11ubuntu1 [45.3 kB] 122s dpkg-preconfigure: unable to re-open stdin: No such file or directory 122s Fetched 2534 kB in 2s (1284 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 ... 136597 files and directories currently installed.) 122s Preparing to unpack .../0-iptables_1.8.11-2ubuntu3_arm64.deb ... 122s Unpacking iptables (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../1-libip4tc2_1.8.11-2ubuntu3_arm64.deb ... 122s Unpacking libip4tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../2-libip6tc2_1.8.11-2ubuntu3_arm64.deb ... 122s Unpacking libip6tc2:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../3-libxtables12_1.8.11-2ubuntu3_arm64.deb ... 122s Unpacking libxtables12:arm64 (1.8.11-2ubuntu3) over (1.8.11-2ubuntu2) ... 122s Preparing to unpack .../4-iproute2_6.18.0-1ubuntu1_arm64.deb ... 122s Unpacking iproute2 (6.18.0-1ubuntu1) over (6.16.0-1ubuntu3) ... 123s Preparing to unpack .../5-libcryptsetup12_2%3a2.8.0-1ubuntu3_arm64.deb ... 123s Unpacking libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 123s Preparing to unpack .../6-wget_1.25.0-2ubuntu4_arm64.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_arm64.deb ... 123s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 123s Preparing to unpack .../8-dracut-install_109-11ubuntu1_arm64.deb ... 123s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 123s Setting up libip4tc2:arm64 (1.8.11-2ubuntu3) ... 123s Setting up wget (1.25.0-2ubuntu4) ... 123s Setting up libip6tc2:arm64 (1.8.11-2ubuntu3) ... 123s Setting up libxtables12:arm64 (1.8.11-2ubuntu3) ... 123s Setting up dracut-install (109-11ubuntu1) ... 123s Setting up libcryptsetup12:arm64 (2:2.8.0-1ubuntu3) ... 123s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 123s Setting up iptables (1.8.11-2ubuntu3) ... 123s Setting up iproute2 (6.18.0-1ubuntu1) ... 123s Processing triggers for man-db (2.13.1-1build1) ... 124s Processing triggers for install-info (7.2-5) ... 124s Processing triggers for libc-bin (2.42-2ubuntu4) ... 124s autopkgtest [23:13:43]: upgrading testbed (apt dist-upgrade and autopurge) 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 125s 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... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [23:13:49]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 19:46:27 UTC 2026 130s autopkgtest [23:13:49]: @@@@@@@@@@@@@@@@@@@@ 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] 133s gpgv: Signature made Sat Apr 19 05:22:19 2025 UTC 133s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 133s gpgv: issuer "tille@debian.org" 133s gpgv: Can't check signature: No public key 133s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-3.dsc: no acceptable signature found 133s autopkgtest [23:13:52]: testing package r-cran-vegan version 2.6-10+dfsg-3 134s autopkgtest [23:13:53]: build not needed 136s autopkgtest [23:13:55]: test run-unit-test: preparing testbed 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Solving dependencies... 137s The following NEW packages will be installed: 137s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 137s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 137s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 137s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 137s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 137s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 137s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 137s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 137s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 137s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 137s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 137s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 137s x11-common xdg-utils zip 137s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 66.3 MB of archives. 137s After this operation, 158 MB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 137s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-dejavu-core all 2.37-8build1 [834 kB] 138s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig-config arm64 2.17.1-3ubuntu1 [38.5 kB] 138s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libfontconfig1 arm64 2.17.1-3ubuntu1 [144 kB] 138s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 fontconfig arm64 2.17.1-3ubuntu1 [181 kB] 138s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 138s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 141s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 141s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libpixman-1-0 arm64 0.46.4-1 [204 kB] 141s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-render0 arm64 1.17.0-2ubuntu1 [16.4 kB] 141s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 libxcb-shm0 arm64 1.17.0-2ubuntu1 [5938 B] 141s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libxrender1 arm64 1:0.9.12-1 [19.5 kB] 141s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libcairo2 arm64 1.18.4-3 [556 kB] 142s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libdatrie1 arm64 0.2.14-1 [19.6 kB] 142s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2build1 [46.8 kB] 142s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 142s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 142s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libgraphite2-3 arm64 1.3.14-11ubuntu1 [72.1 kB] 142s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libharfbuzz0b arm64 12.3.2-1 [510 kB] 142s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 142s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libice6 arm64 2:1.1.1-1build1 [43.0 kB] 142s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8 arm64 2.1.5-4ubuntu3 [161 kB] 142s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 142s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 142s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 142s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 142s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 142s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 145s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu2 [174 kB] 145s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai-data all 0.1.30-1 [155 kB] 145s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libthai0 arm64 0.1.30-1 [18.3 kB] 145s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libpango-1.0-0 arm64 1.57.0-1 [238 kB] 145s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangoft2-1.0-0 arm64 1.57.0-1 [51.5 kB] 145s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 libpangocairo-1.0-0 arm64 1.57.0-1 [27.9 kB] 145s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper2 arm64 2.2.5-0.3build1 [17.3 kB] 145s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 libpaper-utils arm64 2.2.5-0.3build1 [15.4 kB] 145s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libsharpyuv0 arm64 1.5.0-0.1build1 [16.7 kB] 145s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libsm6 arm64 2:1.2.6-1build1 [16.8 kB] 145s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtcl8.6 arm64 8.6.17+dfsg-1build1 [983 kB] 146s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libjbig0 arm64 2.1-6.1ubuntu3 [29.2 kB] 146s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libwebp7 arm64 1.5.0-0.1build1 [205 kB] 146s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libtiff6 arm64 4.7.0-3ubuntu3 [196 kB] 146s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libxft2 arm64 2.3.6-1build2 [43.2 kB] 146s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libxss1 arm64 1:1.2.3-1build4 [7102 B] 146s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libtk8.6 arm64 8.6.17-1 [811 kB] 148s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libxt6t64 arm64 1:1.2.1-1.3 [168 kB] 148s Get:47 http://ftpmaster.internal/ubuntu resolute/universe arm64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 148s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 zip arm64 3.0-15ubuntu3 [170 kB] 148s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 unzip arm64 6.0-29ubuntu1 [176 kB] 148s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 148s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-core arm64 4.5.2-1ubuntu2 [28.6 MB] 183s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-cluster arm64 2.1.8.2-1 [568 kB] 183s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-commonmark arm64 1.9.5-1 [130 kB] 183s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-evaluate all 1.0.5-1 [117 kB] 183s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-xfun arm64 0.55+dfsg-1 [587 kB] 184s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 184s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 184s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 191s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 193s Get:60 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 r-cran-lattice arm64 0.22-9-1 [1399 kB] 195s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-markdown all 1.13-1 [162 kB] 195s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 197s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-matrix arm64 1.7-4-1 [4146 kB] 201s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 204s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-mgcv arm64 1.9-4-1 [3546 kB] 208s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-permute all 0.9-8-1 [237 kB] 208s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-cran-vegan arm64 2.6-10+dfsg-3 [3134 kB] 213s Preconfiguring packages ... 213s Fetched 66.3 MB in 1min 15s (882 kB/s) 213s Selecting previously unselected package fonts-dejavu-mono. 213s (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 ... 136600 files and directories currently installed.) 213s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 213s Unpacking fonts-dejavu-mono (2.37-8build1) ... 213s Selecting previously unselected package fonts-dejavu-core. 213s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 213s Unpacking fonts-dejavu-core (2.37-8build1) ... 213s Selecting previously unselected package fontconfig-config. 213s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_arm64.deb ... 213s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 213s Selecting previously unselected package libfontconfig1:arm64. 213s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_arm64.deb ... 213s Unpacking libfontconfig1:arm64 (2.17.1-3ubuntu1) ... 213s Selecting previously unselected package fontconfig. 213s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_arm64.deb ... 213s Unpacking fontconfig (2.17.1-3ubuntu1) ... 213s Selecting previously unselected package fonts-glyphicons-halflings. 213s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 213s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 213s Selecting previously unselected package fonts-mathjax. 213s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 213s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 213s Selecting previously unselected package libblas3:arm64. 213s Preparing to unpack .../07-libblas3_3.12.1-7ubuntu1_arm64.deb ... 213s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 213s Selecting previously unselected package libpixman-1-0:arm64. 213s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_arm64.deb ... 213s Unpacking libpixman-1-0:arm64 (0.46.4-1) ... 213s Selecting previously unselected package libxcb-render0:arm64. 213s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_arm64.deb ... 213s Unpacking libxcb-render0:arm64 (1.17.0-2ubuntu1) ... 213s Selecting previously unselected package libxcb-shm0:arm64. 213s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_arm64.deb ... 213s Unpacking libxcb-shm0:arm64 (1.17.0-2ubuntu1) ... 213s Selecting previously unselected package libxrender1:arm64. 213s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_arm64.deb ... 213s Unpacking libxrender1:arm64 (1:0.9.12-1) ... 213s Selecting previously unselected package libcairo2:arm64. 213s Preparing to unpack .../12-libcairo2_1.18.4-3_arm64.deb ... 213s Unpacking libcairo2:arm64 (1.18.4-3) ... 214s Selecting previously unselected package libdatrie1:arm64. 214s Preparing to unpack .../13-libdatrie1_0.2.14-1_arm64.deb ... 214s Unpacking libdatrie1:arm64 (0.2.14-1) ... 214s Selecting previously unselected package libdeflate0:arm64. 214s Preparing to unpack .../14-libdeflate0_1.23-2build1_arm64.deb ... 214s Unpacking libdeflate0:arm64 (1.23-2build1) ... 214s Selecting previously unselected package libgfortran5:arm64. 214s Preparing to unpack .../15-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 214s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 214s Selecting previously unselected package libgomp1:arm64. 214s Preparing to unpack .../16-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 214s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 214s Selecting previously unselected package libgraphite2-3:arm64. 214s Preparing to unpack .../17-libgraphite2-3_1.3.14-11ubuntu1_arm64.deb ... 214s Unpacking libgraphite2-3:arm64 (1.3.14-11ubuntu1) ... 214s 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... 220s Processing triggers for man-db (2.13.1-1build1) ... 221s Processing triggers for install-info (7.2-5) ... 222s autopkgtest [23:15:21]: test run-unit-test: [----------------------- 222s 222s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 222s Copyright (C) 2025 The R Foundation for Statistical Computing 222s Platform: aarch64-unknown-linux-gnu 222s 222s R is free software and comes with ABSOLUTELY NO WARRANTY. 222s You are welcome to redistribute it under certain conditions. 222s Type 'license()' or 'licence()' for distribution details. 222s 222s R is a collaborative project with many contributors. 222s Type 'contributors()' for more information and 222s 'citation()' on how to cite R or R packages in publications. 222s 222s Type 'demo()' for some demos, 'help()' for on-line help, or 222s 'help.start()' for an HTML browser interface to help. 222s Type 'q()' to quit R. 222s 222s > Stangle("decision-vegan.Rnw") 222s Writing to file decision-vegan.R 222s > source("decision-vegan.R", echo=TRUE) 222s 222s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 222s 222s > options(SweaveHooks = list(fig = figset)) 222s 222s > options(prompt = "> ", continue = " ") 222s 222s > options(width = 55) 222s 222s > require(vegan) 222s Loading required package: vegan 222s Loading required package: permute 222s Loading required package: lattice 223s 223s > data(sipoo) 223s 223s > mod <- nestedtemp(sipoo) 223s 223s > plot(mod, "i") 223s 223s > x <- mod$c["Falcsubb"] 223s 223s > y <- 1 - mod$r["Svartholm"] 223s 223s > points(x, y, pch = 16, cex = 1.5) 223s 223s > abline(x + y, -1, lty = 2) 223s 223s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 223s 223s > cross <- function(x, a, p) f(x, p) - a + x 223s 223s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 223s 223s > arrows(x, y, r, f(r, mod$p), lwd = 4) 223s 223s > library(vegan) 223s 223s > data(varespec) 223s 223s > data(varechem) 223s 223s > orig <- cca(varespec ~ Al + K, varechem) 223s 223s > plot(orig, dis = c("lc", "bp")) 223s 223s > plot(orig, dis = c("lc", "bp")) 223s 223s > i <- sample(nrow(varespec)) 223s 223s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 223s 223s > plot(shuff, dis = c("lc", "bp")) 223s 223s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 223s + dis = "lc"))) 223s 223s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 223s + dis = "lc"))) 223s 223s > tmp1 <- rda(varespec ~ Al + K, varechem) 223s 223s > i <- sample(nrow(varespec)) 223s 223s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 223s 223s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 223s + dis = "lc"))) 223s 223s > orig 223s Call: cca(formula = varespec ~ Al + K, data = 223s varechem) 223s 223s -- Model Summary -- 223s 223s Inertia Proportion Rank 223s Total 2.0832 1.0000 223s Constrained 0.4760 0.2285 2 223s Unconstrained 1.6072 0.7715 21 223s 223s Inertia is scaled Chi-square 223s 223s -- Eigenvalues -- 223s 223s Eigenvalues for constrained axes: 223s CCA1 CCA2 223s 0.3608 0.1152 223s 223s Eigenvalues for unconstrained axes: 223s CA1 CA2 CA3 CA4 CA5 CA6 CA7 223s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 223s CA8 223s 0.0757 223s (Showing 8 of 21 unconstrained eigenvalues) 223s 223s 223s > shuff 223s Call: cca(formula = varespec[i, ] ~ Al + K, data = 223s varechem) 223s 223s -- Model Summary -- 223s 223s Inertia Proportion Rank 223s Total 2.08320 1.00000 223s Constrained 0.16405 0.07875 2 223s Unconstrained 1.91915 0.92125 21 223s 223s Inertia is scaled Chi-square 223s 223s -- Eigenvalues -- 223s 223s Eigenvalues for constrained axes: 223s CCA1 CCA2 223s 0.10528 0.05877 223s 223s Eigenvalues for unconstrained axes: 223s CA1 CA2 CA3 CA4 CA5 CA6 CA7 223s 0.4817 0.3517 0.1944 0.1897 0.1551 0.1155 0.1119 223s CA8 223s 0.0823 223s (Showing 8 of 21 unconstrained eigenvalues) 223s 223s 223s > plot(procrustes(orig, shuff)) 223s 223s > tmp1 <- rda(varespec ~ ., varechem) 223s 223s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 223s 223s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 223s + scores(tmp2, dis = "lc", choi = 1:14)) 223s 223s > max(residuals(proc)) 223s [1] 3.139821e-14 223s 223s > data(dune) 223s 223s > data(dune.env) 223s 223s > orig <- cca(dune ~ Moisture, dune.env) 223s 223s > plot(orig, dis = "lc") 223s 223s > plot(orig, display = "wa", type = "points") 223s 223s > ordispider(orig, col = "red") 223s 223s > text(orig, dis = "cn", col = "blue") 223s 223s > plot(orig, display = "wa", type = "points") 223s 223s > ordispider(orig, col = "red") 223s 223s > text(orig, dis = "cn", col = "blue") 223s > 223s 223s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 223s Copyright (C) 2025 The R Foundation for Statistical Computing 223s Platform: aarch64-unknown-linux-gnu 223s 223s R is free software and comes with ABSOLUTELY NO WARRANTY. 223s You are welcome to redistribute it under certain conditions. 223s Type 'license()' or 'licence()' for distribution details. 223s 223s R is a collaborative project with many contributors. 223s Type 'contributors()' for more information and 223s 'citation()' on how to cite R or R packages in publications. 223s 223s Type 'demo()' for some demos, 'help()' for on-line help, or 223s 'help.start()' for an HTML browser interface to help. 223s Type 'q()' to quit R. 223s 224s > Stangle("diversity-vegan.Rnw") 224s Writing to file diversity-vegan.R 224s > source("diversity-vegan.R", echo=TRUE) 224s 224s > par(mfrow = c(1, 1)) 224s 224s > options(width = 55) 224s 224s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 224s 224s > options(SweaveHooks = list(fig = figset)) 224s 224s > options(prompt = "> ", continue = " ") 224s 224s > library(vegan) 224s Loading required package: permute 224s Loading required package: lattice 225s 225s > data(BCI) 225s 225s > H <- diversity(BCI) 225s 225s > J <- H/log(specnumber(BCI)) 225s 225s > k <- sample(nrow(BCI), 6) 225s 225s > R <- renyi(BCI[k, ]) 225s 225s > print(plot(R)) 225s 225s > alpha <- fisher.alpha(BCI) 225s 225s > quantile(rowSums(BCI)) 225s 0% 25% 50% 75% 100% 225s 340.0 409.0 428.0 443.5 601.0 225s 225s > Srar <- rarefy(BCI, min(rowSums(BCI))) 225s 225s > S2 <- rarefy(BCI, 2) 225s 225s > all(rank(Srar) == rank(S2)) 225s [1] FALSE 225s 225s > range(diversity(BCI, "simp") - (S2 - 1)) 225s [1] -0.002868298 -0.001330663 225s 225s > data(dune) 225s 225s > data(dune.taxon) 225s 225s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 225s 225s > mod <- taxondive(dune, taxdis) 225s 225s > plot(mod) 225s 225s > tr <- hclust(taxdis, "aver") 225s forced matching of 'tree' labels and 'comm' names 225s 225s > mod <- treedive(dune, tr) 225s 225s > k <- sample(nrow(BCI), 1) 225s 225s > fish <- fisherfit(BCI[k, ]) 225s 225s > fish 225s 225s Fisher log series model 225s No. of species: 81 225s Fisher alpha: 29.02041 225s 225s 225s > plot(fish) 225s 225s > prestondistr(BCI[k, ]) 225s 225s Preston lognormal model 225s Method: maximized likelihood to log2 abundances 225s No. of species: 81 225s 225s mode width S0 225s 0.5985323 2.0883063 19.8892888 225s 225s Frequencies by Octave 225s 0 1 2 3 4 225s Observed 17.00000 24.00000 15.00000 10.00000 9.000000 225s Fitted 19.08892 19.52513 15.87891 10.26744 5.278594 225s 5 6 225s Observed 3.500000 2.5000000 225s Fitted 2.157689 0.7012518 225s 225s 225s > rad <- radfit(BCI[k, ]) 225s 225s > rad 225s 225s RAD models, family poisson 225s No. of species 81, total abundance 444 225s 225s par1 par2 par3 Deviance 225s Null 114.1829 225s Preemption 0.062873 82.1220 225s Lognormal 0.89266 1.301 24.4013 225s Zipf 0.17917 -0.94243 32.6148 225s Mandelbrot 1.4107 -1.508 4.0101 7.7853 225s AIC BIC 225s Null 349.0742 349.0742 225s Preemption 319.0133 321.4078 225s Lognormal 263.2927 268.0816 225s Zipf 271.5062 276.2951 225s Mandelbrot 248.6766 255.8600 225s 225s > print(radlattice(rad)) 225s 225s > sac <- specaccum(BCI) 225s 225s > plot(sac, ci.type = "polygon", ci.col = "yellow") 225s 225s > sac <- specaccum(BCI) 225s 225s > plot(sac, ci.type = "polygon", ci.col = "yellow") 225s 225s > ncol(BCI)/mean(specnumber(BCI)) - 1 225s [1] 1.478519 225s 225s > beta <- vegdist(BCI, binary = TRUE) 225s 225s > mean(beta) 225s [1] 0.3399075 225s 225s > betadiver(help = TRUE) 225s 1 "w" = (b+c)/(2*a+b+c) 225s 2 "-1" = (b+c)/(2*a+b+c) 225s 3 "c" = (b+c)/2 225s 4 "wb" = b+c 225s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 225s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 225s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 225s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 225s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 225s (2*a+b+c))-1 225s 8 "t" = (b+c)/(2*a+b+c) 225s 9 "me" = (b+c)/(2*a+b+c) 225s 10 "j" = a/(a+b+c) 225s 11 "sor" = 2*a/(2*a+b+c) 225s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 225s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 225s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 225s 15 "cc" = (b+c)/(a+b+c) 225s 16 "g" = (b+c)/(a+b+c) 225s 17 "-3" = pmin.int(b,c)/(a+b+c) 225s 18 "l" = (b+c)/2 225s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 225s 20 "hk" = (b+c)/(2*a+b+c) 225s 21 "rlb" = a/(a+c) 225s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 225s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 225s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 225s 225s > z <- betadiver(BCI, "z") 225s 225s > quantile(z) 225s 0% 25% 50% 75% 100% 225s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 225s 225s > data(dune) 225s 225s > data(dune.env) 225s 225s > z <- betadiver(dune, "z") 225s 225s > mod <- with(dune.env, betadisper(z, Management)) 225s 225s > mod 225s 225s Homogeneity of multivariate dispersions 225s 225s Call: betadisper(d = z, group = Management) 225s 225s No. of Positive Eigenvalues: 12 225s No. of Negative Eigenvalues: 7 225s 225s Average distance to median: 225s BF HF NM SF 225s 0.2532 0.2512 0.4406 0.3635 225s 225s Eigenvalues for PCoA axes: 225s (Showing 8 of 19 eigenvalues) 225s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 225s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 225s PCoA7 PCoA8 225s 0.16128 0.08099 225s 225s > boxplot(mod) 225s 225s > specpool(BCI) 225s Species chao chao.se jack1 jack1.se jack2 225s All 225 236.3732 6.54361 245.58 5.650522 247.8722 225s boot boot.se n 225s All 235.6862 3.468888 50 225s 225s > s <- sample(nrow(BCI), 25) 225s 225s > specpool(BCI[s, ]) 225s Species chao chao.se jack1 jack1.se jack2 225s All 204 209.12 3.572935 219.36 5.486857 212.92 225s boot boot.se n 225s All 213.5289 3.860524 25 225s 225s > estimateR(BCI[k, ]) 225s 45 225s S.obs 81.000000 225s S.chao1 118.400000 225s se.chao1 17.143725 225s S.ACE 129.701001 225s se.ACE 6.249946 225s 225s > veiledspec(prestondistr(BCI[k, ])) 225s Extrapolated Observed Veiled 225s 104.11262 81.00000 23.11262 225s 225s > veiledspec(BCI[k, ]) 225s Extrapolated Observed Veiled 225s 127.42578 81.00000 46.42578 225s 225s > smo <- beals(BCI) 225s 225s > j <- which(colnames(BCI) == "Ceiba.pentandra") 225s 225s > plot(beals(BCI, species = j, include = FALSE), BCI[, 225s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 225s 225s > j <- which(colnames(BCI) == "Ceiba.pentandra") 225s 225s > plot(beals(BCI, species = j, include = FALSE), BCI[, 225s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 225s Warning messages: 225s 1: In cor(x > 0) : the standard deviation is zero 225s 2: > 225s In cor(x > 0) : the standard deviation is zero 225s 3: In betadisper(z, Management) : 225s some squared distances are negative and changed to zero 225s 225s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 225s Copyright (C) 2025 The R Foundation for Statistical Computing 225s Platform: aarch64-unknown-linux-gnu 225s 225s R is free software and comes with ABSOLUTELY NO WARRANTY. 225s You are welcome to redistribute it under certain conditions. 225s Type 'license()' or 'licence()' for distribution details. 225s 225s R is a collaborative project with many contributors. 225s Type 'contributors()' for more information and 225s 'citation()' on how to cite R or R packages in publications. 225s 225s Type 'demo()' for some demos, 'help()' for on-line help, or 225s 'help.start()' for an HTML browser interface to help. 225s Type 'q()' to quit R. 225s 226s > Stangle("intro-vegan.Rnw") 226s Writing to file intro-vegan.R 226s > source("intro-vegan.R", echo=TRUE) 226s 226s > par(mfrow = c(1, 1)) 226s 226s > options(width = 72) 226s 226s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 226s 226s > options(SweaveHooks = list(fig = figset)) 226s 226s > options(prompt = "> ", continue = " ") 226s 226s > library(vegan) 226s Loading required package: permute 226s Loading required package: lattice 227s 227s > data(dune) 227s 227s > ord <- decorana(dune) 227s 227s > ord 227s 227s Call: 227s decorana(veg = dune) 227s 227s Detrended correspondence analysis with 26 segments. 227s Rescaling of axes with 4 iterations. 227s Total inertia (scaled Chi-square): 2.1153 227s 227s DCA1 DCA2 DCA3 DCA4 227s Eigenvalues 0.5117 0.3036 0.12125 0.14267 227s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 227s Decorana values 0.5360 0.2869 0.08136 0.04814 227s Axis lengths 3.7004 3.1166 1.30055 1.47888 227s 227s 227s > ord <- metaMDS(dune, trace = FALSE) 227s 227s > ord 227s 227s Call: 227s metaMDS(comm = dune, trace = FALSE) 227s 227s global Multidimensional Scaling using monoMDS 227s 227s Data: dune 227s Distance: bray 227s 227s Dimensions: 2 227s Stress: 0.1183186 227s Stress type 1, weak ties 227s Best solution was repeated 4 times in 20 tries 227s The best solution was from try 11 (random start) 227s Scaling: centring, PC rotation, halfchange scaling 227s Species: expanded scores based on ‘dune’ 227s 227s 227s > plot(ord) 227s 227s > plot(ord) 227s 227s > plot(ord, type = "n") 227s 227s > points(ord, display = "sites", cex = 0.8, pch = 21, 227s + col = "red", bg = "yellow") 227s 227s > text(ord, display = "species", cex = 0.7, col = "blue") 227s 227s > plot(ord, type = "n") 227s 227s > points(ord, display = "sites", cex = 0.8, pch = 21, 227s + col = "red", bg = "yellow") 227s 227s > text(ord, display = "species", cex = 0.7, col = "blue") 227s 227s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 227s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 227s + col = "blue") 227s 227s > data(dune.env) 227s 227s > attach(dune.env) 227s 227s > plot(ord, disp = "sites", type = "n") 227s 227s > ordihull(ord, Management, col = 1:4, lwd = 3) 227s 227s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 227s + lwd = 3) 227s 227s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 227s 227s > ordispider(ord, Management, col = 1:4, label = TRUE) 227s 227s > points(ord, disp = "sites", pch = 21, col = "red", 227s + bg = "yellow", cex = 1.3) 227s 227s > plot(ord, disp = "sites", type = "n") 227s 227s > ordihull(ord, Management, col = 1:4, lwd = 3) 227s 227s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 227s + lwd = 3) 227s 227s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 227s 227s > ordispider(ord, Management, col = 1:4, label = TRUE) 227s 227s > points(ord, disp = "sites", pch = 21, col = "red", 227s + bg = "yellow", cex = 1.3) 227s 227s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 227s + perm = 999) 227s 227s > ord.fit 227s 227s ***VECTORS 227s 227s NMDS1 NMDS2 r2 Pr(>r) 227s A1 0.96474 0.26321 0.3649 0.024 * 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s Permutation: free 227s Number of permutations: 999 227s 227s ***FACTORS: 227s 227s Centroids: 227s NMDS1 NMDS2 227s ManagementBF -0.4534 -0.0102 227s ManagementHF -0.2636 -0.1282 227s ManagementNM 0.2958 0.5790 227s ManagementSF 0.1506 -0.4670 227s 227s Goodness of fit: 227s r2 Pr(>r) 227s Management 0.4134 0.005 ** 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s Permutation: free 227s Number of permutations: 999 227s 227s 227s 227s > plot(ord, dis = "site") 227s 227s > plot(ord.fit) 227s 227s > ordisurf(ord, A1, add = TRUE) 227s 227s Family: gaussian 227s Link function: identity 227s 227s Formula: 227s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 227s 227s Estimated degrees of freedom: 227s 1.59 total = 2.59 227s 227s REML score: 41.58728 227s 227s > plot(ord, dis = "site") 227s 227s > plot(ord.fit) 227s 227s > ordisurf(ord, A1, add = TRUE) 227s 227s Family: gaussian 227s Link function: identity 227s 227s Formula: 227s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 227s 227s Estimated degrees of freedom: 227s 1.59 total = 2.59 227s 227s REML score: 41.58728 227s 227s > ord <- cca(dune ~ A1 + Management, data = dune.env) 227s 227s > ord 227s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 227s 227s -- Model Summary -- 227s 227s Inertia Proportion Rank 227s Total 2.1153 1.0000 227s Constrained 0.7798 0.3686 4 227s Unconstrained 1.3355 0.6314 15 227s 227s Inertia is scaled Chi-square 227s 227s -- Eigenvalues -- 227s 227s Eigenvalues for constrained axes: 227s CCA1 CCA2 CCA3 CCA4 227s 0.3187 0.2372 0.1322 0.0917 227s 227s Eigenvalues for unconstrained axes: 227s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 227s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 227s CA11 CA12 CA13 CA14 CA15 227s 0.0317 0.0178 0.0116 0.0087 0.0047 227s 227s 227s > plot(ord) 227s 227s > plot(ord) 227s 227s > cca(dune ~ ., data = dune.env) 227s 227s Some constraints or conditions were aliased because they were 227s redundant. This can happen if terms are linearly dependent (collinear): 227s ‘Manure^4’ 227s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 227s Manure, data = dune.env) 227s 227s -- Model Summary -- 227s 227s Inertia Proportion Rank 227s Total 2.1153 1.0000 227s Constrained 1.5032 0.7106 12 227s Unconstrained 0.6121 0.2894 7 227s 227s Inertia is scaled Chi-square 227s 227s -- Note -- 227s 227s Some constraints or conditions were aliased because they were 227s redundant. This can happen if terms are linearly dependent 227s (collinear): ‘Manure^4’ 227s 227s -- Eigenvalues -- 227s 227s Eigenvalues for constrained axes: 227s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 227s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 227s CCA11 CCA12 227s 0.0228 0.0108 227s 227s Eigenvalues for unconstrained axes: 227s CA1 CA2 CA3 CA4 CA5 CA6 CA7 227s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 227s 227s 227s > anova(ord) 227s Permutation test for cca under reduced model 227s Permutation: free 227s Number of permutations: 999 227s 227s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 227s Df ChiSquare F Pr(>F) 227s Model 4 0.77978 2.1896 0.002 ** 227s Residual 15 1.33549 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > anova(ord, by = "term", permutations = 199) 227s Permutation test for cca under reduced model 227s Terms added sequentially (first to last) 227s Permutation: free 227s Number of permutations: 199 227s 227s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 227s Df ChiSquare F Pr(>F) 227s A1 1 0.22476 2.5245 0.015 * 227s Management 3 0.55502 2.0780 0.010 ** 227s Residual 15 1.33549 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > anova(ord, by = "mar", permutations = 199) 227s Permutation test for cca under reduced model 227s Marginal effects of terms 227s Permutation: free 227s Number of permutations: 199 227s 227s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 227s Df ChiSquare F Pr(>F) 227s A1 1 0.17594 1.9761 0.050 * 227s Management 3 0.55502 2.0780 0.005 ** 227s Residual 15 1.33549 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > anova(ord, by = "axis", permutations = 499) 227s Permutation test for cca under reduced model 227s Forward tests for axes 227s Permutation: free 227s Number of permutations: 499 227s 227s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 227s Df ChiSquare F Pr(>F) 227s CCA1 1 0.31875 3.5801 0.012 * 227s CCA2 1 0.23718 2.6640 0.130 227s CCA3 1 0.13217 1.4845 0.842 227s CCA4 1 0.09168 1.0297 1.000 227s Residual 15 1.33549 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 227s + data = dune.env) 227s 227s > ord 227s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 227s data = dune.env) 227s 227s -- Model Summary -- 227s 227s Inertia Proportion Rank 227s Total 2.1153 1.0000 227s Conditional 0.6283 0.2970 3 227s Constrained 0.5109 0.2415 4 227s Unconstrained 0.9761 0.4615 12 227s 227s Inertia is scaled Chi-square 227s 227s -- Eigenvalues -- 227s 227s Eigenvalues for constrained axes: 227s CCA1 CCA2 CCA3 CCA4 227s 0.24932 0.12090 0.08160 0.05904 227s 227s Eigenvalues for unconstrained axes: 227s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 227s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 227s CA10 CA11 CA12 227s 0.02102 0.01254 0.00928 227s 227s 227s > anova(ord, by = "term", permutations = 499) 227s Permutation test for cca under reduced model 227s Terms added sequentially (first to last) 227s Permutation: free 227s Number of permutations: 499 227s 227s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 227s Df ChiSquare F Pr(>F) 227s A1 1 0.11543 1.4190 1.000 227s Management 3 0.39543 1.6205 0.002 ** 227s Residual 12 0.97610 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 227s 227s > anova(ord, by = "term", permutations = how) 227s Permutation test for cca under reduced model 227s Terms added sequentially (first to last) 227s Plots: dune.env$Moisture, plot permutation: none 227s Permutation: free 227s Number of permutations: 499 227s 227s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 227s Df ChiSquare F Pr(>F) 227s A1 1 0.11543 1.4190 1.000 227s Management 3 0.39543 1.6205 0.002 ** 227s Residual 12 0.97610 227s --- 227s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 227s 227s > detach(dune.env) 227s > 227s 227s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 227s Copyright (C) 2025 The R Foundation for Statistical Computing 227s Platform: aarch64-unknown-linux-gnu 227s 227s R is free software and comes with ABSOLUTELY NO WARRANTY. 227s You are welcome to redistribute it under certain conditions. 227s Type 'license()' or 'licence()' for distribution details. 227s 227s R is a collaborative project with many contributors. 227s Type 'contributors()' for more information and 227s 'citation()' on how to cite R or R packages in publications. 227s 227s Type 'demo()' for some demos, 'help()' for on-line help, or 227s 'help.start()' for an HTML browser interface to help. 227s Type 'q()' to quit R. 227s 227s > Stangle("partitioning.Rnw") 227s Writing to file partitioning.R 227s > source("partitioning.R", echo=TRUE) 227s 227s > par(mfrow = c(1, 1)) 227s 227s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 227s 227s > options(SweaveHooks = list(fig = figset)) 227s 227s > library(vegan) 227s Loading required package: permute 228s Loading required package: lattice 228s 228s > labs <- paste("Table", 1:4) 228s 228s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 228s 228s > showvarparts(2, bg = cls, Xnames = labs) 228s 228s > showvarparts(3, bg = cls, Xnames = labs) 228s 228s > showvarparts(4, bg = cls, Xnames = labs) 228s > 235s Test cca-object-tests passed 236s Test oecosimu-tests passed 239s Test vegan-tests passed 240s autopkgtest [23:15:39]: test run-unit-test: -----------------------] 240s autopkgtest [23:15:39]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 240s run-unit-test PASS 241s autopkgtest [23:15:40]: test pkg-r-autopkgtest: preparing testbed 241s Reading package lists... 241s Building dependency tree... 241s Reading state information... 241s Solving dependencies... 241s The following NEW packages will be installed: 241s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 241s dctrl-tools g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 241s gcc-15 gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-15 241s gfortran-15-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 241s libasan8 libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 241s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 241s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 241s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 241s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libreadline-dev 241s libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev linux-libc-dev 241s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto zlib1g-dev 241s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 241s Need to get 103 MB of archives. 241s After this operation, 377 MB of additional disk space will be used. 241s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 242s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.19.0-3.3 [1819 kB] 244s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 244s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 244s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 247s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 248s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 248s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 262s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 262s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 262s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 262s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 262s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 262s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 266s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 268s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 272s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 274s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 277s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 280s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 312s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 312s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 312s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 312s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 316s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 337s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 337s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 337s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 337s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 337s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 dctrl-tools arm64 2.24-3build4 [102 kB] 337s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran-15-dev arm64 15.2.0-12ubuntu1 [490 kB] 337s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [12.5 MB] 355s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-15 arm64 15.2.0-12ubuntu1 [18.1 kB] 355s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1022 B] 355s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gfortran arm64 4:15.2.0-4ubuntu1 [1160 B] 355s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 icu-devtools arm64 78.2-1ubuntu1 [207 kB] 355s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas-dev arm64 3.12.1-7ubuntu1 [160 kB] 355s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libbz2-dev arm64 1.0.8-6build2 [34.9 kB] 355s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate-dev arm64 1.23-2build1 [54.3 kB] 355s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 libicu-dev arm64 78.2-1ubuntu1 [12.5 MB] 376s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-turbo8-dev arm64 2.1.5-4ubuntu3 [301 kB] 376s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 376s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 376s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack-dev arm64 3.12.1-7ubuntu1 [4456 kB] 385s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 libncurses-dev arm64 6.6+20251231-1 [391 kB] 385s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-16-0 arm64 10.46-1 [225 kB] 385s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-32-0 arm64 10.46-1 [213 kB] 385s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-posix3 arm64 10.46-1 [7300 B] 385s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 libpcre2-dev arm64 10.46-1 [772 kB] 386s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 libpkgconf3 arm64 1.8.1-4build1 [33.7 kB] 386s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu2 [899 kB] 387s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 libpng-dev arm64 1.6.54-1 [268 kB] 387s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 libreadline-dev arm64 8.3-3 [199 kB] 387s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 libzstd-dev arm64 1.5.7+dfsg-3 [349 kB] 387s Get:55 http://ftpmaster.internal/ubuntu resolute/main arm64 liblzma-dev arm64 5.8.2-2 [180 kB] 387s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf-bin arm64 1.8.1-4build1 [21.7 kB] 387s Get:57 http://ftpmaster.internal/ubuntu resolute/main arm64 pkgconf arm64 1.8.1-4build1 [16.8 kB] 387s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 libtirpc-dev arm64 1.3.6+ds-1 [202 kB] 387s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 387s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 pkg-r-autopkgtest all 20250812 [6158 B] 388s Fetched 103 MB in 2min 26s (704 kB/s) 388s Selecting previously unselected package libc-dev-bin. 388s (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 ... 144587 files and directories currently installed.) 388s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 388s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 388s Selecting previously unselected package linux-libc-dev:arm64. 388s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_arm64.deb ... 388s Unpacking linux-libc-dev:arm64 (6.19.0-3.3) ... 388s Selecting previously unselected package libcrypt-dev:arm64. 388s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 388s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 388s Selecting previously unselected package rpcsvc-proto. 388s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 388s Unpacking rpcsvc-proto (1.4.3-1build1) ... 388s Selecting previously unselected package libc6-dev:arm64. 388s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_arm64.deb ... 388s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 388s Selecting previously unselected package libisl23:arm64. 388s Preparing to unpack .../05-libisl23_0.27-1build1_arm64.deb ... 388s Unpacking libisl23:arm64 (0.27-1build1) ... 388s Selecting previously unselected package libmpc3:arm64. 388s Preparing to unpack .../06-libmpc3_1.3.1-2_arm64.deb ... 388s Unpacking libmpc3:arm64 (1.3.1-2) ... 388s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 388s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 388s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 388s Selecting previously unselected package cpp-15. 388s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 388s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 388s Selecting previously unselected package cpp-aarch64-linux-gnu. 388s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 388s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package cpp. 388s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 388s Unpacking cpp (4:15.2.0-4ubuntu1) ... 388s Selecting previously unselected package libcc1-0:arm64. 388s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 388s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libitm1:arm64. 389s Preparing to unpack .../12-libitm1_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libasan8:arm64. 389s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package liblsan0:arm64. 389s Preparing to unpack .../14-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libtsan2:arm64. 389s Preparing to unpack .../15-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libubsan1:arm64. 389s Preparing to unpack .../16-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libhwasan0:arm64. 389s Preparing to unpack .../17-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package libgcc-15-dev:arm64. 389s Preparing to unpack .../18-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 389s Preparing to unpack .../19-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gcc-15. 389s Preparing to unpack .../20-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 389s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 389s Selecting previously unselected package gcc-aarch64-linux-gnu. 389s Preparing to unpack .../21-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 389s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 389s Selecting previously unselected package gcc. 390s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 390s Unpacking gcc (4:15.2.0-4ubuntu1) ... 390s Selecting previously unselected package libstdc++-15-dev:arm64. 390s Preparing to unpack .../23-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package g++-15-aarch64-linux-gnu. 390s Preparing to unpack .../24-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package g++-15. 390s Preparing to unpack .../25-g++-15_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking g++-15 (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package g++-aarch64-linux-gnu. 390s Preparing to unpack .../26-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 390s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 390s Selecting previously unselected package g++. 390s Preparing to unpack .../27-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 390s Unpacking g++ (4:15.2.0-4ubuntu1) ... 390s Selecting previously unselected package build-essential. 390s Preparing to unpack .../28-build-essential_12.12ubuntu2_arm64.deb ... 390s Unpacking build-essential (12.12ubuntu2) ... 390s Selecting previously unselected package dctrl-tools. 390s Preparing to unpack .../29-dctrl-tools_2.24-3build4_arm64.deb ... 390s Unpacking dctrl-tools (2.24-3build4) ... 390s Selecting previously unselected package libgfortran-15-dev:arm64. 390s Preparing to unpack .../30-libgfortran-15-dev_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package gfortran-15-aarch64-linux-gnu. 390s Preparing to unpack .../31-gfortran-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package gfortran-15. 390s Preparing to unpack .../32-gfortran-15_15.2.0-12ubuntu1_arm64.deb ... 390s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 390s Selecting previously unselected package gfortran-aarch64-linux-gnu. 390s Preparing to unpack .../33-gfortran-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 390s Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 391s Selecting previously unselected package gfortran. 391s Preparing to unpack .../34-gfortran_4%3a15.2.0-4ubuntu1_arm64.deb ... 391s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 391s Selecting previously unselected package icu-devtools. 391s Preparing to unpack .../35-icu-devtools_78.2-1ubuntu1_arm64.deb ... 391s Unpacking icu-devtools (78.2-1ubuntu1) ... 391s Selecting previously unselected package libblas-dev:arm64. 391s Preparing to unpack .../36-libblas-dev_3.12.1-7ubuntu1_arm64.deb ... 391s Unpacking libblas-dev:arm64 (3.12.1-7ubuntu1) ... 391s Selecting previously unselected package libbz2-dev:arm64. 391s Preparing to unpack .../37-libbz2-dev_1.0.8-6build2_arm64.deb ... 391s Unpacking libbz2-dev:arm64 (1.0.8-6build2) ... 391s Selecting previously unselected package libdeflate-dev:arm64. 391s Preparing to unpack .../38-libdeflate-dev_1.23-2build1_arm64.deb ... 391s Unpacking libdeflate-dev:arm64 (1.23-2build1) ... 391s Selecting previously unselected package libicu-dev:arm64. 391s Preparing to unpack .../39-libicu-dev_78.2-1ubuntu1_arm64.deb ... 391s Unpacking libicu-dev:arm64 (78.2-1ubuntu1) ... 391s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 391s Preparing to unpack .../40-libjpeg-turbo8-dev_2.1.5-4ubuntu3_arm64.deb ... 391s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 391s Selecting previously unselected package libjpeg8-dev:arm64. 391s Preparing to unpack .../41-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 391s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 391s Selecting previously unselected package libjpeg-dev:arm64. 391s Preparing to unpack .../42-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 391s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 391s Selecting previously unselected package liblapack-dev:arm64. 391s Preparing to unpack .../43-liblapack-dev_3.12.1-7ubuntu1_arm64.deb ... 391s Unpacking liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 391s Selecting previously unselected package libncurses-dev:arm64. 391s Preparing to unpack .../44-libncurses-dev_6.6+20251231-1_arm64.deb ... 391s Unpacking libncurses-dev:arm64 (6.6+20251231-1) ... 391s Selecting previously unselected package libpcre2-16-0:arm64. 391s Preparing to unpack .../45-libpcre2-16-0_10.46-1_arm64.deb ... 391s Unpacking libpcre2-16-0:arm64 (10.46-1) ... 391s Selecting previously unselected package libpcre2-32-0:arm64. 391s Preparing to unpack .../46-libpcre2-32-0_10.46-1_arm64.deb ... 391s Unpacking libpcre2-32-0:arm64 (10.46-1) ... 391s Selecting previously unselected package libpcre2-posix3:arm64. 392s Preparing to unpack .../47-libpcre2-posix3_10.46-1_arm64.deb ... 392s Unpacking libpcre2-posix3:arm64 (10.46-1) ... 392s Selecting previously unselected package libpcre2-dev:arm64. 392s Preparing to unpack .../48-libpcre2-dev_10.46-1_arm64.deb ... 392s Unpacking libpcre2-dev:arm64 (10.46-1) ... 392s Selecting previously unselected package libpkgconf3:arm64. 392s Preparing to unpack .../49-libpkgconf3_1.8.1-4build1_arm64.deb ... 392s Unpacking libpkgconf3:arm64 (1.8.1-4build1) ... 392s Selecting previously unselected package zlib1g-dev:arm64. 392s Preparing to unpack .../50-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_arm64.deb ... 392s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 392s Selecting previously unselected package libpng-dev:arm64. 392s Preparing to unpack .../51-libpng-dev_1.6.54-1_arm64.deb ... 392s Unpacking libpng-dev:arm64 (1.6.54-1) ... 392s Selecting previously unselected package libreadline-dev:arm64. 392s Preparing to unpack .../52-libreadline-dev_8.3-3_arm64.deb ... 392s Unpacking libreadline-dev:arm64 (8.3-3) ... 392s Selecting previously unselected package libzstd-dev:arm64. 392s Preparing to unpack .../53-libzstd-dev_1.5.7+dfsg-3_arm64.deb ... 392s Unpacking libzstd-dev:arm64 (1.5.7+dfsg-3) ... 392s Selecting previously unselected package liblzma-dev:arm64. 392s Preparing to unpack .../54-liblzma-dev_5.8.2-2_arm64.deb ... 392s Unpacking liblzma-dev:arm64 (5.8.2-2) ... 392s Selecting previously unselected package pkgconf-bin. 392s Preparing to unpack .../55-pkgconf-bin_1.8.1-4build1_arm64.deb ... 392s Unpacking pkgconf-bin (1.8.1-4build1) ... 392s Selecting previously unselected package pkgconf:arm64. 392s Preparing to unpack .../56-pkgconf_1.8.1-4build1_arm64.deb ... 392s Unpacking pkgconf:arm64 (1.8.1-4build1) ... 392s Selecting previously unselected package libtirpc-dev:arm64. 392s Preparing to unpack .../57-libtirpc-dev_1.3.6+ds-1_arm64.deb ... 392s Unpacking libtirpc-dev:arm64 (1.3.6+ds-1) ... 392s Selecting previously unselected package r-base-dev. 392s Preparing to unpack .../58-r-base-dev_4.5.2-1ubuntu2_all.deb ... 392s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 392s Selecting previously unselected package pkg-r-autopkgtest. 392s Preparing to unpack .../59-pkg-r-autopkgtest_20250812_all.deb ... 392s Unpacking pkg-r-autopkgtest (20250812) ... 392s Setting up libzstd-dev:arm64 (1.5.7+dfsg-3) ... 392s Setting up linux-libc-dev:arm64 (6.19.0-3.3) ... 392s Setting up libpcre2-16-0:arm64 (10.46-1) ... 392s Setting up libpcre2-32-0:arm64 (10.46-1) ... 392s Setting up libtirpc-dev:arm64 (1.3.6+ds-1) ... 392s Setting up libpkgconf3:arm64 (1.8.1-4build1) ... 392s Setting up rpcsvc-proto (1.4.3-1build1) ... 392s Setting up libmpc3:arm64 (1.3.1-2) ... 392s Setting up icu-devtools (78.2-1ubuntu1) ... 392s Setting up pkgconf-bin (1.8.1-4build1) ... 392s Setting up liblzma-dev:arm64 (5.8.2-2) ... 392s Setting up libubsan1:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libpcre2-posix3:arm64 (10.46-1) ... 392s Setting up libhwasan0:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libcrypt-dev:arm64 (1:4.5.1-1) ... 392s Setting up libasan8:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libtsan2:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libisl23:arm64 (0.27-1build1) ... 392s Setting up libc-dev-bin (2.42-2ubuntu4) ... 392s Setting up libdeflate-dev:arm64 (1.23-2build1) ... 392s Setting up libcc1-0:arm64 (15.2.0-12ubuntu1) ... 392s Setting up liblsan0:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libblas-dev:arm64 (3.12.1-7ubuntu1) ... 392s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode 392s Setting up dctrl-tools (2.24-3build4) ... 392s Setting up libitm1:arm64 (15.2.0-12ubuntu1) ... 392s Setting up cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 392s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 392s Setting up libgfortran-15-dev:arm64 (15.2.0-12ubuntu1) ... 392s Setting up pkgconf:arm64 (1.8.1-4build1) ... 392s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 392s Setting up liblapack-dev:arm64 (3.12.1-7ubuntu1) ... 392s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode 392s Setting up cpp-15 (15.2.0-12ubuntu1) ... 392s Setting up cpp (4:15.2.0-4ubuntu1) ... 392s Setting up libc6-dev:arm64 (2.42-2ubuntu4) ... 392s Setting up libicu-dev:arm64 (78.2-1ubuntu1) ... 392s Setting up libbz2-dev:arm64 (1.0.8-6build2) ... 392s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-4ubuntu3) ... 392s Setting up libncurses-dev:arm64 (6.6+20251231-1) ... 392s Setting up gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 392s Setting up libpcre2-dev:arm64 (10.46-1) ... 392s Setting up libreadline-dev:arm64 (8.3-3) ... 392s Setting up gcc-15 (15.2.0-12ubuntu1) ... 392s Setting up libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 392s Setting up gfortran-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 392s Setting up g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 392s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 392s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 392s Setting up g++-15 (15.2.0-12ubuntu1) ... 392s Setting up gfortran-15 (15.2.0-12ubuntu1) ... 392s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 392s Setting up libpng-dev:arm64 (1.6.54-1) ... 392s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 392s Setting up gcc (4:15.2.0-4ubuntu1) ... 392s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 392s Setting up gfortran-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 392s Setting up gfortran (4:15.2.0-4ubuntu1) ... 392s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 392s 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 392s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 392s 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 392s Setting up g++ (4:15.2.0-4ubuntu1) ... 392s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 392s Setting up build-essential (12.12ubuntu2) ... 392s Setting up r-base-dev (4.5.2-1ubuntu2) ... 392s Setting up pkg-r-autopkgtest (20250812) ... 392s Processing triggers for libc-bin (2.42-2ubuntu4) ... 392s Processing triggers for man-db (2.13.1-1build1) ... 393s Processing triggers for install-info (7.2-5) ... 394s autopkgtest [23:18:13]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 394s autopkgtest [23:18:13]: test pkg-r-autopkgtest: [----------------------- 394s Test: Try to load the R library vegan 394s 394s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 394s Copyright (C) 2025 The R Foundation for Statistical Computing 394s Platform: aarch64-unknown-linux-gnu 394s 394s R is free software and comes with ABSOLUTELY NO WARRANTY. 394s You are welcome to redistribute it under certain conditions. 394s Type 'license()' or 'licence()' for distribution details. 394s 394s R is a collaborative project with many contributors. 394s Type 'contributors()' for more information and 394s 'citation()' on how to cite R or R packages in publications. 394s 394s Type 'demo()' for some demos, 'help()' for on-line help, or 394s 'help.start()' for an HTML browser interface to help. 394s Type 'q()' to quit R. 394s 394s > library('vegan') 394s Loading required package: permute 394s Loading required package: lattice 395s > 396s autopkgtest [23:18:15]: test pkg-r-autopkgtest: -----------------------] 396s pkg-r-autopkgtest PASS 396s autopkgtest [23:18:15]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 396s autopkgtest [23:18:15]: @@@@@@@@@@@@@@@@@@@@ summary 396s run-unit-test PASS 396s pkg-r-autopkgtest PASS