0s autopkgtest [01:04:23]: starting date and time: 2025-03-04 01:04:23+0000 0s autopkgtest [01:04:23]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:04:23]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.40uh0xed/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-mass,src:r-cran-bayestestr,src:r-cran-dendextend,src:r-cran-glmmtmb,src:r-cran-rmpfr --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=r-cran-mass/7.3-65-1 r-cran-bayestestr/0.15.2-1 r-cran-dendextend/1.19.0+dfsg-1 r-cran-glmmtmb/1.1.10+dfsg-1 r-cran-rmpfr/1.0-0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-21.secgroup --name adt-plucky-amd64-r-cran-vegan-20250304-010423-juju-7f2275-prod-proposed-migration-environment-15-1a4f5085-fd99-4dc4-b06f-bf2d139710e3 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 205s autopkgtest [01:07:48]: testbed dpkg architecture: amd64 205s autopkgtest [01:07:48]: testbed apt version: 2.9.31ubuntu1 208s autopkgtest [01:07:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 208s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 208s autopkgtest [01:07:49]: testbed release detected to be: None 208s autopkgtest [01:07:49]: updating testbed package index (apt update) 208s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 208s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 208s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 208s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [472 kB] 208s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [2420 B] 208s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [51.1 kB] 208s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.4 kB] 208s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [69.1 kB] 208s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [103 kB] 208s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [13.2 kB] 208s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [246 kB] 208s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [458 kB] 208s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [10.9 kB] 208s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [23.5 kB] 208s Fetched 1578 kB in 1s (1792 kB/s) 208s Reading package lists... 209s + lsb_release --codename --short 209s + RELEASE=plucky 209s + cat 209s + [ plucky != trusty ] 209s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 209s Calculating upgrade... 210s Calculating upgrade... 210s The following packages will be upgraded: 210s wireless-regdb 210s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 210s Need to get 7290 B of archives. 210s After this operation, 1024 B of additional disk space will be used. 210s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 wireless-regdb all 2024.10.07-0ubuntu2 [7290 B] 211s Fetched 7290 B in 0s (48.8 kB/s) 211s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 211s + /usr/lib/apt/apt-helper analyze-pattern ?true 211s (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 ... 109140 files and directories currently installed.) 211s Preparing to unpack .../wireless-regdb_2024.10.07-0ubuntu2_all.deb ... 211s Unpacking wireless-regdb (2024.10.07-0ubuntu2) over (2024.10.07-0ubuntu1) ... 211s Setting up wireless-regdb (2024.10.07-0ubuntu2) ... 211s Processing triggers for man-db (2.13.0-1) ... 211s + uname -r 211s + sed s/\./\\./g 211s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 211s + apt list ?obsolete 211s + tail -n+2 211s + grep -v ^linux-.*6\.12\.0-16-generic.* 211s + cut -d/ -f1 211s + true 211s + obsolete_pkgs= 211s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 211s Reading package lists... 211s Building dependency tree... 211s Reading state information... 212s Solving dependencies... 212s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 212s + grep -q trusty /etc/lsb-release 212s + [ ! -d /usr/share/doc/unattended-upgrades ] 212s + [ ! -d /usr/share/doc/lxd ] 212s + [ ! -d /usr/share/doc/lxd-client ] 212s + [ ! -d /usr/share/doc/snapd ] 212s + type iptables 212s + cat 212s + chmod 755 /etc/rc.local 212s + . /etc/rc.local 212s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 212s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 212s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 212s + uname -m 212s + [ x86_64 = ppc64le ] 212s + [ -d /run/systemd/system ] 212s + systemd-detect-virt --quiet --vm 212s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 212s + cat 212s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 212s + echo COMPRESS=lz4 212s autopkgtest [01:07:55]: upgrading testbed (apt dist-upgrade and autopurge) 212s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 213s Starting 2 pkgProblemResolver with broken count: 0 213s Done 213s Entering ResolveByKeep 213s 213s Calculating upgrade... 213s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 213s Reading package lists... 214s Building dependency tree... 214s Reading state information... 214s Starting pkgProblemResolver with broken count: 0 214s Starting 2 pkgProblemResolver with broken count: 0 214s Done 214s Solving dependencies... 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s autopkgtest [01:08:00]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 14 15:11:11 UTC 2025 219s autopkgtest [01:08:00]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 219s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (dsc) [2204 B] 219s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (tar) [1205 kB] 219s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (diff) [6312 B] 219s gpgv: Signature made Sun Sep 1 23:45:51 2024 UTC 219s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 219s gpgv: issuer "plessy@debian.org" 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-8+dfsg-1.dsc: no acceptable signature found 219s autopkgtest [01:08:02]: testing package r-cran-vegan version 2.6-8+dfsg-1 220s autopkgtest [01:08:03]: build not needed 223s autopkgtest [01:08:06]: test run-unit-test: preparing testbed 223s Reading package lists... 223s Building dependency tree... 223s Reading state information... 223s Starting pkgProblemResolver with broken count: 0 223s Starting 2 pkgProblemResolver with broken count: 0 223s Done 224s The following NEW packages will be installed: 224s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 224s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 224s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 224s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 224s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 224s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 224s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 224s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 224s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 224s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 224s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 224s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 224s x11-common xdg-utils zip 224s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 224s Need to get 68.6 MB of archives. 224s After this operation, 165 MB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 224s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 224s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 224s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 224s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 224s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 224s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 225s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 225s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 225s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 225s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 225s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 225s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 225s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 225s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 225s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 225s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250213-1ubuntu1 [148 kB] 225s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 225s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 225s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 225s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 225s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 225s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 225s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 225s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 225s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 225s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 225s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 225s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 225s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 225s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 225s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.1-1 [255 kB] 225s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [52.6 kB] 225s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [29.1 kB] 225s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 225s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 225s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 225s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 225s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 225s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 225s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 225s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 225s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 225s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 225s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 225s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 225s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 225s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 225s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 225s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 225s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.2-1build1 [28.9 MB] 227s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.8-1 [579 kB] 227s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.2-2 [137 kB] 227s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 227s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.50+dfsg-1 [568 kB] 227s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 227s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 227s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 227s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 227s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 227s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-markdown all 1.13-1 [162 kB] 227s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 227s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-2-1 [4456 kB] 227s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 227s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 228s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-permute all 0.9-7-1 [228 kB] 228s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vegan amd64 2.6-8+dfsg-1 [3132 kB] 228s Preconfiguring packages ... 228s Fetched 68.6 MB in 4s (16.8 MB/s) 228s Selecting previously unselected package fonts-dejavu-mono. 228s (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 ... 109140 files and directories currently installed.) 228s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-mono (2.37-8) ... 228s Selecting previously unselected package fonts-dejavu-core. 228s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 228s Unpacking fonts-dejavu-core (2.37-8) ... 228s Selecting previously unselected package fontconfig-config. 228s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 229s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package libfontconfig1:amd64. 229s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 229s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package fontconfig. 229s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 229s Unpacking fontconfig (2.15.0-2ubuntu1) ... 229s Selecting previously unselected package fonts-glyphicons-halflings. 229s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 229s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 229s Selecting previously unselected package fonts-mathjax. 229s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 229s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 229s Selecting previously unselected package libblas3:amd64. 229s Preparing to unpack .../07-libblas3_3.12.1-2_amd64.deb ... 229s Unpacking libblas3:amd64 (3.12.1-2) ... 229s Selecting previously unselected package libpixman-1-0:amd64. 229s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_amd64.deb ... 229s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 229s Selecting previously unselected package libxcb-render0:amd64. 229s Preparing to unpack .../09-libxcb-render0_1.17.0-2_amd64.deb ... 229s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 229s Selecting previously unselected package libxcb-shm0:amd64. 229s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_amd64.deb ... 229s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 229s Selecting previously unselected package libxrender1:amd64. 229s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 229s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 229s Selecting previously unselected package libcairo2:amd64. 229s Preparing to unpack .../12-libcairo2_1.18.2-2_amd64.deb ... 229s Unpacking libcairo2:amd64 (1.18.2-2) ... 229s Selecting previously unselected package libdatrie1:amd64. 229s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_amd64.deb ... 229s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 229s Selecting previously unselected package libdeflate0:amd64. 229s Preparing to unpack .../14-libdeflate0_1.23-1_amd64.deb ... 229s Unpacking libdeflate0:amd64 (1.23-1) ... 229s Selecting previously unselected package libgfortran5:amd64. 229s Preparing to unpack .../15-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 229s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 229s Selecting previously unselected package libgomp1:amd64. 229s Preparing to unpack .../16-libgomp1_15-20250213-1ubuntu1_amd64.deb ... 229s Unpacking libgomp1:amd64 (15-20250213-1ubuntu1) ... 229s Selecting previously unselected package libgraphite2-3:amd64. 229s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 229s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 229s Selecting 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run-unit-test: [----------------------- 238s 238s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 238s Copyright (C) 2024 The R Foundation for Statistical Computing 238s Platform: x86_64-pc-linux-gnu 238s 238s R is free software and comes with ABSOLUTELY NO WARRANTY. 238s You are welcome to redistribute it under certain conditions. 238s Type 'license()' or 'licence()' for distribution details. 238s 238s R is a collaborative project with many contributors. 238s Type 'contributors()' for more information and 238s 'citation()' on how to cite R or R packages in publications. 238s 238s Type 'demo()' for some demos, 'help()' for on-line help, or 238s 'help.start()' for an HTML browser interface to help. 238s Type 'q()' to quit R. 238s 238s > Stangle("decision-vegan.Rnw") 238s Writing to file decision-vegan.R 238s > source("decision-vegan.R", echo=TRUE) 238s 238s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 238s 238s > options(SweaveHooks = list(fig = figset)) 238s 238s > options(prompt = "> ", continue = " ") 238s 238s > options(width = 55) 238s 238s > require(vegan) 238s Loading required package: vegan 238s Loading required package: permute 238s Loading required package: lattice 239s 239s > data(sipoo) 239s This is vegan 2.6-8 239s 239s > mod <- nestedtemp(sipoo) 239s 239s > plot(mod, "i") 239s 239s > x <- mod$c["Falcsubb"] 239s 239s > y <- 1 - mod$r["Svartholm"] 239s 239s > points(x, y, pch = 16, cex = 1.5) 239s 239s > abline(x + y, -1, lty = 2) 239s 239s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 239s 239s > cross <- function(x, a, p) f(x, p) - a + x 239s 239s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 239s 239s > arrows(x, y, r, f(r, mod$p), lwd = 4) 239s 239s > library(vegan) 239s 239s > data(varespec) 239s 239s > data(varechem) 239s 239s > orig <- cca(varespec ~ Al + K, varechem) 239s 239s > plot(orig, dis = c("lc", "bp")) 239s 239s > plot(orig, dis = c("lc", "bp")) 239s 239s > i <- sample(nrow(varespec)) 239s 239s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 239s 239s > plot(shuff, dis = c("lc", "bp")) 239s 239s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 239s + dis = "lc"))) 239s 239s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 239s + dis = "lc"))) 239s 239s > tmp1 <- rda(varespec ~ Al + K, varechem) 239s 239s > i <- sample(nrow(varespec)) 239s 239s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 239s 239s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 239s + dis = "lc"))) 239s 239s > orig 239s Call: cca(formula = varespec ~ Al + K, data = 239s varechem) 239s 239s -- Model Summary -- 239s 239s Inertia Proportion Rank 239s Total 2.0832 1.0000 239s Constrained 0.4760 0.2285 2 239s Unconstrained 1.6072 0.7715 21 239s 239s Inertia is scaled Chi-square 239s 239s -- Eigenvalues -- 239s 239s Eigenvalues for constrained axes: 239s CCA1 CCA2 239s 0.3608 0.1152 239s 239s Eigenvalues for unconstrained axes: 239s CA1 CA2 CA3 CA4 CA5 CA6 CA7 239s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 239s CA8 239s 0.0757 239s (Showing 8 of 21 unconstrained eigenvalues) 239s 239s 239s > shuff 239s Call: cca(formula = varespec[i, ] ~ Al + K, data = 239s varechem) 239s 239s -- Model Summary -- 239s 239s Inertia Proportion Rank 239s Total 2.0832 1.0000 239s Constrained 0.3402 0.1633 2 239s Unconstrained 1.7430 0.8367 21 239s 239s Inertia is scaled Chi-square 239s 239s -- Eigenvalues -- 239s 239s Eigenvalues for constrained axes: 239s CCA1 CCA2 239s 0.27759 0.06264 239s 239s Eigenvalues for unconstrained axes: 239s CA1 CA2 CA3 CA4 CA5 CA6 CA7 239s 0.3614 0.2667 0.2313 0.1740 0.1578 0.1130 0.1030 239s CA8 239s 0.0857 239s (Showing 8 of 21 unconstrained eigenvalues) 239s 239s 239s > plot(procrustes(orig, shuff)) 239s 239s > tmp1 <- rda(varespec ~ ., varechem) 239s 239s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 239s 239s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 239s + scores(tmp2, dis = "lc", choi = 1:14)) 239s 239s > max(residuals(proc)) 239s [1] 4.58403e-14 239s 239s > data(dune) 239s 239s > data(dune.env) 239s 239s > orig <- cca(dune ~ Moisture, dune.env) 239s 239s > plot(orig, dis = "lc") 239s 239s > plot(orig, display = "wa", type = "points") 239s 239s > ordispider(orig, col = "red") 239s 239s > text(orig, dis = "cn", col = "blue") 239s 239s > plot(orig, display = "wa", type = "points") 239s 239s > ordispider(orig, col = "red") 239s 239s > text(orig, dis = "cn", col = "blue") 239s > 239s 239s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 239s Copyright (C) 2024 The R Foundation for Statistical Computing 239s Platform: x86_64-pc-linux-gnu 239s 239s R is free software and comes with ABSOLUTELY NO WARRANTY. 239s You are welcome to redistribute it under certain conditions. 239s Type 'license()' or 'licence()' for distribution details. 239s 239s R is a collaborative project with many contributors. 239s Type 'contributors()' for more information and 239s 'citation()' on how to cite R or R packages in publications. 239s 239s Type 'demo()' for some demos, 'help()' for on-line help, or 239s 'help.start()' for an HTML browser interface to help. 239s Type 'q()' to quit R. 239s 239s > Stangle("diversity-vegan.Rnw") 239s Writing to file diversity-vegan.R 239s > source("diversity-vegan.R", echo=TRUE) 239s 239s > par(mfrow = c(1, 1)) 239s 239s > options(width = 55) 239s 239s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 239s 239s > options(SweaveHooks = list(fig = figset)) 239s 239s > options(prompt = "> ", continue = " ") 239s 239s > library(vegan) 239s Loading required package: permute 239s Loading required package: lattice 240s This is vegan 2.6-8 240s 240s > data(BCI) 240s 240s > H <- diversity(BCI) 240s 240s > J <- H/log(specnumber(BCI)) 240s 240s > k <- sample(nrow(BCI), 6) 240s 240s > R <- renyi(BCI[k, ]) 240s 240s > print(plot(R)) 240s 240s > alpha <- fisher.alpha(BCI) 240s 240s > quantile(rowSums(BCI)) 240s 0% 25% 50% 75% 100% 240s 340.0 409.0 428.0 443.5 601.0 240s 240s > Srar <- rarefy(BCI, min(rowSums(BCI))) 240s 240s > S2 <- rarefy(BCI, 2) 240s 240s > all(rank(Srar) == rank(S2)) 240s [1] FALSE 240s 240s > range(diversity(BCI, "simp") - (S2 - 1)) 240s [1] -0.002868298 -0.001330663 240s 240s > data(dune) 240s 240s > data(dune.taxon) 240s 240s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 240s 240s > mod <- taxondive(dune, taxdis) 240s 240s > plot(mod) 240s 240s > tr <- hclust(taxdis, "aver") 240s 240s > mod <- treedive(dune, tr) 240s forced matching of 'tree' labels and 'comm' names 240s 240s > k <- sample(nrow(BCI), 1) 240s 240s > fish <- fisherfit(BCI[k, ]) 240s 240s > fish 240s 240s Fisher log series model 240s No. of species: 81 240s Fisher alpha: 30.28666 240s 240s 240s > plot(fish) 240s 240s > prestondistr(BCI[k, ]) 240s 240s Preston lognormal model 240s Method: maximized likelihood to log2 abundances 240s No. of species: 81 240s 240s mode width S0 240s 0.797735 1.924434 20.356166 240s 240s Frequencies by Octave 240s 0 1 2 3 4 240s Observed 17.00000 22.50000 14.00000 15.00000 5.500000 240s Fitted 18.68024 20.24404 16.74728 10.57605 5.098416 240s 5 6 240s Observed 6.0000 1.0000000 240s Fitted 1.8762 0.5270545 240s 240s 240s > rad <- radfit(BCI[k, ]) 240s 240s > rad 240s 240s RAD models, family poisson 240s No. of species 81, total abundance 409 240s 240s par1 par2 par3 Deviance AIC 240s Null 77.934 312.822 240s Preemption 0.057227 63.597 300.485 240s Lognormal 0.91394 1.2125 18.375 257.263 240s Zipf 0.1606 -0.89023 29.217 268.105 240s Mandelbrot 1.3026 -1.4527 4.5336 11.587 252.475 240s BIC 240s Null 312.822 240s Preemption 302.879 240s Lognormal 262.052 240s Zipf 272.894 240s Mandelbrot 259.658 240s 240s > print(radlattice(rad)) 240s 240s > sac <- specaccum(BCI) 240s 240s > plot(sac, ci.type = "polygon", ci.col = "yellow") 240s 240s > sac <- specaccum(BCI) 240s 240s > plot(sac, ci.type = "polygon", ci.col = "yellow") 240s 240s > ncol(BCI)/mean(specnumber(BCI)) - 1 240s [1] 1.478519 240s 240s > beta <- vegdist(BCI, binary = TRUE) 240s 240s > mean(beta) 240s [1] 0.3399075 240s 240s > betadiver(help = TRUE) 240s 1 "w" = (b+c)/(2*a+b+c) 240s 2 "-1" = (b+c)/(2*a+b+c) 240s 3 "c" = (b+c)/2 240s 4 "wb" = b+c 240s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 240s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 240s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 240s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 240s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 240s (2*a+b+c))-1 240s 8 "t" = (b+c)/(2*a+b+c) 240s 9 "me" = (b+c)/(2*a+b+c) 240s 10 "j" = a/(a+b+c) 240s 11 "sor" = 2*a/(2*a+b+c) 240s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 240s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 240s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 240s 15 "cc" = (b+c)/(a+b+c) 240s 16 "g" = (b+c)/(a+b+c) 240s 17 "-3" = pmin.int(b,c)/(a+b+c) 240s 18 "l" = (b+c)/2 240s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 240s 20 "hk" = (b+c)/(2*a+b+c) 240s 21 "rlb" = a/(a+c) 240s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 240s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 240s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 240s 240s > z <- betadiver(BCI, "z") 240s 240s > quantile(z) 240s 0% 25% 50% 75% 100% 240s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 240s 240s > data(dune) 240s 240s > data(dune.env) 240s 240s > z <- betadiver(dune, "z") 240s 240s > mod <- with(dune.env, betadisper(z, Management)) 240s 240s > mod 240s 240s Homogeneity of multivariate dispersions 240s 240s Call: betadisper(d = z, group = Management) 240s 240s No. of Positive Eigenvalues: 12 240s No. of Negative Eigenvalues: 7 240s 240s Average distance to median: 240s BF HF NM SF 240s 0.2532 0.2512 0.4406 0.3635 240s 240s Eigenvalues for PCoA axes: 240s (Showing 8 of 19 eigenvalues) 240s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 240s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 240s PCoA7 PCoA8 240s 0.16128 0.08099 240s 240s > boxplot(mod) 240s 240s > specpool(BCI) 240s Species chao chao.se jack1 jack1.se jack2 240s All 225 236.3732 6.54361 245.58 5.650522 247.8722 240s boot boot.se n 240s All 235.6862 3.468888 50 240s 240s > s <- sample(nrow(BCI), 25) 240s 240s > specpool(BCI[s, ]) 240s Species chao chao.se jack1 jack1.se jack2 240s All 211 239.8343 14.24427 238.84 7.05453 253.1767 240s boot boot.se n 240s All 223.7356 3.829209 25 240s 240s > estimateR(BCI[k, ]) 240s 44 240s S.obs 81.000000 240s S.chao1 127.750000 240s se.chao1 21.873671 240s S.ACE 122.485974 240s se.ACE 5.852501 240s 240s > veiledspec(prestondistr(BCI[k, ])) 240s Extrapolated Observed Veiled 240s 98.1949 81.0000 17.1949 240s 240s > veiledspec(BCI[k, ]) 240s Extrapolated Observed Veiled 240s 111.86104 81.00000 30.86104 240s 240s > smo <- beals(BCI) 241s 241s > j <- which(colnames(BCI) == "Ceiba.pentandra") 241s 241s > plot(beals(BCI, species = j, include = FALSE), BCI[, 241s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 241s 241s > j <- which(colnames(BCI) == "Ceiba.pentandra") 241s 241s > plot(beals(BCI, species = j, include = FALSE), BCI[, 241s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 241s Warning messages: 241s 1: In cor(x > 0) : the standard deviation is zero 241s 2: In cor(x > 0) : the standard deviation is zero 241s 3: In betadisper(z, Management) : 241s some squared distances are negative and changed to zero 241s > 241s 241s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 241s Copyright (C) 2024 The R Foundation for Statistical Computing 241s Platform: x86_64-pc-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 241s > Stangle("intro-vegan.Rnw") 241s Writing to file intro-vegan.R 241s > source("intro-vegan.R", echo=TRUE) 241s 241s > par(mfrow = c(1, 1)) 241s 241s > options(width = 72) 241s 241s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 241s 241s > options(SweaveHooks = list(fig = figset)) 241s 241s > options(prompt = "> ", continue = " ") 241s 241s > library(vegan) 241s Loading required package: permute 241s Loading required package: lattice 242s This is vegan 2.6-8 242s 242s > data(dune) 242s 242s > ord <- decorana(dune) 242s 242s > ord 242s 242s Call: 242s decorana(veg = dune) 242s 242s Detrended correspondence analysis with 26 segments. 242s Rescaling of axes with 4 iterations. 242s Total inertia (scaled Chi-square): 2.1153 242s 242s DCA1 DCA2 DCA3 DCA4 242s Eigenvalues 0.5117 0.3036 0.12125 0.14267 242s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 242s Decorana values 0.5360 0.2869 0.08136 0.04814 242s Axis lengths 3.7004 3.1166 1.30055 1.47888 242s 242s 242s > ord <- metaMDS(dune, trace = FALSE) 242s 242s > ord 242s 242s Call: 242s metaMDS(comm = dune, trace = FALSE) 242s 242s global Multidimensional Scaling using monoMDS 242s 242s Data: dune 242s Distance: bray 242s 242s Dimensions: 2 242s Stress: 0.1183186 242s Stress type 1, weak ties 242s Best solution was repeated 2 times in 20 tries 242s The best solution was from try 18 (random start) 242s Scaling: centring, PC rotation, halfchange scaling 242s Species: expanded scores based on ‘dune’ 242s 242s 242s > plot(ord) 242s 242s > plot(ord) 242s 242s > plot(ord, type = "n") 242s 242s > points(ord, display = "sites", cex = 0.8, pch = 21, 242s + col = "red", bg = "yellow") 242s 242s > text(ord, display = "species", cex = 0.7, col = "blue") 242s 242s > plot(ord, type = "n") 242s 242s > points(ord, display = "sites", cex = 0.8, pch = 21, 242s + col = "red", bg = "yellow") 242s 242s > text(ord, display = "species", cex = 0.7, col = "blue") 242s 242s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 242s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 242s + col = "blue") 242s 242s > data(dune.env) 242s 242s > attach(dune.env) 242s 242s > plot(ord, disp = "sites", type = "n") 242s 242s > ordihull(ord, Management, col = 1:4, lwd = 3) 242s 242s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 242s + lwd = 3) 242s 242s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 242s 242s > ordispider(ord, Management, col = 1:4, label = TRUE) 242s 242s > points(ord, disp = "sites", pch = 21, col = "red", 242s + bg = "yellow", cex = 1.3) 242s 242s > plot(ord, disp = "sites", type = "n") 242s 242s > ordihull(ord, Management, col = 1:4, lwd = 3) 242s 242s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 242s + lwd = 3) 242s 242s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 242s 242s > ordispider(ord, Management, col = 1:4, label = TRUE) 242s 242s > points(ord, disp = "sites", pch = 21, col = "red", 242s + bg = "yellow", cex = 1.3) 242s 242s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 242s + perm = 999) 242s 242s > ord.fit 242s 242s ***VECTORS 242s 242s NMDS1 NMDS2 r2 Pr(>r) 242s A1 0.96473 0.26323 0.3649 0.019 * 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s Permutation: free 242s Number of permutations: 999 242s 242s ***FACTORS: 242s 242s Centroids: 242s NMDS1 NMDS2 242s ManagementBF -0.4534 -0.0102 242s ManagementHF -0.2636 -0.1282 242s ManagementNM 0.2958 0.5790 242s ManagementSF 0.1506 -0.4670 242s 242s Goodness of fit: 242s r2 Pr(>r) 242s Management 0.4134 0.004 ** 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s Permutation: free 242s Number of permutations: 999 242s 242s 242s 242s > plot(ord, dis = "site") 242s 242s > plot(ord.fit) 242s 242s > ordisurf(ord, A1, add = TRUE) 242s 242s Family: gaussian 242s Link function: identity 242s 242s Formula: 242s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 242s 242s Estimated degrees of freedom: 242s 1.59 total = 2.59 242s 242s REML score: 41.58727 242s 242s > plot(ord, dis = "site") 242s 242s > plot(ord.fit) 242s 242s > ordisurf(ord, A1, add = TRUE) 242s 242s Family: gaussian 242s Link function: identity 242s 242s Formula: 242s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 242s 242s Estimated degrees of freedom: 242s 1.59 total = 2.59 242s 242s REML score: 41.58727 242s 242s > ord <- cca(dune ~ A1 + Management, data = dune.env) 242s 242s > ord 242s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 242s 242s -- Model Summary -- 242s 242s Inertia Proportion Rank 242s Total 2.1153 1.0000 242s Constrained 0.7798 0.3686 4 242s Unconstrained 1.3355 0.6314 15 242s 242s Inertia is scaled Chi-square 242s 242s -- Eigenvalues -- 242s 242s Eigenvalues for constrained axes: 242s CCA1 CCA2 CCA3 CCA4 242s 0.3187 0.2372 0.1322 0.0917 242s 242s Eigenvalues for unconstrained axes: 242s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 242s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 242s CA11 CA12 CA13 CA14 CA15 242s 0.0317 0.0178 0.0116 0.0087 0.0047 242s 242s 242s > plot(ord) 242s 242s > plot(ord) 242s 242s > cca(dune ~ ., data = dune.env) 242s 242s Some constraints or conditions were aliased because they were 242s redundant. This can happen if terms are linearly dependent (colliCall: cca(formula = dune ~ A1 + Moisture + Management + Use + 242s Manure, data = dune.env) 242s 242s -- Model Summary -- 242s 242s Inertia Proportion Rank 242s Total 2.1153 1.0000 242s Constrained 1.5032 0.7106 12 242s Unconstrained 0.6121 0.2894 7 242s 242s Inertia is scaled Chi-square 242s 242s -- Note -- 242s 242s Some constraints or conditions were aliased because they were 242s redundant. This can happen if terms are linearly dependent 242s (collinear): ‘Manure^4’ 242s 242s -- Eigenvalues -- 242s 242s Eigenvalues for constrained axes: 242s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 242s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 242s CCA11 CCA12 242s 0.0228 0.0108 242s 242s Eigenvalues for unconstrained axes: 242s CA1 CA2 CA3 CA4 CA5 CA6 CA7 242s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 242s 242s 242s > anova(ord) 242s near): 242s ‘Manure^4’ 242s Permutation test for cca under reduced model 242s Permutation: free 242s Number of permutations: 999 242s 242s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 242s Df ChiSquare F Pr(>F) 242s Model 4 0.77978 2.1896 0.001 *** 242s Residual 15 1.33549 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > anova(ord, by = "term", permutations = 199) 242s Permutation test for cca under reduced model 242s Terms added sequentially (first to last) 242s Permutation: free 242s Number of permutations: 199 242s 242s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 242s Df ChiSquare F Pr(>F) 242s A1 1 0.22476 2.5245 0.015 * 242s Management 3 0.55502 2.0780 0.005 ** 242s Residual 15 1.33549 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > anova(ord, by = "mar", permutations = 199) 242s Permutation test for cca under reduced model 242s Marginal effects of terms 242s Permutation: free 242s Number of permutations: 199 242s 242s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 242s Df ChiSquare F Pr(>F) 242s A1 1 0.17594 1.9761 0.015 * 242s Management 3 0.55502 2.0780 0.010 ** 242s Residual 15 1.33549 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > anova(ord, by = "axis", permutations = 499) 242s Permutation test for cca under reduced model 242s Forward tests for axes 242s Permutation: free 242s Number of permutations: 499 242s 242s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 242s Df ChiSquare F Pr(>F) 242s CCA1 1 0.31875 3.5801 0.018 * 242s CCA2 1 0.23718 2.6640 0.154 242s CCA3 1 0.13217 1.4845 0.876 242s CCA4 1 0.09168 1.0297 1.000 242s Residual 15 1.33549 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 242s + data = dune.env) 242s 242s > ord 242s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 242s data = dune.env) 242s 242s -- Model Summary -- 242s 242s Inertia Proportion Rank 242s Total 2.1153 1.0000 242s Conditional 0.6283 0.2970 3 242s Constrained 0.5109 0.2415 4 242s Unconstrained 0.9761 0.4615 12 242s 242s Inertia is scaled Chi-square 242s 242s -- Eigenvalues -- 242s 242s Eigenvalues for constrained axes: 242s CCA1 CCA2 CCA3 CCA4 242s 0.24932 0.12090 0.08160 0.05904 242s 242s Eigenvalues for unconstrained axes: 242s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 242s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 242s CA10 CA11 CA12 242s 0.02102 0.01254 0.00928 242s 242s 242s > anova(ord, by = "term", permutations = 499) 242s Permutation test for cca under reduced model 242s Terms added sequentially (first to last) 242s Permutation: free 242s Number of permutations: 499 242s 242s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 242s Df ChiSquare F Pr(>F) 242s A1 1 0.11543 1.4190 1.000 242s Management 3 0.39543 1.6205 0.002 ** 242s Residual 12 0.97610 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 242s 242s > anova(ord, by = "term", permutations = how) 242s Permutation test for cca under reduced model 242s Terms added sequentially (first to last) 242s Plots: dune.env$Moisture, plot permutation: none 242s Permutation: free 242s Number of permutations: 499 242s 242s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 242s Df ChiSquare F Pr(>F) 242s A1 1 0.11543 1.4190 1.000 242s Management 3 0.39543 1.6205 0.002 ** 242s Residual 12 0.97610 242s --- 242s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 242s 242s > detach(dune.env) 242s > 242s 242s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 242s Copyright (C) 2024 The R Foundation for Statistical Computing 242s Platform: x86_64-pc-linux-gnu 242s 242s R is free software and comes with ABSOLUTELY NO WARRANTY. 242s You are welcome to redistribute it under certain conditions. 242s Type 'license()' or 'licence()' for distribution details. 242s 242s R is a collaborative project with many contributors. 242s Type 'contributors()' for more information and 242s 'citation()' on how to cite R or R packages in publications. 242s 242s Type 'demo()' for some demos, 'help()' for on-line help, or 242s 'help.start()' for an HTML browser interface to help. 242s Type 'q()' to quit R. 242s 243s > Stangle("partitioning.Rnw") 243s Writing to file partitioning.R 243s > source("partitioning.R", echo=TRUE) 243s 243s > par(mfrow = c(1, 1)) 243s 243s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 243s 243s > options(SweaveHooks = list(fig = figset)) 243s 243s > library(vegan) 243s Loading required package: permute 243s Loading required package: lattice 244s 244s > labs <- paste("Table", 1:4) 244s 244s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 244s 244s > showvarparts(2, bg = cls, Xnames = labs) 244s 244s > showvarparts(3, bg = cls, Xnames = labs) 244s This is vegan 2.6-8 244s 244s > showvarparts(4, bg = cls, Xnames = labs) 244s > 250s Test cca-object-tests passed 251s Test oecosimu-tests passed 254s Test vegan-tests passed 254s autopkgtest [01:08:37]: test run-unit-test: -----------------------] 255s autopkgtest [01:08:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 255s run-unit-test PASS 255s autopkgtest [01:08:38]: test pkg-r-autopkgtest: preparing testbed 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s Starting pkgProblemResolver with broken count: 0 256s Starting 2 pkgProblemResolver with broken count: 0 256s Done 256s The following NEW packages will be installed: 256s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 256s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 256s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 256s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 256s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 256s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 256s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 256s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 256s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 256s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 256s r-base-dev zlib1g-dev 256s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 256s Need to get 103 MB of archives. 256s After this operation, 363 MB of additional disk space will be used. 256s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 257s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 258s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 258s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 258s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 258s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250213-1ubuntu1 [47.0 kB] 258s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250213-1ubuntu1 [28.5 kB] 258s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250213-1ubuntu1 [3059 kB] 258s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250213-1ubuntu1 [1356 kB] 258s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250213-1ubuntu1 [2757 kB] 258s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250213-1ubuntu1 [1206 kB] 258s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250213-1ubuntu1 [1678 kB] 258s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250213-1ubuntu1 [152 kB] 258s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 258s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 258s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 258s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 258s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 258s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 258s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 259s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 259s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 259s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 259s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 259s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 259s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 259s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 259s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 259s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 259s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 259s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 259s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 259s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 259s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 259s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 259s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 259s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 259s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 259s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 259s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-1 [424 kB] 259s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 259s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 259s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 259s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 259s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 259s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 259s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 259s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 259s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.3-1 [189 kB] 260s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 260s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 260s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 260s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.2-1build1 [4342 B] 260s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 260s Fetched 103 MB in 3s (31.0 MB/s) 260s Selecting previously unselected package libisl23:amd64. 260s (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 ... 117155 files and directories currently installed.) 260s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 260s Unpacking libisl23:amd64 (0.27-1) ... 260s Selecting previously unselected package libmpc3:amd64. 260s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 260s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 260s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 260s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 260s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 260s Selecting previously unselected package cpp-14. 260s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 260s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 260s Selecting previously unselected package cpp-x86-64-linux-gnu. 260s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 260s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 260s Selecting previously unselected package cpp. 260s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 260s Unpacking cpp (4:14.2.0-1ubuntu1) ... 260s Selecting previously unselected package libcc1-0:amd64. 260s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_amd64.deb ... 260s Unpacking libcc1-0:amd64 (15-20250213-1ubuntu1) ... 260s Selecting previously unselected package libitm1:amd64. 260s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_amd64.deb ... 260s Unpacking libitm1:amd64 (15-20250213-1ubuntu1) ... 260s Selecting previously unselected package libasan8:amd64. 260s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_amd64.deb ... 260s Unpacking libasan8:amd64 (15-20250213-1ubuntu1) ... 260s Selecting previously unselected package liblsan0:amd64. 260s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_amd64.deb ... 260s Unpacking liblsan0:amd64 (15-20250213-1ubuntu1) ... 260s Selecting previously unselected package libtsan2:amd64. 260s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_amd64.deb ... 260s Unpacking libtsan2:amd64 (15-20250213-1ubuntu1) ... 261s Selecting previously unselected package libubsan1:amd64. 261s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_amd64.deb ... 261s Unpacking libubsan1:amd64 (15-20250213-1ubuntu1) ... 261s Selecting previously unselected package libhwasan0:amd64. 261s Preparing to unpack .../12-libhwasan0_15-20250213-1ubuntu1_amd64.deb ... 261s Unpacking libhwasan0:amd64 (15-20250213-1ubuntu1) ... 261s Selecting previously unselected package libquadmath0:amd64. 261s Preparing to unpack .../13-libquadmath0_15-20250213-1ubuntu1_amd64.deb ... 261s Unpacking libquadmath0:amd64 (15-20250213-1ubuntu1) ... 261s Selecting previously unselected package libgcc-14-dev:amd64. 261s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 261s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 261s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 261s Selecting previously unselected package gcc-14. 261s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 261s Selecting previously unselected package gcc-x86-64-linux-gnu. 261s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 261s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 261s Selecting previously unselected package gcc. 261s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 261s Unpacking gcc (4:14.2.0-1ubuntu1) ... 261s Selecting previously unselected package libstdc++-14-dev:amd64. 261s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 261s Selecting previously unselected package g++-14-x86-64-linux-gnu. 261s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 261s Selecting previously unselected package g++-14. 261s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_amd64.deb ... 261s Unpacking g++-14 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package g++-x86-64-linux-gnu. 262s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 262s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package g++. 262s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 262s Unpacking g++ (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package build-essential. 262s Preparing to unpack .../24-build-essential_12.10ubuntu1_amd64.deb ... 262s Unpacking build-essential (12.10ubuntu1) ... 262s Selecting previously unselected package dctrl-tools. 262s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 262s Unpacking dctrl-tools (2.24-3build3) ... 262s Selecting previously unselected package libgfortran-14-dev:amd64. 262s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 262s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 262s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 262s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gfortran-14. 262s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 262s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 262s Selecting previously unselected package gfortran-x86-64-linux-gnu. 262s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 262s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package gfortran. 262s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 262s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 262s Selecting previously unselected package icu-devtools. 262s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 262s Unpacking icu-devtools (76.1-1ubuntu2) ... 262s Selecting previously unselected package libblas-dev:amd64. 262s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 262s Unpacking libblas-dev:amd64 (3.12.1-2) ... 262s Selecting previously unselected package libbz2-dev:amd64. 262s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 262s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 262s Selecting previously unselected package libdeflate-dev:amd64. 262s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 262s Unpacking libdeflate-dev:amd64 (1.23-1) ... 262s Selecting previously unselected package libicu-dev:amd64. 262s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 262s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 262s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 262s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 262s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 262s Selecting previously unselected package libjpeg8-dev:amd64. 262s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 262s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 262s Selecting previously unselected package libjpeg-dev:amd64. 262s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 262s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 262s Selecting previously unselected package liblapack-dev:amd64. 262s Preparing to unpack .../39-liblapack-dev_3.12.1-2_amd64.deb ... 262s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 263s Selecting previously unselected package libncurses-dev:amd64. 263s Preparing to unpack .../40-libncurses-dev_6.5+20250216-1_amd64.deb ... 263s Unpacking libncurses-dev:amd64 (6.5+20250216-1) ... 263s Selecting previously unselected package libpcre2-16-0:amd64. 263s Preparing to unpack .../41-libpcre2-16-0_10.45-1_amd64.deb ... 263s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 263s Selecting previously unselected package libpcre2-32-0:amd64. 263s Preparing to unpack .../42-libpcre2-32-0_10.45-1_amd64.deb ... 263s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 263s Selecting previously unselected package libpcre2-posix3:amd64. 263s Preparing to unpack .../43-libpcre2-posix3_10.45-1_amd64.deb ... 263s Unpacking libpcre2-posix3:amd64 (10.45-1) ... 263s Selecting previously unselected package libpcre2-dev:amd64. 263s Preparing to unpack .../44-libpcre2-dev_10.45-1_amd64.deb ... 263s Unpacking libpcre2-dev:amd64 (10.45-1) ... 263s Selecting previously unselected package libpkgconf3:amd64. 263s Preparing to unpack .../45-libpkgconf3_1.8.1-4_amd64.deb ... 263s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 263s Selecting previously unselected package zlib1g-dev:amd64. 263s Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 263s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 263s Selecting previously unselected package libpng-dev:amd64. 263s Preparing to unpack .../47-libpng-dev_1.6.47-1_amd64.deb ... 263s Unpacking libpng-dev:amd64 (1.6.47-1) ... 263s Selecting previously unselected package libreadline-dev:amd64. 263s Preparing to unpack .../48-libreadline-dev_8.2-6_amd64.deb ... 263s Unpacking libreadline-dev:amd64 (8.2-6) ... 263s Selecting previously unselected package liblzma-dev:amd64. 263s Preparing to unpack .../49-liblzma-dev_5.6.3-1_amd64.deb ... 263s Unpacking liblzma-dev:amd64 (5.6.3-1) ... 263s Selecting previously unselected package pkgconf-bin. 263s Preparing to unpack .../50-pkgconf-bin_1.8.1-4_amd64.deb ... 263s Unpacking pkgconf-bin (1.8.1-4) ... 263s Selecting previously unselected package pkgconf:amd64. 263s Preparing to unpack .../51-pkgconf_1.8.1-4_amd64.deb ... 263s Unpacking pkgconf:amd64 (1.8.1-4) ... 263s Selecting previously unselected package libtirpc-dev:amd64. 263s Preparing to unpack .../52-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 263s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 263s Selecting previously unselected package r-base-dev. 263s Preparing to unpack .../53-r-base-dev_4.4.2-1build1_all.deb ... 263s Unpacking r-base-dev (4.4.2-1build1) ... 263s Selecting previously unselected package pkg-r-autopkgtest. 263s Preparing to unpack .../54-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 263s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 263s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 263s Setting up libncurses-dev:amd64 (6.5+20250216-1) ... 263s Setting up libreadline-dev:amd64 (8.2-6) ... 263s Setting up libpcre2-16-0:amd64 (10.45-1) ... 263s Setting up libpcre2-32-0:amd64 (10.45-1) ... 263s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 263s Setting up libpkgconf3:amd64 (1.8.1-4) ... 263s Setting up libquadmath0:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libmpc3:amd64 (1.3.1-1build2) ... 263s Setting up icu-devtools (76.1-1ubuntu2) ... 263s Setting up pkgconf-bin (1.8.1-4) ... 263s Setting up liblzma-dev:amd64 (5.6.3-1) ... 263s Setting up libubsan1:amd64 (15-20250213-1ubuntu1) ... 263s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 263s Setting up libpcre2-posix3:amd64 (10.45-1) ... 263s Setting up libhwasan0:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libasan8:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libtsan2:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 263s Setting up libisl23:amd64 (0.27-1) ... 263s Setting up libdeflate-dev:amd64 (1.23-1) ... 263s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 263s Setting up libcc1-0:amd64 (15-20250213-1ubuntu1) ... 263s Setting up liblsan0:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libblas-dev:amd64 (3.12.1-2) ... 263s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 263s Setting up dctrl-tools (2.24-3build3) ... 263s Setting up libitm1:amd64 (15-20250213-1ubuntu1) ... 263s Setting up libbz2-dev:amd64 (1.0.8-6) ... 263s Setting up libpcre2-dev:amd64 (10.45-1) ... 263s Setting up libpng-dev:amd64 (1.6.47-1) ... 263s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 263s Setting up pkgconf:amd64 (1.8.1-4) ... 263s Setting up liblapack-dev:amd64 (3.12.1-2) ... 263s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 263s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 263s Setting up cpp-14 (14.2.0-17ubuntu3) ... 263s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 263s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 263s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 263s Setting up cpp (4:14.2.0-1ubuntu1) ... 263s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 263s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Setting up gcc-14 (14.2.0-17ubuntu3) ... 263s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 263s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 263s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Setting up g++-14 (14.2.0-17ubuntu3) ... 263s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 263s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 263s Setting up gcc (4:14.2.0-1ubuntu1) ... 263s Setting up g++ (4:14.2.0-1ubuntu1) ... 263s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 263s Setting up build-essential (12.10ubuntu1) ... 263s Setting up gfortran (4:14.2.0-1ubuntu1) ... 263s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 263s 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 263s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 263s 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 263s Setting up r-base-dev (4.4.2-1build1) ... 263s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 263s Processing triggers for libc-bin (2.40-4ubuntu1) ... 263s Processing triggers for man-db (2.13.0-1) ... 264s Processing triggers for install-info (7.1.1-1) ... 265s autopkgtest [01:08:48]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 265s autopkgtest [01:08:48]: test pkg-r-autopkgtest: [----------------------- 265s Test: Try to load the R library vegan 265s 265s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 265s Copyright (C) 2024 The R Foundation for Statistical Computing 265s Platform: x86_64-pc-linux-gnu 265s 265s R is free software and comes with ABSOLUTELY NO WARRANTY. 265s You are welcome to redistribute it under certain conditions. 265s Type 'license()' or 'licence()' for distribution details. 265s 265s R is a collaborative project with many contributors. 265s Type 'contributors()' for more information and 265s 'citation()' on how to cite R or R packages in publications. 265s 265s Type 'demo()' for some demos, 'help()' for on-line help, or 265s 'help.start()' for an HTML browser interface to help. 265s Type 'q()' to quit R. 265s 266s > library('vegan') 266s Loading required package: permute 266s Loading required package: lattice 266s This is vegan 2.6-8 266s > 266s > 266s Other tests are currently unsupported! 266s They will be progressively added. 267s autopkgtest [01:08:50]: test pkg-r-autopkgtest: -----------------------] 267s autopkgtest [01:08:50]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 267s pkg-r-autopkgtest PASS 268s autopkgtest [01:08:51]: @@@@@@@@@@@@@@@@@@@@ summary 268s run-unit-test PASS 268s pkg-r-autopkgtest PASS 413s nova [W] Skipping flock for amd64 413s Creating nova instance adt-plucky-amd64-r-cran-vegan-20250304-010423-juju-7f2275-prod-proposed-migration-environment-15-1a4f5085-fd99-4dc4-b06f-bf2d139710e3 from image adt/ubuntu-plucky-amd64-server-20250303.img (UUID 4b11e980-bc59-4d67-9099-b69112741ead)... 413s nova [W] Timed out waiting for 67d95d6e-02ea-4678-83c4-6e894eb0cfbb to get deleted.