0s autopkgtest [23:57:19]: starting date and time: 2025-03-03 23:57:19+0000 0s autopkgtest [23:57:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:57:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3hwakiko/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-43.secgroup --name adt-plucky-arm64-r-cran-vegan-20250303-235719-juju-7f2275-prod-proposed-migration-environment-15-e1067047-25b8-41ed-b868-5faf4712402f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 117s autopkgtest [23:59:16]: testbed dpkg architecture: arm64 117s autopkgtest [23:59:16]: testbed apt version: 2.9.31ubuntu1 118s autopkgtest [23:59:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s autopkgtest [23:59:17]: testbed release detected to be: None 119s autopkgtest [23:59:18]: updating testbed package index (apt update) 119s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 119s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 119s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 119s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [472 kB] 120s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [2420 B] 120s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [51.1 kB] 120s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.4 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [89.8 kB] 120s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [25.4 kB] 120s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [448 kB] 120s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.7 kB] 120s Fetched 1236 kB in 1s (1470 kB/s) 121s Reading package lists... 121s + lsb_release --codename --short 121s + RELEASE=plucky 121s + cat 121s + [ plucky != trusty ] 121s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Calculating upgrade... 122s Calculating upgrade... 122s The following packages will be upgraded: 122s wireless-regdb 123s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 7290 B of archives. 123s After this operation, 1024 B of additional disk space will be used. 123s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 wireless-regdb all 2024.10.07-0ubuntu2 [7290 B] 123s Fetched 7290 B in 0s (50.7 kB/s) 123s (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 ... 116830 files and directories currently installed.) 123s Preparing to unpack .../wireless-regdb_2024.10.07-0ubuntu2_all.deb ... 123s Unpacking wireless-regdb (2024.10.07-0ubuntu2) over (2024.10.07-0ubuntu1) ... 123s Setting up wireless-regdb (2024.10.07-0ubuntu2) ... 123s Processing triggers for man-db (2.13.0-1) ... 124s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 124s + /usr/lib/apt/apt-helper analyze-pattern ?true 124s + uname -r 124s + sed s/\./\\./g 124s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 124s + apt list ?obsolete 124s + tail -n+2 124s + cut+ -d/grep -v ^linux-.*6\.12\.0-16-generic.* 124s -f1 124s + true 124s + obsolete_pkgs= 124s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Solving dependencies... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s + grep -q trusty /etc/lsb-release 125s + [ ! -d /usr/share/doc/unattended-upgrades ] 125s + [ ! -d /usr/share/doc/lxd ] 125s + [ ! -d /usr/share/doc/lxd-client ] 125s + [ ! -d /usr/share/doc/snapd ] 125s + type iptables 125s + cat 125s + chmod 755 /etc/rc.local 125s + . /etc/rc.local 125s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 125s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 125s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 125s + uname -m 125s + [ aarch64 = ppc64le ] 125s + [ -d /run/systemd/system ] 125s + systemd-detect-virt --quiet --vm 125s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 125s + cat 125s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 125s + echo COMPRESS=lz4 125s autopkgtest [23:59:24]: upgrading testbed (apt dist-upgrade and autopurge) 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 127s Entering ResolveByKeep 127s 127s Calculating upgrade... 128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 128s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Starting pkgProblemResolver with broken count: 0 129s Starting 2 pkgProblemResolver with broken count: 0 129s Done 129s Solving dependencies... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s autopkgtest [23:59:31]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP PREEMPT_DYNAMIC Fri Feb 14 14:51:45 UTC 2025 132s autopkgtest [23:59:31]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 134s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (dsc) [2204 B] 134s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (tar) [1205 kB] 134s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (diff) [6312 B] 134s gpgv: Signature made Sun Sep 1 23:45:51 2024 UTC 134s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 134s gpgv: issuer "plessy@debian.org" 134s gpgv: Can't check signature: No public key 134s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-8+dfsg-1.dsc: no acceptable signature found 135s autopkgtest [23:59:34]: testing package r-cran-vegan version 2.6-8+dfsg-1 135s autopkgtest [23:59:34]: build not needed 136s autopkgtest [23:59:35]: test run-unit-test: preparing testbed 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 138s The following NEW packages will be installed: 138s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 138s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 138s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 138s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 138s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 138s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 138s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 138s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 138s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 138s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 138s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 138s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 138s x11-common xdg-utils zip 138s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 138s Need to get 65.4 MB of archives. 138s After this operation, 158 MB of additional disk space will be used. 138s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 139s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 139s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 139s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 139s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 139s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 139s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 139s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 139s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 139s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 139s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 139s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 139s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 139s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250213-1ubuntu1 [443 kB] 139s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250213-1ubuntu1 [146 kB] 139s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 139s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 139s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 139s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 139s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 139s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 139s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 139s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 139s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 139s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 139s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 139s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 139s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 139s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 139s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.1-1 [238 kB] 139s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [49.6 kB] 139s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [27.6 kB] 139s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 139s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 139s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 139s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 139s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 139s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 139s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 139s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 139s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 139s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 139s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 139s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 139s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 139s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 139s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 139s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 139s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.2-1build1 [28.4 MB] 140s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cluster arm64 2.1.8-1 [568 kB] 140s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.2-2 [129 kB] 140s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 140s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.50+dfsg-1 [567 kB] 140s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 140s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 140s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 140s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 140s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 140s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-markdown all 1.13-1 [162 kB] 140s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 r-cran-mass arm64 7.3-65-1 [1109 kB] 141s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-2-1 [4153 kB] 141s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 141s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 141s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-permute all 0.9-7-1 [228 kB] 141s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vegan arm64 2.6-8+dfsg-1 [3129 kB] 141s Preconfiguring packages ... 141s Fetched 65.4 MB in 3s (23.7 MB/s) 141s Selecting previously unselected package fonts-dejavu-mono. 141s (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 ... 116830 files and directories currently installed.) 141s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 141s Unpacking fonts-dejavu-mono (2.37-8) ... 141s Selecting previously unselected package fonts-dejavu-core. 141s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 141s Unpacking fonts-dejavu-core (2.37-8) ... 141s Selecting previously unselected package fontconfig-config. 141s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 142s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 142s Selecting previously unselected package libfontconfig1:arm64. 142s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 142s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 142s Selecting previously unselected package fontconfig. 142s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 142s Unpacking fontconfig (2.15.0-2ubuntu1) ... 142s Selecting previously unselected package fonts-glyphicons-halflings. 142s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 142s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 142s Selecting previously unselected package fonts-mathjax. 142s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 142s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 142s Selecting previously unselected package libblas3:arm64. 142s Preparing to unpack .../07-libblas3_3.12.1-2_arm64.deb ... 142s Unpacking libblas3:arm64 (3.12.1-2) ... 142s Selecting previously unselected package libpixman-1-0:arm64. 142s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_arm64.deb ... 142s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 142s Selecting previously unselected package libxcb-render0:arm64. 142s Preparing to unpack .../09-libxcb-render0_1.17.0-2_arm64.deb ... 142s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 142s Selecting previously unselected package libxcb-shm0:arm64. 142s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_arm64.deb ... 142s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 142s Selecting previously unselected package libxrender1:arm64. 142s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 142s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 142s Selecting previously unselected package libcairo2:arm64. 142s Preparing to unpack .../12-libcairo2_1.18.2-2_arm64.deb ... 142s Unpacking libcairo2:arm64 (1.18.2-2) ... 142s Selecting previously unselected package libdatrie1:arm64. 142s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_arm64.deb ... 142s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 142s Selecting previously unselected package libdeflate0:arm64. 142s Preparing to unpack .../14-libdeflate0_1.23-1_arm64.deb ... 142s Unpacking libdeflate0:arm64 (1.23-1) ... 142s Selecting previously unselected package libgfortran5:arm64. 142s Preparing to unpack .../15-libgfortran5_15-20250213-1ubuntu1_arm64.deb ... 142s Unpacking libgfortran5:arm64 (15-20250213-1ubuntu1) ... 142s Selecting previously unselected package libgomp1:arm64. 142s Preparing to unpack .../16-libgomp1_15-20250213-1ubuntu1_arm64.deb ... 142s Unpacking libgomp1:arm64 (15-20250213-1ubuntu1) ... 142s Selecting previously unselected package libgraphite2-3:arm64. 142s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 142s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 142s Selecting previously unselected package libharfbuzz0b:arm64. 142s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_arm64.deb ... 142s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 143s Selecting previously unselected package x11-common. 143s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 143s Unpacking x11-common (1:7.7+23ubuntu3) ... 143s Selecting previously unselected package libice6:arm64. 143s Preparing to unpack .../20-libice6_2%3a1.1.1-1_arm64.deb ... 143s Unpacking libice6:arm64 (2:1.1.1-1) ... 143s Selecting previously unselected package libjpeg-turbo8:arm64. 143s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 143s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 143s Selecting previously unselected package libjpeg8:arm64. 143s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ... 143s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 143s Selecting previously unselected package libjs-bootstrap. 143s Preparing to unpack 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run-unit-test: [----------------------- 151s 151s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 151s Copyright (C) 2024 The R Foundation for Statistical Computing 151s Platform: aarch64-unknown-linux-gnu 151s 151s R is free software and comes with ABSOLUTELY NO WARRANTY. 151s You are welcome to redistribute it under certain conditions. 151s Type 'license()' or 'licence()' for distribution details. 151s 151s R is a collaborative project with many contributors. 151s Type 'contributors()' for more information and 151s 'citation()' on how to cite R or R packages in publications. 151s 151s Type 'demo()' for some demos, 'help()' for on-line help, or 151s 'help.start()' for an HTML browser interface to help. 151s Type 'q()' to quit R. 151s 151s > Stangle("decision-vegan.Rnw") 151s Writing to file decision-vegan.R 151s > source("decision-vegan.R", echo=TRUE) 151s 151s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 151s 151s > options(SweaveHooks = list(fig = figset)) 151s 151s > options(prompt = "> ", continue = " ") 151s 151s > options(width = 55) 151s 151s > require(vegan) 151s Loading required package: vegan 151s Loading required package: permute 151s Loading required package: lattice 152s This is vegan 2.6-8 152s 152s > data(sipoo) 152s 152s > mod <- nestedtemp(sipoo) 152s 152s > plot(mod, "i") 152s 152s > x <- mod$c["Falcsubb"] 152s 152s > y <- 1 - mod$r["Svartholm"] 152s 152s > points(x, y, pch = 16, cex = 1.5) 152s 152s > abline(x + y, -1, lty = 2) 152s 152s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 152s 152s > cross <- function(x, a, p) f(x, p) - a + x 152s 152s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 153s 153s > arrows(x, y, r, f(r, mod$p), lwd = 4) 153s 153s > library(vegan) 153s 153s > data(varespec) 153s 153s > data(varechem) 153s 153s > orig <- cca(varespec ~ Al + K, varechem) 153s 153s > plot(orig, dis = c("lc", "bp")) 153s 153s > plot(orig, dis = c("lc", "bp")) 153s 153s > i <- sample(nrow(varespec)) 153s 153s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 153s 153s > plot(shuff, dis = c("lc", "bp")) 153s 153s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 153s + dis = "lc"))) 153s 153s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 153s + dis = "lc"))) 153s 153s > tmp1 <- rda(varespec ~ Al + K, varechem) 153s 153s > i <- sample(nrow(varespec)) 153s 153s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 153s 153s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 153s + dis = "lc"))) 153s 153s > orig 153s Call: cca(formula = varespec ~ Al + K, data = 153s varechem) 153s 153s -- Model Summary -- 153s 153s Inertia Proportion Rank 153s Total 2.0832 1.0000 153s Constrained 0.4760 0.2285 2 153s Unconstrained 1.6072 0.7715 21 153s 153s Inertia is scaled Chi-square 153s 153s -- Eigenvalues -- 153s 153s Eigenvalues for constrained axes: 153s CCA1 CCA2 153s 0.3608 0.1152 153s 153s Eigenvalues for unconstrained axes: 153s CA1 CA2 CA3 CA4 CA5 CA6 CA7 153s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 153s CA8 153s 0.0757 153s (Showing 8 of 21 unconstrained eigenvalues) 153s 153s 153s > shuff 153s Call: cca(formula = varespec[i, ] ~ Al + K, data = 153s varechem) 153s 153s -- Model Summary -- 153s 153s Inertia Proportion Rank 153s Total 2.08320 1.00000 153s Constrained 0.09433 0.04528 2 153s Unconstrained 1.98887 0.95472 21 153s 153s Inertia is scaled Chi-square 153s 153s -- Eigenvalues -- 153s 153s Eigenvalues for constrained axes: 153s CCA1 CCA2 153s 0.07171 0.02262 153s 153s Eigenvalues for unconstrained axes: 153s CA1 CA2 CA3 CA4 CA5 CA6 CA7 153s 0.5192 0.3289 0.2309 0.1954 0.1760 0.1169 0.1089 153s CA8 153s 0.0811 153s (Showing 8 of 21 unconstrained eigenvalues) 153s 153s 153s > plot(procrustes(orig, shuff)) 153s 153s > tmp1 <- rda(varespec ~ ., varechem) 153s 153s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 153s 153s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 153s + scores(tmp2, dis = "lc", choi = 1:14)) 153s 153s > max(residuals(proc)) 153s [1] 2.543974e-14 153s 153s > data(dune) 153s 153s > data(dune.env) 153s 153s > orig <- cca(dune ~ Moisture, dune.env) 153s 153s > plot(orig, dis = "lc") 153s 153s > plot(orig, display = "wa", type = "points") 153s 153s > ordispider(orig, col = "red") 153s 153s > text(orig, dis = "cn", col = "blue") 153s 153s > plot(orig, display = "wa", type = "points") 153s 153s > ordispider(orig, col = "red") 153s 153s > text(orig, dis = "cn", col = "blue") 153s > 153s 153s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 153s Copyright (C) 2024 The R Foundation for Statistical Computing 153s Platform: aarch64-unknown-linux-gnu 153s 153s R is free software and comes with ABSOLUTELY NO WARRANTY. 153s You are welcome to redistribute it under certain conditions. 153s Type 'license()' or 'licence()' for distribution details. 153s 153s R is a collaborative project with many contributors. 153s Type 'contributors()' for more information and 153s 'citation()' on how to cite R or R packages in publications. 153s 153s Type 'demo()' for some demos, 'help()' for on-line help, or 153s 'help.start()' for an HTML browser interface to help. 153s Type 'q()' to quit R. 153s 153s > Stangle("diversity-vegan.Rnw") 153s Writing to file diversity-vegan.R 153s > source("diversity-vegan.R", echo=TRUE) 153s 153s > par(mfrow = c(1, 1)) 153s 153s > options(width = 55) 153s 153s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 153s 153s > options(SweaveHooks = list(fig = figset)) 153s 153s > options(prompt = "> ", continue = " ") 153s 153s > library(vegan) 153s Loading required package: permute 153s Loading required package: lattice 154s This is vegan 2.6-8 154s 154s > data(BCI) 154s 154s > H <- diversity(BCI) 154s 154s > J <- H/log(specnumber(BCI)) 154s 154s > k <- sample(nrow(BCI), 6) 154s 154s > R <- renyi(BCI[k, ]) 154s 154s > print(plot(R)) 154s 154s > alpha <- fisher.alpha(BCI) 154s 154s > quantile(rowSums(BCI)) 154s 0% 25% 50% 75% 100% 154s 340.0 409.0 428.0 443.5 601.0 154s 154s > Srar <- rarefy(BCI, min(rowSums(BCI))) 154s 154s > S2 <- rarefy(BCI, 2) 154s 154s > all(rank(Srar) == rank(S2)) 154s [1] FALSE 154s 154s > range(diversity(BCI, "simp") - (S2 - 1)) 154s [1] -0.002868298 -0.001330663 154s 154s > data(dune) 154s 154s > data(dune.taxon) 154s 154s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 154s 154s > mod <- taxondive(dune, taxdis) 154s 154s > plot(mod) 154s 154s > tr <- hclust(taxdis, "aver") 154s 154s > mod <- treedive(dune, tr) 154s forced matching of 'tree' labels and 'comm' names 154s 154s > k <- sample(nrow(BCI), 1) 154s 154s > fish <- fisherfit(BCI[k, ]) 154s 154s > fish 154s 154s Fisher log series model 154s No. of species: 86 154s Fisher alpha: 35.54363 154s 154s 154s > plot(fish) 154s 154s > prestondistr(BCI[k, ]) 154s 154s Preston lognormal model 154s Method: maximized likelihood to log2 abundances 154s No. of species: 86 154s 154s mode width S0 154s 0.7090315 1.7052549 23.8984091 154s 154s Frequencies by Octave 154s 0 1 2 3 4 154s Observed 18.50000 26.00000 18.50000 14.500000 6.000000 154s Fitted 21.91936 23.55303 17.94385 9.692462 3.711953 154s 5 6 154s Observed 0.500000 2.0000000 154s Fitted 1.007908 0.1940389 154s 154s 154s > rad <- radfit(BCI[k, ]) 154s 154s > rad 154s 154s RAD models, family poisson 154s No. of species 86, total abundance 364 154s 154s par1 par2 par3 Deviance 154s Null 117.880 154s Preemption 0.052888 124.438 154s Lognormal 0.68438 1.2574 36.783 154s Zipf 0.173 -0.93219 15.446 154s Mandelbrot 0.24126 -1.0276 0.52084 13.861 154s AIC BIC 154s Null 355.738 355.738 154s Preemption 364.295 366.750 154s Lognormal 278.640 283.549 154s Zipf 257.303 262.212 154s Mandelbrot 257.718 265.081 154s 154s > print(radlattice(rad)) 154s 154s > sac <- specaccum(BCI) 154s 154s > plot(sac, ci.type = "polygon", ci.col = "yellow") 154s 154s > sac <- specaccum(BCI) 155s 155s > plot(sac, ci.type = "polygon", ci.col = "yellow") 155s 155s > ncol(BCI)/mean(specnumber(BCI)) - 1 155s [1] 1.478519 155s 155s > beta <- vegdist(BCI, binary = TRUE) 155s 155s > mean(beta) 155s [1] 0.3399075 155s 155s > betadiver(help = TRUE) 155s 1 "w" = (b+c)/(2*a+b+c) 155s 2 "-1" = (b+c)/(2*a+b+c) 155s 3 "c" = (b+c)/2 155s 4 "wb" = b+c 155s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 155s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 155s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 155s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 155s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 155s (2*a+b+c))-1 155s 8 "t" = (b+c)/(2*a+b+c) 155s 9 "me" = (b+c)/(2*a+b+c) 155s 10 "j" = a/(a+b+c) 155s 11 "sor" = 2*a/(2*a+b+c) 155s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 155s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 155s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 155s 15 "cc" = (b+c)/(a+b+c) 155s 16 "g" = (b+c)/(a+b+c) 155s 17 "-3" = pmin.int(b,c)/(a+b+c) 155s 18 "l" = (b+c)/2 155s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 155s 20 "hk" = (b+c)/(2*a+b+c) 155s 21 "rlb" = a/(a+c) 155s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 155s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 155s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 155s 155s > z <- betadiver(BCI, "z") 155s 155s > quantile(z) 155s 0% 25% 50% 75% 100% 155s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 155s 155s > data(dune) 155s 155s > data(dune.env) 155s 155s > z <- betadiver(dune, "z") 155s 155s > mod <- with(dune.env, betadisper(z, Management)) 155s 155s > mod 155s 155s Homogeneity of multivariate dispersions 155s 155s Call: betadisper(d = z, group = Management) 155s 155s No. of Positive Eigenvalues: 12 155s No. of Negative Eigenvalues: 7 155s 155s Average distance to median: 155s BF HF NM SF 155s 0.2532 0.2512 0.4406 0.3635 155s 155s Eigenvalues for PCoA axes: 155s (Showing 8 of 19 eigenvalues) 155s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 155s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 155s PCoA7 PCoA8 155s 0.16128 0.08099 155s 155s > boxplot(mod) 155s 155s > specpool(BCI) 155s Species chao chao.se jack1 jack1.se jack2 155s All 225 236.3732 6.54361 245.58 5.650522 247.8722 155s boot boot.se n 155s All 235.6862 3.468888 50 155s 155s > s <- sample(nrow(BCI), 25) 155s 155s > specpool(BCI[s, ]) 155s Species chao chao.se jack1 jack1.se jack2 155s All 204 233.4982 15.57145 228.96 7.523403 243.1817 155s boot boot.se n 155s All 215.4157 4.015733 25 155s 155s > estimateR(BCI[k, ]) 155s 29 155s S.obs 86.00000 155s S.chao1 127.62500 155s se.chao1 18.31906 155s S.ACE 127.05647 155s se.ACE 5.85267 155s 155s > veiledspec(prestondistr(BCI[k, ])) 155s Extrapolated Observed Veiled 155s 102.15232 86.00000 16.15232 155s 155s > veiledspec(BCI[k, ]) 155s Extrapolated Observed Veiled 155s 108.8758 86.0000 22.8758 155s 155s > smo <- beals(BCI) 155s 155s > j <- which(colnames(BCI) == "Ceiba.pentandra") 155s 155s > plot(beals(BCI, species = j, include = FALSE), BCI[, 155s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 155s 155s > j <- which(colnames(BCI) == "Ceiba.pentandra") 155s 155s > plot(beals(BCI, species = j, include = FALSE), BCI[, 155s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 155s > 155s Warning messages: 155s 1: In cor(x > 0) : the standard deviation is zero 155s 2: In cor(x > 0) : the standard deviation is zero 155s 3: In betadisper(z, Management) : 155s some squared distances are negative and changed to zero 155s 155s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 155s Copyright (C) 2024 The R Foundation for Statistical Computing 155s Platform: aarch64-unknown-linux-gnu 155s 155s R is free software and comes with ABSOLUTELY NO WARRANTY. 155s You are welcome to redistribute it under certain conditions. 155s Type 'license()' or 'licence()' for distribution details. 155s 155s R is a collaborative project with many contributors. 155s Type 'contributors()' for more information and 155s 'citation()' on how to cite R or R packages in publications. 155s 155s Type 'demo()' for some demos, 'help()' for on-line help, or 155s 'help.start()' for an HTML browser interface to help. 155s Type 'q()' to quit R. 155s 155s > Stangle("intro-vegan.Rnw") 155s Writing to file intro-vegan.R 155s > source("intro-vegan.R", echo=TRUE) 155s 155s > par(mfrow = c(1, 1)) 155s 155s > options(width = 72) 155s 155s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 155s 155s > options(SweaveHooks = list(fig = figset)) 155s 155s > options(prompt = "> ", continue = " ") 155s 155s > library(vegan) 155s Loading required package: permute 155s Loading required package: lattice 156s This is vegan 2.6-8 156s 156s > data(dune) 156s 156s > ord <- decorana(dune) 156s 156s > ord 156s 156s Call: 156s decorana(veg = dune) 156s 156s Detrended correspondence analysis with 26 segments. 156s Rescaling of axes with 4 iterations. 156s Total inertia (scaled Chi-square): 2.1153 156s 156s DCA1 DCA2 DCA3 DCA4 156s Eigenvalues 0.5117 0.3036 0.12125 0.14267 156s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 156s Decorana values 0.5360 0.2869 0.08136 0.04814 156s Axis lengths 3.7004 3.1166 1.30055 1.47888 156s 156s 156s > ord <- metaMDS(dune, trace = FALSE) 156s 156s > ord 156s 156s Call: 156s metaMDS(comm = dune, trace = FALSE) 156s 156s global Multidimensional Scaling using monoMDS 156s 156s Data: dune 156s Distance: bray 156s 156s Dimensions: 2 156s Stress: 0.1183186 156s Stress type 1, weak ties 156s Best solution was repeated 3 times in 20 tries 156s The best solution was from try 8 (random start) 156s Scaling: centring, PC rotation, halfchange scaling 156s Species: expanded scores based on ‘dune’ 156s 156s 156s > plot(ord) 156s 156s > plot(ord) 156s 156s > plot(ord, type = "n") 156s 156s > points(ord, display = "sites", cex = 0.8, pch = 21, 156s + col = "red", bg = "yellow") 156s 156s > text(ord, display = "species", cex = 0.7, col = "blue") 156s 156s > plot(ord, type = "n") 156s 156s > points(ord, display = "sites", cex = 0.8, pch = 21, 156s + col = "red", bg = "yellow") 156s 156s > text(ord, display = "species", cex = 0.7, col = "blue") 156s 156s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 156s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 156s + col = "blue") 156s 156s > data(dune.env) 156s 156s > attach(dune.env) 156s 156s > plot(ord, disp = "sites", type = "n") 156s 156s > ordihull(ord, Management, col = 1:4, lwd = 3) 156s 156s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 156s + lwd = 3) 156s 156s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 156s 156s > ordispider(ord, Management, col = 1:4, label = TRUE) 156s 156s > points(ord, disp = "sites", pch = 21, col = "red", 156s + bg = "yellow", cex = 1.3) 156s 156s > plot(ord, disp = "sites", type = "n") 156s 156s > ordihull(ord, Management, col = 1:4, lwd = 3) 156s 156s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 156s + lwd = 3) 156s 156s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 156s 156s > ordispider(ord, Management, col = 1:4, label = TRUE) 156s 156s > points(ord, disp = "sites", pch = 21, col = "red", 156s + bg = "yellow", cex = 1.3) 156s 156s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 156s + perm = 999) 156s 156s > ord.fit 156s 156s ***VECTORS 156s 156s NMDS1 NMDS2 r2 Pr(>r) 156s A1 0.96474 0.26322 0.3649 0.022 * 156s --- 156s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 156s Permutation: free 156s Number of permutations: 999 156s 156s ***FACTORS: 156s 156s Centroids: 156s NMDS1 NMDS2 156s ManagementBF -0.4534 -0.0102 156s ManagementHF -0.2636 -0.1282 156s ManagementNM 0.2958 0.5790 156s ManagementSF 0.1506 -0.4670 156s 156s Goodness of fit: 156s r2 Pr(>r) 156s Management 0.4134 0.004 ** 156s --- 156s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 156s Permutation: free 156s Number of permutations: 999 156s 156s 156s 156s > plot(ord, dis = "site") 156s 156s > plot(ord.fit) 156s 156s > ordisurf(ord, A1, add = TRUE) 156s 156s Family: gaussian 156s Link function: identity 156s 156s Formula: 156s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 156s 156s Estimated degrees of freedom: 156s 1.59 total = 2.59 156s 156s REML score: 41.58728 156s 156s > plot(ord, dis = "site") 156s 156s > plot(ord.fit) 156s 156s > ordisurf(ord, A1, add = TRUE) 156s 156s Family: gaussian 156s Link function: identity 156s 156s Formula: 156s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 156s 156s Estimated degrees of freedom: 156s 1.59 total = 2.59 156s 156s REML score: 41.58728 156s 156s > ord <- cca(dune ~ A1 + Management, data = dune.env) 156s 156s > ord 156s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 156s 156s -- Model Summary -- 156s 156s Inertia Proportion Rank 156s Total 2.1153 1.0000 156s Constrained 0.7798 0.3686 4 156s Unconstrained 1.3355 0.6314 15 156s 156s Inertia is scaled Chi-square 156s 156s -- Eigenvalues -- 156s 156s Eigenvalues for constrained axes: 156s CCA1 CCA2 CCA3 CCA4 156s 0.3187 0.2372 0.1322 0.0917 156s 156s Eigenvalues for unconstrained axes: 156s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 156s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 156s CA11 CA12 CA13 CA14 CA15 156s 0.0317 0.0178 0.0116 0.0087 0.0047 156s 156s 156s > plot(ord) 156s 156s > plot(ord) 156s 156s > cca(dune ~ ., data = dune.env) 156s 156s Some constraints or conditions were aliased because they were 156s redundant. This can happen if terms are linearly dependent (collinear): 156s ‘Manure^4’ 156s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 156s Manure, data = dune.env) 156s 156s -- Model Summary -- 156s 156s Inertia Proportion Rank 156s Total 2.1153 1.0000 156s Constrained 1.5032 0.7106 12 156s Unconstrained 0.6121 0.2894 7 156s 156s Inertia is scaled Chi-square 156s 156s -- Note -- 156s 156s Some constraints or conditions were aliased because they were 156s redundant. This can happen if terms are linearly dependent 156s (collinear): ‘Manure^4’ 156s 156s -- Eigenvalues -- 156s 156s Eigenvalues for constrained axes: 156s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 156s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 156s CCA11 CCA12 156s 0.0228 0.0108 156s 156s Eigenvalues for unconstrained axes: 156s CA1 CA2 CA3 CA4 CA5 CA6 CA7 156s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 156s 156s 156s > anova(ord) 156s Permutation test for cca under reduced model 156s Permutation: free 156s Number of permutations: 999 156s 156s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 156s Df ChiSquare F Pr(>F) 156s Model 4 0.77978 2.1896 0.001 *** 156s Residual 15 1.33549 156s --- 156s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 156s 156s > anova(ord, by = "term", permutations = 199) 156s Permutation test for cca under reduced model 156s Terms added sequentially (first to last) 156s Permutation: free 156s Number of permutations: 199 156s 156s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 156s Df ChiSquare F Pr(>F) 156s A1 1 0.22476 2.5245 0.01 ** 156s Management 3 0.55502 2.0780 0.01 ** 156s Residual 15 1.33549 156s --- 156s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 156s 156s > anova(ord, by = "mar", permutations = 199) 156s Permutation test for cca under reduced model 156s Marginal effects of terms 156s Permutation: free 156s Number of permutations: 199 156s 156s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 156s Df ChiSquare F Pr(>F) 156s A1 1 0.17594 1.9761 0.055 . 156s Management 3 0.55502 2.0780 0.005 ** 156s Residual 15 1.33549 156s --- 156s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 156s 156s > anova(ord, by = "axis", permutations = 499) 157s Permutation test for cca under reduced model 157s Forward tests for axes 157s Permutation: free 157s Number of permutations: 499 157s 157s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 157s Df ChiSquare F Pr(>F) 157s CCA1 1 0.31875 3.5801 0.008 ** 157s CCA2 1 0.23718 2.6640 0.126 157s CCA3 1 0.13217 1.4845 0.838 157s CCA4 1 0.09168 1.0297 1.000 157s Residual 15 1.33549 157s --- 157s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 157s 157s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 157s + data = dune.env) 157s 157s > ord 157s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 157s data = dune.env) 157s 157s -- Model Summary -- 157s 157s Inertia Proportion Rank 157s Total 2.1153 1.0000 157s Conditional 0.6283 0.2970 3 157s Constrained 0.5109 0.2415 4 157s Unconstrained 0.9761 0.4615 12 157s 157s Inertia is scaled Chi-square 157s 157s -- Eigenvalues -- 157s 157s Eigenvalues for constrained axes: 157s CCA1 CCA2 CCA3 CCA4 157s 0.24932 0.12090 0.08160 0.05904 157s 157s Eigenvalues for unconstrained axes: 157s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 157s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 157s CA10 CA11 CA12 157s 0.02102 0.01254 0.00928 157s 157s 157s > anova(ord, by = "term", permutations = 499) 157s Permutation test for cca under reduced model 157s Terms added sequentially (first to last) 157s Permutation: free 157s Number of permutations: 499 157s 157s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 157s Df ChiSquare F Pr(>F) 157s A1 1 0.11543 1.4190 1.000 157s Management 3 0.39543 1.6205 0.002 ** 157s Residual 12 0.97610 157s --- 157s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 157s 157s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 157s 157s > anova(ord, by = "term", permutations = how) 157s Permutation test for cca under reduced model 157s Terms added sequentially (first to last) 157s Plots: dune.env$Moisture, plot permutation: none 157s Permutation: free 157s Number of permutations: 499 157s 157s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 157s Df ChiSquare F Pr(>F) 157s A1 1 0.11543 1.4190 1.000 157s Management 3 0.39543 1.6205 0.002 ** 157s Residual 12 0.97610 157s --- 157s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 157s 157s > detach(dune.env) 157s > 157s 157s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 157s Copyright (C) 2024 The R Foundation for Statistical Computing 157s Platform: aarch64-unknown-linux-gnu 157s 157s R is free software and comes with ABSOLUTELY NO WARRANTY. 157s You are welcome to redistribute it under certain conditions. 157s Type 'license()' or 'licence()' for distribution details. 157s 157s R is a collaborative project with many contributors. 157s Type 'contributors()' for more information and 157s 'citation()' on how to cite R or R packages in publications. 157s 157s Type 'demo()' for some demos, 'help()' for on-line help, or 157s 'help.start()' for an HTML browser interface to help. 157s Type 'q()' to quit R. 157s 157s > Stangle("partitioning.Rnw") 157s Writing to file partitioning.R 157s > source("partitioning.R", echo=TRUE) 157s 157s > par(mfrow = c(1, 1)) 157s 157s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 157s 157s > options(SweaveHooks = list(fig = figset)) 157s 157s > library(vegan) 157s Loading required package: permute 157s Loading required package: lattice 158s This is vegan 2.6-8 158s 158s > labs <- paste("Table", 1:4) 158s 158s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 158s 158s > showvarparts(2, bg = cls, Xnames = labs) 158s 158s > showvarparts(3, bg = cls, Xnames = labs) 158s 158s > showvarparts(4, bg = cls, Xnames = labs) 158s > 165s Test cca-object-tests passed 166s Test oecosimu-tests passed 170s Test vegan-tests passed 170s autopkgtest [00:00:09]: test run-unit-test: -----------------------] 172s autopkgtest [00:00:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 172s run-unit-test PASS 173s autopkgtest [00:00:12]: test pkg-r-autopkgtest: preparing testbed 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s The following NEW packages will be installed: 175s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 175s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 175s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 175s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 175s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 175s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 175s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 175s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 175s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 175s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 175s zlib1g-dev 175s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 92.7 MB of archives. 175s After this operation, 334 MB of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 175s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 176s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 176s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 176s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 176s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250213-1ubuntu1 [44.2 kB] 176s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250213-1ubuntu1 [28.0 kB] 176s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250213-1ubuntu1 [2928 kB] 176s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250213-1ubuntu1 [1319 kB] 176s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250213-1ubuntu1 [2695 kB] 176s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250213-1ubuntu1 [1178 kB] 176s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250213-1ubuntu1 [1642 kB] 176s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 176s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 177s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 177s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 177s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 177s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 177s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 177s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 177s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 177s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 177s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 177s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 177s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 177s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 177s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 177s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 177s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 177s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 177s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 177s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 177s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 177s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 177s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 177s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 177s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 177s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 178s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-1 [389 kB] 178s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 178s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 178s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 178s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 178s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 178s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 178s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 178s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 178s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.3-1 [180 kB] 178s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 178s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 178s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 178s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.2-1build1 [4342 B] 178s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 178s Fetched 92.7 MB in 3s (31.0 MB/s) 178s Selecting previously unselected package libisl23:arm64. 178s (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 ... 124803 files and directories currently installed.) 178s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 178s Unpacking libisl23:arm64 (0.27-1) ... 178s Selecting previously unselected package libmpc3:arm64. 178s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 178s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 178s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 178s Preparing to unpack .../02-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 178s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 179s Selecting previously unselected package cpp-14. 179s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 179s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 179s Selecting previously unselected package cpp-aarch64-linux-gnu. 179s Preparing to unpack .../04-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 179s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 179s Selecting previously unselected package cpp. 179s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 179s Unpacking cpp (4:14.2.0-1ubuntu1) ... 179s Selecting previously unselected package libcc1-0:arm64. 179s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libcc1-0:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libitm1:arm64. 179s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libitm1:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libasan8:arm64. 179s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libasan8:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package liblsan0:arm64. 179s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking liblsan0:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libtsan2:arm64. 179s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libtsan2:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libubsan1:arm64. 179s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libubsan1:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libhwasan0:arm64. 179s Preparing to unpack .../12-libhwasan0_15-20250213-1ubuntu1_arm64.deb ... 179s Unpacking libhwasan0:arm64 (15-20250213-1ubuntu1) ... 179s Selecting previously unselected package libgcc-14-dev:arm64. 179s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 179s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 179s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 179s Preparing to unpack .../14-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 179s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 180s Selecting previously unselected package gcc-14. 180s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 180s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 180s Selecting previously unselected package gcc-aarch64-linux-gnu. 180s Preparing to unpack .../16-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 180s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 180s Selecting previously unselected package gcc. 180s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 180s Unpacking gcc (4:14.2.0-1ubuntu1) ... 180s Selecting previously unselected package libstdc++-14-dev:arm64. 180s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 180s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 180s Selecting previously unselected package g++-14-aarch64-linux-gnu. 180s Preparing to unpack .../19-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 180s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 181s Selecting previously unselected package g++-14. 181s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu3_arm64.deb ... 181s Unpacking g++-14 (14.2.0-17ubuntu3) ... 181s Selecting previously unselected package g++-aarch64-linux-gnu. 181s Preparing to unpack .../21-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 181s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Selecting previously unselected package g++. 181s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 181s Unpacking g++ (4:14.2.0-1ubuntu1) ... 181s Selecting previously unselected package build-essential. 181s Preparing to unpack .../23-build-essential_12.10ubuntu1_arm64.deb ... 181s Unpacking build-essential (12.10ubuntu1) ... 181s Selecting previously unselected package dctrl-tools. 181s Preparing to unpack .../24-dctrl-tools_2.24-3build3_arm64.deb ... 181s Unpacking dctrl-tools (2.24-3build3) ... 181s Selecting previously unselected package libgfortran-14-dev:arm64. 181s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 181s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 181s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 181s Preparing to unpack .../26-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 181s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 181s Selecting previously unselected package gfortran-14. 181s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 181s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 181s Selecting previously unselected package gfortran-aarch64-linux-gnu. 181s Preparing to unpack .../28-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 181s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 181s Selecting previously unselected package gfortran. 181s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 181s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 181s Selecting previously unselected package icu-devtools. 181s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_arm64.deb ... 181s Unpacking icu-devtools (76.1-1ubuntu2) ... 181s Selecting previously unselected package libblas-dev:arm64. 181s Preparing to unpack .../31-libblas-dev_3.12.1-2_arm64.deb ... 181s Unpacking libblas-dev:arm64 (3.12.1-2) ... 181s Selecting previously unselected package libbz2-dev:arm64. 181s Preparing to unpack .../32-libbz2-dev_1.0.8-6_arm64.deb ... 181s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 181s Selecting previously unselected package libdeflate-dev:arm64. 181s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 181s Unpacking libdeflate-dev:arm64 (1.23-1) ... 181s Selecting previously unselected package libicu-dev:arm64. 181s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 181s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 181s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 181s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 181s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 181s Selecting previously unselected package libjpeg8-dev:arm64. 181s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 181s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 181s Selecting previously unselected package libjpeg-dev:arm64. 182s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 182s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 182s Selecting previously unselected package liblapack-dev:arm64. 182s Preparing to unpack .../38-liblapack-dev_3.12.1-2_arm64.deb ... 182s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 182s Selecting previously unselected package libncurses-dev:arm64. 182s Preparing to unpack .../39-libncurses-dev_6.5+20250216-1_arm64.deb ... 182s Unpacking libncurses-dev:arm64 (6.5+20250216-1) ... 182s Selecting previously unselected package libpcre2-16-0:arm64. 182s Preparing to unpack .../40-libpcre2-16-0_10.45-1_arm64.deb ... 182s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 182s Selecting previously unselected package libpcre2-32-0:arm64. 182s Preparing to unpack .../41-libpcre2-32-0_10.45-1_arm64.deb ... 182s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 182s Selecting previously unselected package libpcre2-posix3:arm64. 182s Preparing to unpack .../42-libpcre2-posix3_10.45-1_arm64.deb ... 182s Unpacking libpcre2-posix3:arm64 (10.45-1) ... 182s Selecting previously unselected package libpcre2-dev:arm64. 182s Preparing to unpack .../43-libpcre2-dev_10.45-1_arm64.deb ... 182s Unpacking libpcre2-dev:arm64 (10.45-1) ... 182s Selecting previously unselected package libpkgconf3:arm64. 182s Preparing to unpack .../44-libpkgconf3_1.8.1-4_arm64.deb ... 182s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 182s Selecting previously unselected package zlib1g-dev:arm64. 182s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 182s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 182s Selecting previously unselected package libpng-dev:arm64. 182s Preparing to unpack .../46-libpng-dev_1.6.47-1_arm64.deb ... 182s Unpacking libpng-dev:arm64 (1.6.47-1) ... 182s Selecting previously unselected package libreadline-dev:arm64. 182s Preparing to unpack .../47-libreadline-dev_8.2-6_arm64.deb ... 182s Unpacking libreadline-dev:arm64 (8.2-6) ... 182s Selecting previously unselected package liblzma-dev:arm64. 182s Preparing to unpack .../48-liblzma-dev_5.6.3-1_arm64.deb ... 182s Unpacking liblzma-dev:arm64 (5.6.3-1) ... 182s Selecting previously unselected package pkgconf-bin. 182s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_arm64.deb ... 182s Unpacking pkgconf-bin (1.8.1-4) ... 182s Selecting previously unselected package pkgconf:arm64. 182s Preparing to unpack .../50-pkgconf_1.8.1-4_arm64.deb ... 182s Unpacking pkgconf:arm64 (1.8.1-4) ... 182s Selecting previously unselected package libtirpc-dev:arm64. 182s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 182s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 182s Selecting previously unselected package r-base-dev. 182s Preparing to unpack .../52-r-base-dev_4.4.2-1build1_all.deb ... 182s Unpacking r-base-dev (4.4.2-1build1) ... 182s Selecting previously unselected package pkg-r-autopkgtest. 182s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 182s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 182s Setting up libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 182s Setting up libncurses-dev:arm64 (6.5+20250216-1) ... 183s Setting up libreadline-dev:arm64 (8.2-6) ... 183s Setting up libpcre2-16-0:arm64 (10.45-1) ... 183s Setting up libpcre2-32-0:arm64 (10.45-1) ... 183s Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 183s Setting up libpkgconf3:arm64 (1.8.1-4) ... 183s Setting up libmpc3:arm64 (1.3.1-1build2) ... 183s Setting up icu-devtools (76.1-1ubuntu2) ... 183s Setting up pkgconf-bin (1.8.1-4) ... 183s Setting up liblzma-dev:arm64 (5.6.3-1) ... 183s Setting up libubsan1:arm64 (15-20250213-1ubuntu1) ... 183s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 183s Setting up libpcre2-posix3:arm64 (10.45-1) ... 183s Setting up libhwasan0:arm64 (15-20250213-1ubuntu1) ... 183s Setting up libasan8:arm64 (15-20250213-1ubuntu1) ... 183s Setting up libtsan2:arm64 (15-20250213-1ubuntu1) ... 183s Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... 183s Setting up libisl23:arm64 (0.27-1) ... 183s Setting up libdeflate-dev:arm64 (1.23-1) ... 183s Setting up libicu-dev:arm64 (76.1-1ubuntu2) ... 183s Setting up libcc1-0:arm64 (15-20250213-1ubuntu1) ... 183s Setting up liblsan0:arm64 (15-20250213-1ubuntu1) ... 183s Setting up libblas-dev:arm64 (3.12.1-2) ... 183s 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 183s Setting up dctrl-tools (2.24-3build3) ... 183s Setting up libitm1:arm64 (15-20250213-1ubuntu1) ... 183s Setting up libbz2-dev:arm64 (1.0.8-6) ... 183s Setting up libpcre2-dev:arm64 (10.45-1) ... 183s Setting up libpng-dev:arm64 (1.6.47-1) ... 183s Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... 183s Setting up pkgconf:arm64 (1.8.1-4) ... 183s Setting up liblapack-dev:arm64 (3.12.1-2) ... 183s 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 183s Setting up cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 183s Setting up libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 183s Setting up libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 183s Setting up libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 183s Setting up cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 183s Setting up cpp-14 (14.2.0-17ubuntu3) ... 183s Setting up cpp (4:14.2.0-1ubuntu1) ... 183s Setting up gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 183s Setting up gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 183s Setting up g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 183s Setting up gcc-14 (14.2.0-17ubuntu3) ... 183s Setting up gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 183s Setting up g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 183s Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 183s Setting up g++-14 (14.2.0-17ubuntu3) ... 183s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 183s Setting up gcc (4:14.2.0-1ubuntu1) ... 183s Setting up g++ (4:14.2.0-1ubuntu1) ... 183s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 183s Setting up build-essential (12.10ubuntu1) ... 183s Setting up gfortran (4:14.2.0-1ubuntu1) ... 183s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 183s 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 183s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 183s 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 183s Setting up r-base-dev (4.4.2-1build1) ... 183s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 183s Processing triggers for libc-bin (2.40-4ubuntu1) ... 183s Processing triggers for man-db (2.13.0-1) ... 184s Processing triggers for install-info (7.1.1-1) ... 185s autopkgtest [00:00:24]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 185s autopkgtest [00:00:24]: test pkg-r-autopkgtest: [----------------------- 185s Test: Try to load the R library vegan 185s 185s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 185s Copyright (C) 2024 The R Foundation for Statistical Computing 185s Platform: aarch64-unknown-linux-gnu 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 186s > library('vegan') 186s Loading required package: permute 186s Loading required package: lattice 187s This is vegan 2.6-8 187s > 187s > 187s Other tests are currently unsupported! 187s They will be progressively added. 187s autopkgtest [00:00:26]: test pkg-r-autopkgtest: -----------------------] 187s autopkgtest [00:00:26]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 187s pkg-r-autopkgtest PASS 188s autopkgtest [00:00:27]: @@@@@@@@@@@@@@@@@@@@ summary 188s run-unit-test PASS 188s pkg-r-autopkgtest PASS 219s nova [W] Using flock in prodstack6-arm64 219s Creating nova instance adt-plucky-arm64-r-cran-vegan-20250303-235719-juju-7f2275-prod-proposed-migration-environment-15-e1067047-25b8-41ed-b868-5faf4712402f from image adt/ubuntu-plucky-arm64-server-20250303.img (UUID f7e4c905-561c-4e09-ba06-583f90f0368b)... 219s nova [W] Timed out waiting for 85b535de-3ed8-4c19-b219-5997066f648e to get deleted.