0s autopkgtest [07:30:56]: starting date and time: 2025-02-19 07:30:56+0000 0s autopkgtest [07:30:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [07:30:56]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xx7nsikp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-vegan --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-vegan/2.6-10+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-1.secgroup --name adt-plucky-ppc64el-r-cran-vegan-20250219-073056-juju-7f2275-prod-proposed-migration-environment-15-903d55fa-516b-4ee9-9058-c3fc4ed172cf --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 122s autopkgtest [07:32:58]: testbed dpkg architecture: ppc64el 122s autopkgtest [07:32:58]: testbed apt version: 2.9.29 122s autopkgtest [07:32:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 123s autopkgtest [07:32:59]: testbed release detected to be: None 123s autopkgtest [07:32:59]: updating testbed package index (apt update) 124s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 124s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 124s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 124s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [734 kB] 124s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [73.3 kB] 124s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 124s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [91.9 kB] 124s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B] 124s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [638 kB] 124s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [6324 B] 125s Fetched 1673 kB in 1s (1654 kB/s) 125s Reading package lists... 126s + lsb_release --codename --short 126s + RELEASE=plucky 126s + cat 126s + [ plucky != trusty ] 126s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 126s The following NEW packages will be installed: 126s libapt-pkg7.0 126s The following packages will be upgraded: 126s apt apt-utils dhcpcd-base rsyslog 127s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 3731 kB of archives. 127s After this operation, 3926 kB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libapt-pkg7.0 ppc64el 2.9.30 [1152 kB] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el apt ppc64el 2.9.30 [1439 kB] 127s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el apt-utils ppc64el 2.9.30 [228 kB] 127s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el dhcpcd-base ppc64el 1:10.1.0-7 [280 kB] 127s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el rsyslog ppc64el 8.2412.0-2ubuntu1 [632 kB] 127s Fetched 3731 kB in 1s (5162 kB/s) 127s Selecting previously unselected package libapt-pkg7.0:ppc64el. 128s (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 ... 106322 files and directories currently installed.) 128s Preparing to unpack .../libapt-pkg7.0_2.9.30_ppc64el.deb ... 128s Unpacking libapt-pkg7.0:ppc64el (2.9.30) ... 128s Setting up libapt-pkg7.0:ppc64el (2.9.30) ... 128s (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 ... 106371 files and directories currently installed.) 128s Preparing to unpack .../apt_2.9.30_ppc64el.deb ... 128s Unpacking apt (2.9.30) over (2.9.29) ... 128s Setting up apt (2.9.30) ... 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 106371 files and directories currently installed.) 129s Preparing to unpack .../apt-utils_2.9.30_ppc64el.deb ... 129s Unpacking apt-utils (2.9.30) over (2.9.29) ... 129s Preparing to unpack .../dhcpcd-base_1%3a10.1.0-7_ppc64el.deb ... 129s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-6) ... 129s Preparing to unpack .../rsyslog_8.2412.0-2ubuntu1_ppc64el.deb ... 129s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 129s Setting up apt-utils (2.9.30) ... 129s Setting up rsyslog (8.2412.0-2ubuntu1) ... 129s info: The user `syslog' is already a member of `adm'. 130s Setting up dhcpcd-base (1:10.1.0-7) ... 130s Processing triggers for man-db (2.13.0-1) ... 132s Processing triggers for libc-bin (2.40-4ubuntu1) ... 132s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 132s + /usr/lib/apt/apt-helper analyze-pattern ?true 132s + uname -r 132s + sed s/\./\\./g 132s + running_kernel_pattern=^linux-.*6\.12\.0-15-generic.* 132s + apt list ?obsolete 132s + tail -n+2 132s + cut -d/ -f1 132s + grep -v ^linux-.*6\.12\.0-15-generic.* 133s + true 133s + obsolete_pkgs= 133s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove 133s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s + grep -q trusty /etc/lsb-release 134s + [ ! -d /usr/share/doc/unattended-upgrades ] 134s + [ ! -d /usr/share/doc/lxd ] 134s + [ ! -d /usr/share/doc/lxd-client ] 134s + [ ! -d /usr/share/doc/snapd ] 134s + type iptables 134s + cat 134s + chmod 755 /etc/rc.local 134s + . /etc/rc.local 134s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 134s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 134s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 134s + uname -m 134s + [ ppc64le = ppc64le ] 134s + systemctl is-active keyboard-setup.service 134s + [ active = failed ] 134s + [ -d /run/systemd/system ] 134s + systemd-detect-virt --quiet --vm 134s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 134s + cat 134s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 134s + echo COMPRESS=lz4 134s autopkgtest [07:33:10]: upgrading testbed (apt dist-upgrade and autopurge) 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 135s Starting 2 pkgProblemResolver with broken count: 0 135s Done 135s Entering ResolveByKeep 135s 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Starting pkgProblemResolver with broken count: 0 136s Starting 2 pkgProblemResolver with broken count: 0 136s Done 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s autopkgtest [07:33:12]: rebooting testbed after setup commands that affected boot 170s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 177s autopkgtest [07:33:53]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 16:32:08 UTC 2025 179s autopkgtest [07:33:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 181s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (dsc) [2211 B] 181s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (tar) [1207 kB] 181s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (diff) [6328 B] 182s gpgv: Signature made Sun Feb 2 23:43:24 2025 UTC 182s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 182s gpgv: issuer "plessy@debian.org" 182s gpgv: Can't check signature: No public key 182s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1.dsc: no acceptable signature found 182s autopkgtest [07:33:58]: testing package r-cran-vegan version 2.6-10+dfsg-1 182s autopkgtest [07:33:58]: build not needed 184s autopkgtest [07:34:00]: test run-unit-test: preparing testbed 184s Reading package lists... 184s Building dependency tree... 184s Reading state information... 185s Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 185s The following NEW packages will be installed: 185s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 185s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 185s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 185s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 185s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 185s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 185s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 185s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 185s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 185s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 185s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 185s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 185s x11-common xdg-utils zip 185s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 185s Need to get 68.8 MB of archives. 185s After this operation, 170 MB of additional disk space will be used. 185s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-2ubuntu1 [37.5 kB] 186s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-2ubuntu1 [188 kB] 186s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig ppc64el 2.15.0-2ubuntu1 [192 kB] 186s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 186s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 186s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.1-2 [239 kB] 186s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB] 186s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB] 186s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B] 186s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB] 186s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB] 186s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdatrie1 ppc64el 0.2.13-3build1 [22.7 kB] 186s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.23-1 [63.4 kB] 186s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250213-1ubuntu1 [613 kB] 186s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 15-20250213-1ubuntu1 [168 kB] 186s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB] 186s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.2.0-1 [598 kB] 186s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB] 186s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libice6 ppc64el 2:1.1.1-1 [49.9 kB] 186s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-3ubuntu2 [215 kB] 186s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 186s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 186s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 186s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 186s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 186s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.1-2 [2813 kB] 186s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-5ubuntu1 [298 kB] 186s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai-data all 0.1.29-2build1 [158 kB] 186s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libthai0 ppc64el 0.1.29-2build1 [21.8 kB] 186s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpango-1.0-0 ppc64el 1.56.1-1 [277 kB] 186s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangoft2-1.0-0 ppc64el 1.56.1-1 [58.6 kB] 186s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpangocairo-1.0-0 ppc64el 1.56.1-1 [30.6 kB] 186s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper2 ppc64el 2.2.5-0.3 [18.0 kB] 186s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpaper-utils ppc64el 2.2.5-0.3 [15.6 kB] 186s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.5.0-0.1 [22.3 kB] 186s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsm6 ppc64el 2:1.2.4-1 [18.4 kB] 186s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.16+dfsg-1 [1201 kB] 187s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB] 187s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.5.0-0.1 [315 kB] 187s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB] 187s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB] 187s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B] 187s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.16-1 [946 kB] 187s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxt6t64 ppc64el 1:1.2.1-1.2build1 [202 kB] 187s Get:47 http://ftpmaster.internal/ubuntu plucky/universe ppc64el node-normalize.css all 8.0.1-5 [10.8 kB] 187s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el zip ppc64el 3.0-14ubuntu2 [196 kB] 187s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el unzip ppc64el 6.0-28ubuntu6 [200 kB] 187s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 187s Get:51 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-core ppc64el 4.4.2-1build1 [28.9 MB] 189s Get:52 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-cluster ppc64el 2.1.8-1 [586 kB] 189s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-commonmark ppc64el 1.9.2-2 [141 kB] 189s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-evaluate all 1.0.3-1 [114 kB] 189s Get:55 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-xfun ppc64el 0.50+dfsg-1 [569 kB] 189s Get:56 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-highr all 0.11+dfsg-1 [38.5 kB] 189s Get:57 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-yaml ppc64el 2.3.10-1 [123 kB] 189s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 189s Get:59 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-knitr all 1.49+dfsg-1 [859 kB] 189s Get:60 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-lattice ppc64el 0.22-6-1 [1340 kB] 189s Get:61 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-markdown all 1.13-1 [162 kB] 189s Get:62 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-mass ppc64el 7.3-64-1 [1117 kB] 189s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-matrix ppc64el 1.7-2-1 [4536 kB] 190s Get:64 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-nlme ppc64el 3.1.167-1 [2329 kB] 190s Get:65 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-mgcv ppc64el 1.9-1-1 [3393 kB] 190s Get:66 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-cran-permute all 0.9-7-1 [228 kB] 190s Get:67 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el r-cran-vegan ppc64el 2.6-10+dfsg-1 [3151 kB] 190s Preconfiguring packages ... 190s Fetched 68.8 MB in 5s (13.2 MB/s) 191s Selecting previously unselected package fonts-dejavu-mono. 191s (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 ... 106371 files and directories currently installed.) 191s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 191s Unpacking fonts-dejavu-mono (2.37-8) ... 191s Selecting previously unselected package fonts-dejavu-core. 191s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 191s Unpacking fonts-dejavu-core (2.37-8) ... 191s Selecting previously unselected package fontconfig-config. 191s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_ppc64el.deb ... 191s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 191s Selecting previously unselected package libfontconfig1:ppc64el. 191s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_ppc64el.deb ... 191s Unpacking libfontconfig1:ppc64el (2.15.0-2ubuntu1) ... 191s Selecting previously unselected package fontconfig. 191s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_ppc64el.deb ... 191s Unpacking fontconfig (2.15.0-2ubuntu1) ... 191s Selecting previously unselected package fonts-glyphicons-halflings. 191s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 191s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 191s Selecting previously unselected package fonts-mathjax. 191s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 191s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 191s Selecting previously unselected package libblas3:ppc64el. 191s Preparing to unpack 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using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 194s Setting up fonts-dejavu-mono (2.37-8) ... 194s Setting up libtcl8.6:ppc64el (8.6.16+dfsg-1) ... 194s Setting up fonts-dejavu-core (2.37-8) ... 194s Setting up libjpeg-turbo8:ppc64el (2.1.5-3ubuntu2) ... 194s Setting up libgfortran5:ppc64el (15-20250213-1ubuntu1) ... 194s Setting up libwebp7:ppc64el (1.5.0-0.1) ... 194s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ... 194s Setting up libharfbuzz0b:ppc64el (10.2.0-1) ... 194s Setting up libthai-data (0.1.29-2build1) ... 194s Setting up libxss1:ppc64el (1:1.2.3-1build3) ... 194s Setting up libpaper2:ppc64el (2.2.5-0.3) ... 194s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 194s Setting up node-normalize.css (8.0.1-5) ... 194s Setting up xdg-utils (1.2.1-2ubuntu1) ... 194s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 194s Setting up libjs-bootstrap (3.4.1+dfsg-3) ... 194s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 194s Setting up libice6:ppc64el (2:1.1.1-1) ... 194s Setting up liblapack3:ppc64el (3.12.1-2) ... 194s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 194s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 194s Setting up libpaper-utils (2.2.5-0.3) ... 194s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 194s Setting up libthai0:ppc64el (0.1.29-2build1) ... 194s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ... 194s Setting up libfontconfig1:ppc64el (2.15.0-2ubuntu1) ... 194s Setting up libsm6:ppc64el (2:1.2.4-1) ... 194s Setting up fontconfig (2.15.0-2ubuntu1) ... 196s Regenerating fonts cache... done. 196s Setting up libxft2:ppc64el (2.3.6-1build1) ... 196s Setting up libtk8.6:ppc64el (8.6.16-1) ... 197s Setting up libpango-1.0-0:ppc64el (1.56.1-1) ... 197s Setting up libcairo2:ppc64el (1.18.2-2) ... 197s Setting up libxt6t64:ppc64el (1:1.2.1-1.2build1) ... 197s Setting up libpangoft2-1.0-0:ppc64el (1.56.1-1) ... 197s Setting up libpangocairo-1.0-0:ppc64el (1.56.1-1) ... 197s Setting up r-base-core (4.4.2-1build1) ... 197s Creating config file /etc/R/Renviron with new version 197s Setting up r-cran-lattice (0.22-6-1) ... 197s Setting up r-cran-nlme (3.1.167-1) ... 197s Setting up r-cran-cluster (2.1.8-1) ... 197s Setting up r-cran-commonmark (1.9.2-2) ... 197s Setting up r-cran-permute (0.9-7-1) ... 197s Setting up r-cran-xfun (0.50+dfsg-1) ... 197s Setting up r-cran-yaml (2.3.10-1) ... 197s Setting up r-cran-evaluate (1.0.3-1) ... 197s Setting up r-cran-highr (0.11+dfsg-1) ... 197s Setting up r-cran-mass (7.3-64-1) ... 197s Setting up r-cran-markdown (1.13-1) ... 197s Setting up r-cran-matrix (1.7-2-1) ... 197s Setting up r-cran-knitr (1.49+dfsg-1) ... 197s Setting up r-cran-mgcv (1.9-1-1) ... 197s Setting up r-cran-vegan (2.6-10+dfsg-1) ... 197s Processing triggers for libc-bin (2.40-4ubuntu1) ... 197s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for install-info (7.1.1-1) ... 199s autopkgtest [07:34:15]: test run-unit-test: [----------------------- 200s 200s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 200s Copyright (C) 2024 The R Foundation for Statistical Computing 200s Platform: powerpc64le-unknown-linux-gnu 200s 200s R is free software and comes with ABSOLUTELY NO WARRANTY. 200s You are welcome to redistribute it under certain conditions. 200s Type 'license()' or 'licence()' for distribution details. 200s 200s R is a collaborative project with many contributors. 200s Type 'contributors()' for more information and 200s 'citation()' on how to cite R or R packages in publications. 200s 200s Type 'demo()' for some demos, 'help()' for on-line help, or 200s 'help.start()' for an HTML browser interface to help. 200s Type 'q()' to quit R. 200s 200s > Stangle("decision-vegan.Rnw") 200s Writing to file decision-vegan.R 200s > source("decision-vegan.R", echo=TRUE) 200s 200s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 200s 200s > options(SweaveHooks = list(fig = figset)) 200s 200s > options(prompt = "> ", continue = " ") 200s 200s > options(width = 55) 200s 200s > require(vegan) 200s Loading required package: vegan 200s Loading required package: permute 200s Loading required package: lattice 201s 201s > data(sipoo) 201s 201s > mod <- nestedtemp(sipoo) 201s 201s > plot(mod, "i") 201s 201s > x <- mod$c["Falcsubb"] 201s 201s > y <- 1 - mod$r["Svartholm"] 201s 201s > points(x, y, pch = 16, cex = 1.5) 201s 201s > abline(x + y, -1, lty = 2) 201s 201s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 201s 201s > cross <- function(x, a, p) f(x, p) - a + x 201s 201s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 201s 201s > arrows(x, y, r, f(r, mod$p), lwd = 4) 201s 201s > library(vegan) 201s 201s > data(varespec) 201s 201s > data(varechem) 201s 201s > orig <- cca(varespec ~ Al + K, varechem) 201s 201s > plot(orig, dis = c("lc", "bp")) 201s 201s > plot(orig, dis = c("lc", "bp")) 201s 201s > i <- sample(nrow(varespec)) 201s 201s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 201s 201s > plot(shuff, dis = c("lc", "bp")) 201s 201s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 201s + dis = "lc"))) 201s 201s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 201s + dis = "lc"))) 201s 201s > tmp1 <- rda(varespec ~ Al + K, varechem) 201s 201s > i <- sample(nrow(varespec)) 201s 201s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 201s 201s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 201s + dis = "lc"))) 201s 201s > orig 201s Call: cca(formula = varespec ~ Al + K, data = 201s varechem) 201s 201s -- Model Summary -- 201s 201s Inertia Proportion Rank 201s Total 2.0832 1.0000 201s Constrained 0.4760 0.2285 2 201s Unconstrained 1.6072 0.7715 21 201s 201s Inertia is scaled Chi-square 201s 201s -- Eigenvalues -- 201s 201s Eigenvalues for constrained axes: 201s CCA1 CCA2 201s 0.3608 0.1152 201s 201s Eigenvalues for unconstrained axes: 201s CA1 CA2 CA3 CA4 CA5 CA6 CA7 201s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 201s CA8 201s 0.0757 201s (Showing 8 of 21 unconstrained eigenvalues) 201s 201s 201s > shuff 201s Call: cca(formula = varespec[i, ] ~ Al + K, data = 201s varechem) 201s 201s -- Model Summary -- 201s 201s Inertia Proportion Rank 201s Total 2.08320 1.00000 201s Constrained 0.20035 0.09617 2 201s Unconstrained 1.88285 0.90383 21 201s 201s Inertia is scaled Chi-square 201s 201s -- Eigenvalues -- 201s 201s Eigenvalues for constrained axes: 201s CCA1 CCA2 201s 0.14266 0.05769 201s 201s Eigenvalues for unconstrained axes: 201s CA1 CA2 CA3 CA4 CA5 CA6 CA7 201s 0.4964 0.3540 0.2194 0.1761 0.1460 0.1148 0.1029 201s CA8 201s 0.0738 201s (Showing 8 of 21 unconstrained eigenvalues) 201s 201s 201s > plot(procrustes(orig, shuff)) 201s 201s > tmp1 <- rda(varespec ~ ., varechem) 201s 201s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 201s 201s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 201s + scores(tmp2, dis = "lc", choi = 1:14)) 201s 201s > max(residuals(proc)) 201s [1] 2.746358e-14 201s 201s > data(dune) 201s 201s > data(dune.env) 201s 201s > orig <- cca(dune ~ Moisture, dune.env) 201s 201s > plot(orig, dis = "lc") 201s 201s > plot(orig, display = "wa", type = "points") 201s 201s > ordispider(orig, col = "red") 201s 201s > text(orig, dis = "cn", col = "blue") 201s 201s > plot(orig, display = "wa", type = "points") 201s 201s > ordispider(orig, col = "red") 201s 201s > text(orig, dis = "cn", col = "blue") 201s > 201s 201s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 201s Copyright (C) 2024 The R Foundation for Statistical Computing 201s Platform: powerpc64le-unknown-linux-gnu 201s 201s R is free software and comes with ABSOLUTELY NO WARRANTY. 201s You are welcome to redistribute it under certain conditions. 201s Type 'license()' or 'licence()' for distribution details. 201s 201s R is a collaborative project with many contributors. 201s Type 'contributors()' for more information and 201s 'citation()' on how to cite R or R packages in publications. 201s 201s Type 'demo()' for some demos, 'help()' for on-line help, or 201s 'help.start()' for an HTML browser interface to help. 201s Type 'q()' to quit R. 201s 201s > Stangle("diversity-vegan.Rnw") 201s Writing to file diversity-vegan.R 201s > source("diversity-vegan.R", echo=TRUE) 201s 201s > par(mfrow = c(1, 1)) 201s 201s > options(width = 55) 201s 201s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 201s 201s > options(SweaveHooks = list(fig = figset)) 201s 201s > options(prompt = "> ", continue = " ") 201s 201s > library(vegan) 201s Loading required package: permute 201s Loading required package: lattice 202s 202s > data(BCI) 202s 202s > H <- diversity(BCI) 202s 202s > J <- H/log(specnumber(BCI)) 202s 202s > k <- sample(nrow(BCI), 6) 202s 202s > R <- renyi(BCI[k, ]) 202s 202s > print(plot(R)) 202s 202s > alpha <- fisher.alpha(BCI) 202s 202s > quantile(rowSums(BCI)) 202s 0% 25% 50% 75% 100% 202s 340.0 409.0 428.0 443.5 601.0 202s 202s > Srar <- rarefy(BCI, min(rowSums(BCI))) 202s 202s > S2 <- rarefy(BCI, 2) 202s 202s > all(rank(Srar) == rank(S2)) 202s [1] FALSE 202s 202s > range(diversity(BCI, "simp") - (S2 - 1)) 202s [1] -0.002868298 -0.001330663 202s 202s > data(dune) 202s 202s > data(dune.taxon) 202s 202s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 202s forced matching of 'tree' labels and 'comm' names 202s 202s > mod <- taxondive(dune, taxdis) 202s 202s > plot(mod) 202s 202s > tr <- hclust(taxdis, "aver") 202s 202s > mod <- treedive(dune, tr) 202s 202s > k <- sample(nrow(BCI), 1) 203s 203s > fish <- fisherfit(BCI[k, ]) 203s 203s > fish 203s 203s Fisher log series model 203s No. of species: 92 203s Fisher alpha: 35.88776 203s 203s 203s > plot(fish) 203s 203s > prestondistr(BCI[k, ]) 203s 203s Preston lognormal model 203s Method: maximized likelihood to log2 abundances 203s No. of species: 92 203s 203s mode width S0 203s 0.8352028 1.7913322 24.1844800 203s 203s Frequencies by Octave 203s 0 1 2 3 4 203s Observed 17.50000 27.00000 24.000 7.50000 10.000000 203s Fitted 21.69362 24.08235 19.576 11.65218 5.078656 203s 5 6 203s Observed 4.500000 1.5000000 203s Fitted 1.620871 0.3787968 203s 203s 203s > rad <- radfit(BCI[k, ]) 203s 203s > rad 203s 203s RAD models, family poisson 203s No. of species 92, total abundance 430 203s 203s par1 par2 par3 Deviance 203s Null 85.9601 203s Preemption 0.049495 70.0645 203s Lognormal 0.86697 1.1832 28.5832 203s Zipf 0.14615 -0.86285 37.0519 203s Mandelbrot 1.6203 -1.4888 5.7543 5.8926 203s AIC BIC 203s Null 348.6007 348.6007 203s Preemption 334.7051 337.2269 203s Lognormal 295.2238 300.2674 203s Zipf 303.6925 308.7361 203s Mandelbrot 274.5332 282.0986 203s 203s > print(radlattice(rad)) 203s 203s > sac <- specaccum(BCI) 203s 203s > plot(sac, ci.type = "polygon", ci.col = "yellow") 203s 203s > sac <- specaccum(BCI) 203s 203s > plot(sac, ci.type = "polygon", ci.col = "yellow") 203s 203s > ncol(BCI)/mean(specnumber(BCI)) - 1 203s [1] 1.478519 203s 203s > beta <- vegdist(BCI, binary = TRUE) 203s 203s > mean(beta) 203s [1] 0.3399075 203s 203s > betadiver(help = TRUE) 203s 1 "w" = (b+c)/(2*a+b+c) 203s 2 "-1" = (b+c)/(2*a+b+c) 203s 3 "c" = (b+c)/2 203s 4 "wb" = b+c 203s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 203s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 203s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 203s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 203s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 203s (2*a+b+c))-1 203s 8 "t" = (b+c)/(2*a+b+c) 203s 9 "me" = (b+c)/(2*a+b+c) 203s 10 "j" = a/(a+b+c) 203s 11 "sor" = 2*a/(2*a+b+c) 203s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 203s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 203s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 203s 15 "cc" = (b+c)/(a+b+c) 203s 16 "g" = (b+c)/(a+b+c) 203s 17 "-3" = pmin.int(b,c)/(a+b+c) 203s 18 "l" = (b+c)/2 203s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 203s 20 "hk" = (b+c)/(2*a+b+c) 203s 21 "rlb" = a/(a+c) 203s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 203s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 203s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 203s 203s > z <- betadiver(BCI, "z") 203s 203s > quantile(z) 203s 0% 25% 50% 75% 100% 203s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 203s 203s > data(dune) 203s 203s > data(dune.env) 203s 203s > z <- betadiver(dune, "z") 203s 203s > mod <- with(dune.env, betadisper(z, Management)) 203s 203s > mod 203s 203s Homogeneity of multivariate dispersions 203s 203s Call: betadisper(d = z, group = Management) 203s 203s No. of Positive Eigenvalues: 12 203s No. of Negative Eigenvalues: 7 203s 203s Average distance to median: 203s BF HF NM SF 203s 0.2532 0.2512 0.4406 0.3635 203s 203s Eigenvalues for PCoA axes: 203s (Showing 8 of 19 eigenvalues) 203s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 203s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 203s PCoA7 PCoA8 203s 0.16128 0.08099 203s 203s > boxplot(mod) 203s 203s > specpool(BCI) 203s Species chao chao.se jack1 jack1.se jack2 203s All 225 236.3732 6.54361 245.58 5.650522 247.8722 203s boot boot.se n 203s All 235.6862 3.468888 50 203s 203s > s <- sample(nrow(BCI), 25) 203s 203s > specpool(BCI[s, ]) 203s Species chao chao.se jack1 jack1.se jack2 203s All 204 240.6982 18.57122 231.84 7.704959 248.8217 203s boot boot.se n 203s All 216.3225 3.74559 25 203s 203s > estimateR(BCI[k, ]) 203s 36 203s S.obs 92.000000 203s S.chao1 121.750000 203s se.chao1 13.262409 203s S.ACE 136.318712 203s se.ACE 6.669613 203s 203s > veiledspec(prestondistr(BCI[k, ])) 203s Extrapolated Observed Veiled 203s 108.59325 92.00000 16.59325 203s 203s > veiledspec(BCI[k, ]) 203s Extrapolated Observed Veiled 203s 120.52468 92.00000 28.52468 203s 203s > smo <- beals(BCI) 203s 203s > j <- which(colnames(BCI) == "Ceiba.pentandra") 203s 203s > plot(beals(BCI, species = j, include = FALSE), BCI[, 203s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 203s 203s > j <- which(colnames(BCI) == "Ceiba.pentandra") 203s 203s > plot(beals(BCI, species = j, include = FALSE), BCI[, 203s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 203s > 203s Warning messages: 203s 1: In cor(x > 0) : the standard deviation is zero 203s 2: In cor(x > 0) : the standard deviation is zero 203s 3: In betadisper(z, Management) : 203s some squared distances are negative and changed to zero 203s 203s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 203s Copyright (C) 2024 The R Foundation for Statistical Computing 203s Platform: powerpc64le-unknown-linux-gnu 203s 203s R is free software and comes with ABSOLUTELY NO WARRANTY. 203s You are welcome to redistribute it under certain conditions. 203s Type 'license()' or 'licence()' for distribution details. 203s 203s R is a collaborative project with many contributors. 203s Type 'contributors()' for more information and 203s 'citation()' on how to cite R or R packages in publications. 203s 203s Type 'demo()' for some demos, 'help()' for on-line help, or 203s 'help.start()' for an HTML browser interface to help. 203s Type 'q()' to quit R. 203s 203s > Stangle("intro-vegan.Rnw") 203s Writing to file intro-vegan.R 203s > source("intro-vegan.R", echo=TRUE) 203s 203s > par(mfrow = c(1, 1)) 203s 203s > options(width = 72) 203s 203s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 203s 203s > options(SweaveHooks = list(fig = figset)) 203s 203s > options(prompt = "> ", continue = " ") 203s 203s > library(vegan) 203s Loading required package: permute 203s Loading required package: lattice 204s 204s > data(dune) 204s 204s > ord <- decorana(dune) 204s 204s > ord 204s 204s Call: 204s decorana(veg = dune) 204s 204s Detrended correspondence analysis with 26 segments. 204s Rescaling of axes with 4 iterations. 204s Total inertia (scaled Chi-square): 2.1153 204s 204s DCA1 DCA2 DCA3 DCA4 204s Eigenvalues 0.5117 0.3036 0.12125 0.14267 204s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 204s Decorana values 0.5360 0.2869 0.08136 0.04814 204s Axis lengths 3.7004 3.1166 1.30055 1.47888 204s 204s 204s > ord <- metaMDS(dune, trace = FALSE) 204s 204s > ord 204s 204s Call: 204s metaMDS(comm = dune, trace = FALSE) 204s 204s global Multidimensional Scaling using monoMDS 204s 204s Data: dune 204s Distance: bray 204s 204s Dimensions: 2 204s Stress: 0.1183186 204s Stress type 1, weak ties 204s Best solution was repeated 5 times in 20 tries 204s The best solution was from try 3 (random start) 204s Scaling: centring, PC rotation, halfchange scaling 204s Species: expanded scores based on ‘dune’ 204s 204s 204s > plot(ord) 204s 204s > plot(ord) 204s 204s > plot(ord, type = "n") 204s 204s > points(ord, display = "sites", cex = 0.8, pch = 21, 204s + col = "red", bg = "yellow") 204s 204s > text(ord, display = "species", cex = 0.7, col = "blue") 204s 204s > plot(ord, type = "n") 204s 204s > points(ord, display = "sites", cex = 0.8, pch = 21, 204s + col = "red", bg = "yellow") 204s 204s > text(ord, display = "species", cex = 0.7, col = "blue") 204s 204s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 204s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 204s + col = "blue") 204s 204s > data(dune.env) 204s 204s > attach(dune.env) 204s 204s > plot(ord, disp = "sites", type = "n") 204s 204s > ordihull(ord, Management, col = 1:4, lwd = 3) 204s 204s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 204s + lwd = 3) 204s 204s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 204s 204s > ordispider(ord, Management, col = 1:4, label = TRUE) 204s 204s > points(ord, disp = "sites", pch = 21, col = "red", 204s + bg = "yellow", cex = 1.3) 204s 204s > plot(ord, disp = "sites", type = "n") 204s 204s > ordihull(ord, Management, col = 1:4, lwd = 3) 204s 204s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 204s + lwd = 3) 204s 204s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 204s 204s > ordispider(ord, Management, col = 1:4, label = TRUE) 204s 204s > points(ord, disp = "sites", pch = 21, col = "red", 204s + bg = "yellow", cex = 1.3) 204s 204s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 204s + perm = 999) 204s 204s > ord.fit 204s 204s ***VECTORS 204s 204s NMDS1 NMDS2 r2 Pr(>r) 204s A1 0.96474 0.26322 0.3649 0.017 * 204s --- 204s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 204s Permutation: free 204s Number of permutations: 999 204s 204s ***FACTORS: 204s 204s Centroids: 204s NMDS1 NMDS2 204s ManagementBF -0.4534 -0.0102 204s ManagementHF -0.2636 -0.1282 204s ManagementNM 0.2958 0.5790 204s ManagementSF 0.1506 -0.4670 204s 204s Goodness of fit: 204s r2 Pr(>r) 204s Management 0.4134 0.007 ** 204s --- 204s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 204s Permutation: free 204s Number of permutations: 999 204s 204s 204s 204s > plot(ord, dis = "site") 204s 204s > plot(ord.fit) 204s 204s > ordisurf(ord, A1, add = TRUE) 204s 204s Family: gaussian 204s Link function: identity 204s 204s Formula: 204s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 204s 204s Estimated degrees of freedom: 204s 1.59 total = 2.59 204s 204s REML score: 41.58727 204s 204s > plot(ord, dis = "site") 204s 204s > plot(ord.fit) 204s 204s > ordisurf(ord, A1, add = TRUE) 204s 204s Family: gaussian 204s Link function: identity 204s 204s Formula: 204s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 204s 204s Estimated degrees of freedom: 204s 1.59 total = 2.59 204s 204s REML score: 41.58727 204s 204s > ord <- cca(dune ~ A1 + Management, data = dune.env) 204s 204s > ord 204s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 204s 204s -- Model Summary -- 204s 204s Inertia Proportion Rank 204s Total 2.1153 1.0000 204s Constrained 0.7798 0.3686 4 204s Unconstrained 1.3355 0.6314 15 204s 204s Inertia is scaled Chi-square 204s 204s -- Eigenvalues -- 204s 204s Eigenvalues for constrained axes: 204s CCA1 CCA2 CCA3 CCA4 204s 0.3187 0.2372 0.1322 0.0917 204s 204s Eigenvalues for unconstrained axes: 204s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 204s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 204s CA11 CA12 CA13 CA14 CA15 204s 0.0317 0.0178 0.0116 0.0087 0.0047 204s 204s 204s > plot(ord) 204s 204s > plot(ord) 204s 204s > cca(dune ~ ., data = dune.env) 204s 204s Some constraints or conditions were aliased because they were 204s redundant. This can happen if terms are linearly dependent (collinear): 204s ‘Manure^4’ 204s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 204s Manure, data = dune.env) 204s 204s -- Model Summary -- 204s 204s Inertia Proportion Rank 204s Total 2.1153 1.0000 204s Constrained 1.5032 0.7106 12 204s Unconstrained 0.6121 0.2894 7 204s 204s Inertia is scaled Chi-square 204s 204s -- Note -- 204s 204s Some constraints or conditions were aliased because they were 204s redundant. This can happen if terms are linearly dependent 204s (collinear): ‘Manure^4’ 204s 204s -- Eigenvalues -- 204s 204s Eigenvalues for constrained axes: 204s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 204s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 204s CCA11 CCA12 204s 0.0228 0.0108 204s 204s Eigenvalues for unconstrained axes: 204s CA1 CA2 CA3 CA4 CA5 CA6 CA7 204s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 204s 204s 204s > anova(ord) 205s Permutation test for cca under reduced model 205s Permutation: free 205s Number of permutations: 999 205s 205s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 205s Df ChiSquare F Pr(>F) 205s Model 4 0.77978 2.1896 0.001 *** 205s Residual 15 1.33549 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > anova(ord, by = "term", permutations = 199) 205s Permutation test for cca under reduced model 205s Terms added sequentially (first to last) 205s Permutation: free 205s Number of permutations: 199 205s 205s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 205s Df ChiSquare F Pr(>F) 205s A1 1 0.22476 2.5245 0.01 ** 205s Management 3 0.55502 2.0780 0.01 ** 205s Residual 15 1.33549 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > anova(ord, by = "mar", permutations = 199) 205s Permutation test for cca under reduced model 205s Marginal effects of terms 205s Permutation: free 205s Number of permutations: 199 205s 205s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 205s Df ChiSquare F Pr(>F) 205s A1 1 0.17594 1.9761 0.050 * 205s Management 3 0.55502 2.0780 0.005 ** 205s Residual 15 1.33549 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > anova(ord, by = "axis", permutations = 499) 205s Permutation test for cca under reduced model 205s Forward tests for axes 205s Permutation: free 205s Number of permutations: 499 205s 205s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 205s Df ChiSquare F Pr(>F) 205s CCA1 1 0.31875 3.5801 0.016 * 205s CCA2 1 0.23718 2.6640 0.118 205s CCA3 1 0.13217 1.4845 0.840 205s CCA4 1 0.09168 1.0297 1.000 205s Residual 15 1.33549 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 205s + data = dune.env) 205s 205s > ord 205s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 205s data = dune.env) 205s 205s -- Model Summary -- 205s 205s Inertia Proportion Rank 205s Total 2.1153 1.0000 205s Conditional 0.6283 0.2970 3 205s Constrained 0.5109 0.2415 4 205s Unconstrained 0.9761 0.4615 12 205s 205s Inertia is scaled Chi-square 205s 205s -- Eigenvalues -- 205s 205s Eigenvalues for constrained axes: 205s CCA1 CCA2 CCA3 CCA4 205s 0.24932 0.12090 0.08160 0.05904 205s 205s Eigenvalues for unconstrained axes: 205s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 205s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 205s CA10 CA11 CA12 205s 0.02102 0.01254 0.00928 205s 205s 205s > anova(ord, by = "term", permutations = 499) 205s Permutation test for cca under reduced model 205s Terms added sequentially (first to last) 205s Permutation: free 205s Number of permutations: 499 205s 205s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 205s Df ChiSquare F Pr(>F) 205s A1 1 0.11543 1.4190 1.000 205s Management 3 0.39543 1.6205 0.002 ** 205s Residual 12 0.97610 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 205s 205s > anova(ord, by = "term", permutations = how) 205s Permutation test for cca under reduced model 205s Terms added sequentially (first to last) 205s Plots: dune.env$Moisture, plot permutation: none 205s Permutation: free 205s Number of permutations: 499 205s 205s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 205s Df ChiSquare F Pr(>F) 205s A1 1 0.11543 1.4190 1.000 205s Management 3 0.39543 1.6205 0.002 ** 205s Residual 12 0.97610 205s --- 205s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 205s 205s > detach(dune.env) 205s > 205s 205s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 205s Copyright (C) 2024 The R Foundation for Statistical Computing 205s Platform: powerpc64le-unknown-linux-gnu 205s 205s R is free software and comes with ABSOLUTELY NO WARRANTY. 205s You are welcome to redistribute it under certain conditions. 205s Type 'license()' or 'licence()' for distribution details. 205s 205s R is a collaborative project with many contributors. 205s Type 'contributors()' for more information and 205s 'citation()' on how to cite R or R packages in publications. 205s 205s Type 'demo()' for some demos, 'help()' for on-line help, or 205s 'help.start()' for an HTML browser interface to help. 205s Type 'q()' to quit R. 205s 205s > Stangle("partitioning.Rnw") 205s Writing to file partitioning.R 205s > source("partitioning.R", echo=TRUE) 205s 205s > par(mfrow = c(1, 1)) 205s 205s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 205s 205s > options(SweaveHooks = list(fig = figset)) 205s 205s > library(vegan) 205s Loading required package: permute 205s Loading required package: lattice 206s 206s > labs <- paste("Table", 1:4) 206s 206s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 206s 206s > showvarparts(2, bg = cls, Xnames = labs) 206s 206s > showvarparts(3, bg = cls, Xnames = labs) 206s 206s > showvarparts(4, bg = cls, Xnames = labs) 206s > 213s --- cca-object-tests.Rout.save_ 2025-02-19 07:34:29.819259765 +0000 213s +++ cca-object-tests.Rout_ 2025-02-19 07:34:29.819259765 +0000 213s @@ -1,4 +1,4 @@ 213s - 213s + 213s 213s R is free software and comes with ABSOLUTELY NO WARRANTY. 213s You are welcome to redistribute it under certain conditions. 214s autopkgtest [07:34:30]: test run-unit-test: -----------------------] 214s autopkgtest [07:34:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 214s run-unit-test FAIL non-zero exit status 1 215s autopkgtest [07:34:31]: test pkg-r-autopkgtest: preparing testbed 215s Reading package lists... 215s Building dependency tree... 215s Reading state information... 215s Starting pkgProblemResolver with broken count: 0 215s Starting 2 pkgProblemResolver with broken count: 0 215s Done 215s The following NEW packages will be installed: 215s build-essential cpp cpp-14 cpp-14-powerpc64le-linux-gnu 215s cpp-powerpc64le-linux-gnu dctrl-tools g++ g++-14 215s g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14 215s gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gfortran gfortran-14 215s gfortran-14-powerpc64le-linux-gnu gfortran-powerpc64le-linux-gnu 215s icu-devtools libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev 215s libgcc-14-dev libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 215s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 215s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 215s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 215s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 215s r-base-dev zlib1g-dev 216s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 216s Need to get 93.4 MB of archives. 216s After this operation, 349 MB of additional disk space will be used. 216s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB] 216s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB] 216s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu1 [10.5 MB] 217s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-17ubuntu1 [1038 B] 217s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [5566 B] 217s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.2.0-1ubuntu1 [22.4 kB] 217s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 15-20250213-1ubuntu1 [48.7 kB] 217s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 15-20250213-1ubuntu1 [32.4 kB] 217s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 15-20250213-1ubuntu1 [3009 kB] 218s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 15-20250213-1ubuntu1 [1377 kB] 218s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 15-20250213-1ubuntu1 [2734 kB] 218s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 15-20250213-1ubuntu1 [1234 kB] 218s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 15-20250213-1ubuntu1 [160 kB] 218s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-17ubuntu1 [1620 kB] 219s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu1 [20.6 MB] 222s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-17ubuntu1 [536 kB] 222s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [1226 B] 222s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.2.0-1ubuntu1 [5012 B] 222s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-17ubuntu1 [2677 kB] 222s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu1 [12.0 MB] 224s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-17ubuntu1 [21.8 kB] 224s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [966 B] 224s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.2.0-1ubuntu1 [1088 B] 224s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B] 224s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el dctrl-tools ppc64el 2.24-3build3 [109 kB] 224s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran-14-dev ppc64el 14.2.0-17ubuntu1 [621 kB] 224s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-14-powerpc64le-linux-gnu ppc64el 14.2.0-17ubuntu1 [11.3 MB] 226s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-14 ppc64el 14.2.0-17ubuntu1 [13.6 kB] 226s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran-powerpc64le-linux-gnu ppc64el 4:14.2.0-1ubuntu1 [1024 B] 226s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el gfortran ppc64el 4:14.2.0-1ubuntu1 [1166 B] 226s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el icu-devtools ppc64el 76.1-1ubuntu2 [251 kB] 226s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas-dev ppc64el 3.12.1-2 [318 kB] 226s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbz2-dev ppc64el 1.0.8-6 [50.2 kB] 226s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate-dev ppc64el 1.23-1 [70.8 kB] 226s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el libicu-dev ppc64el 76.1-1ubuntu2 [12.9 MB] 228s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8-dev ppc64el 2.1.5-3ubuntu2 [358 kB] 228s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8-dev ppc64el 8c-2ubuntu11 [1484 B] 228s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-dev ppc64el 8c-2ubuntu11 [1486 B] 228s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack-dev ppc64el 3.12.1-2 [6076 kB] 229s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el libncurses-dev ppc64el 6.5+20250125-2 [484 kB] 229s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-16-0 ppc64el 10.42-4ubuntu3 [254 kB] 229s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-32-0 ppc64el 10.42-4ubuntu3 [238 kB] 229s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-posix3 ppc64el 10.42-4ubuntu3 [7108 B] 229s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpcre2-dev ppc64el 10.42-4ubuntu3 [817 kB] 229s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpkgconf3 ppc64el 1.8.1-4 [37.1 kB] 229s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 229s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpng-dev ppc64el 1.6.46-4 [329 kB] 229s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el libreadline-dev ppc64el 8.2-6 [230 kB] 229s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblzma-dev ppc64el 5.6.3-1 [208 kB] 229s Get:50 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf-bin ppc64el 1.8.1-4 [22.5 kB] 229s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el pkgconf ppc64el 1.8.1-4 [16.7 kB] 229s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.3 [223 kB] 229s Get:53 http://ftpmaster.internal/ubuntu plucky/universe ppc64el r-base-dev all 4.4.2-1build1 [4342 B] 229s Get:54 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 230s Fetched 93.4 MB in 14s (6650 kB/s) 230s Selecting previously unselected package libisl23:ppc64el. 230s (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 ... 114344 files and directories currently installed.) 230s Preparing to unpack .../00-libisl23_0.27-1_ppc64el.deb ... 230s Unpacking libisl23:ppc64el (0.27-1) ... 230s Selecting previously unselected package libmpc3:ppc64el. 230s Preparing to unpack .../01-libmpc3_1.3.1-1build2_ppc64el.deb ... 230s Unpacking libmpc3:ppc64el (1.3.1-1build2) ... 230s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu. 230s Preparing to unpack .../02-cpp-14-powerpc64le-linux-gnu_14.2.0-17ubuntu1_ppc64el.deb ... 230s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 230s Selecting previously unselected package cpp-14. 230s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu1_ppc64el.deb ... 230s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 230s Selecting previously unselected package cpp-powerpc64le-linux-gnu. 230s Preparing to unpack .../04-cpp-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 230s Unpacking cpp-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package cpp. 230s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 230s Unpacking cpp (4:14.2.0-1ubuntu1) ... 230s Selecting previously unselected package libcc1-0:ppc64el. 230s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libcc1-0:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libitm1:ppc64el. 230s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libitm1:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libasan8:ppc64el. 230s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libasan8:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package liblsan0:ppc64el. 230s Preparing to unpack .../09-liblsan0_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking liblsan0:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libtsan2:ppc64el. 230s Preparing to unpack .../10-libtsan2_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libtsan2:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libubsan1:ppc64el. 230s Preparing to unpack .../11-libubsan1_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libubsan1:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libquadmath0:ppc64el. 230s Preparing to unpack .../12-libquadmath0_15-20250213-1ubuntu1_ppc64el.deb ... 230s Unpacking libquadmath0:ppc64el (15-20250213-1ubuntu1) ... 230s Selecting previously unselected package libgcc-14-dev:ppc64el. 230s Preparing to unpack .../13-libgcc-14-dev_14.2.0-17ubuntu1_ppc64el.deb ... 230s Unpacking libgcc-14-dev:ppc64el (14.2.0-17ubuntu1) ... 230s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu. 230s Preparing to unpack .../14-gcc-14-powerpc64le-linux-gnu_14.2.0-17ubuntu1_ppc64el.deb ... 230s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package gcc-14. 231s Preparing to unpack .../15-gcc-14_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package gcc-powerpc64le-linux-gnu. 231s Preparing to unpack .../16-gcc-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking gcc-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package gcc. 231s Preparing to unpack .../17-gcc_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking gcc (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package libstdc++-14-dev:ppc64el. 231s Preparing to unpack .../18-libstdc++-14-dev_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking libstdc++-14-dev:ppc64el (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package g++-14-powerpc64le-linux-gnu. 231s Preparing to unpack .../19-g++-14-powerpc64le-linux-gnu_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package g++-14. 231s Preparing to unpack .../20-g++-14_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking g++-14 (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package g++-powerpc64le-linux-gnu. 231s Preparing to unpack .../21-g++-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking g++-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package g++. 231s Preparing to unpack .../22-g++_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking g++ (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package build-essential. 231s Preparing to unpack .../23-build-essential_12.10ubuntu1_ppc64el.deb ... 231s Unpacking build-essential (12.10ubuntu1) ... 231s Selecting previously unselected package dctrl-tools. 231s Preparing to unpack .../24-dctrl-tools_2.24-3build3_ppc64el.deb ... 231s Unpacking dctrl-tools (2.24-3build3) ... 231s Selecting previously unselected package libgfortran-14-dev:ppc64el. 231s Preparing to unpack .../25-libgfortran-14-dev_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking libgfortran-14-dev:ppc64el (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package gfortran-14-powerpc64le-linux-gnu. 231s Preparing to unpack .../26-gfortran-14-powerpc64le-linux-gnu_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking gfortran-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package gfortran-14. 231s Preparing to unpack .../27-gfortran-14_14.2.0-17ubuntu1_ppc64el.deb ... 231s Unpacking gfortran-14 (14.2.0-17ubuntu1) ... 231s Selecting previously unselected package gfortran-powerpc64le-linux-gnu. 231s Preparing to unpack .../28-gfortran-powerpc64le-linux-gnu_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking gfortran-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package gfortran. 231s Preparing to unpack .../29-gfortran_4%3a14.2.0-1ubuntu1_ppc64el.deb ... 231s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 231s Selecting previously unselected package icu-devtools. 231s Preparing to unpack .../30-icu-devtools_76.1-1ubuntu2_ppc64el.deb ... 231s Unpacking icu-devtools (76.1-1ubuntu2) ... 231s Selecting previously unselected package libblas-dev:ppc64el. 231s Preparing to unpack .../31-libblas-dev_3.12.1-2_ppc64el.deb ... 231s Unpacking libblas-dev:ppc64el (3.12.1-2) ... 231s Selecting previously unselected package libbz2-dev:ppc64el. 231s Preparing to unpack .../32-libbz2-dev_1.0.8-6_ppc64el.deb ... 231s Unpacking libbz2-dev:ppc64el (1.0.8-6) ... 231s Selecting previously unselected package libdeflate-dev:ppc64el. 231s Preparing to unpack .../33-libdeflate-dev_1.23-1_ppc64el.deb ... 231s Unpacking libdeflate-dev:ppc64el (1.23-1) ... 231s Selecting previously unselected package libicu-dev:ppc64el. 231s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_ppc64el.deb ... 231s Unpacking libicu-dev:ppc64el (76.1-1ubuntu2) ... 232s Selecting previously unselected package libjpeg-turbo8-dev:ppc64el. 232s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_ppc64el.deb ... 232s Unpacking libjpeg-turbo8-dev:ppc64el (2.1.5-3ubuntu2) ... 232s Selecting previously unselected package libjpeg8-dev:ppc64el. 232s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_ppc64el.deb ... 232s Unpacking libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 232s Selecting previously unselected package libjpeg-dev:ppc64el. 232s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_ppc64el.deb ... 232s Unpacking libjpeg-dev:ppc64el (8c-2ubuntu11) ... 232s Selecting previously unselected package liblapack-dev:ppc64el. 232s Preparing to unpack .../38-liblapack-dev_3.12.1-2_ppc64el.deb ... 232s Unpacking liblapack-dev:ppc64el (3.12.1-2) ... 232s Selecting previously unselected package libncurses-dev:ppc64el. 232s Preparing to unpack .../39-libncurses-dev_6.5+20250125-2_ppc64el.deb ... 232s Unpacking libncurses-dev:ppc64el (6.5+20250125-2) ... 232s Selecting previously unselected package libpcre2-16-0:ppc64el. 232s Preparing to unpack .../40-libpcre2-16-0_10.42-4ubuntu3_ppc64el.deb ... 232s Unpacking libpcre2-16-0:ppc64el (10.42-4ubuntu3) ... 232s Selecting previously unselected package libpcre2-32-0:ppc64el. 232s Preparing to unpack .../41-libpcre2-32-0_10.42-4ubuntu3_ppc64el.deb ... 232s Unpacking libpcre2-32-0:ppc64el (10.42-4ubuntu3) ... 232s Selecting previously unselected package libpcre2-posix3:ppc64el. 232s Preparing to unpack .../42-libpcre2-posix3_10.42-4ubuntu3_ppc64el.deb ... 232s Unpacking libpcre2-posix3:ppc64el (10.42-4ubuntu3) ... 232s Selecting previously unselected package libpcre2-dev:ppc64el. 232s Preparing to unpack .../43-libpcre2-dev_10.42-4ubuntu3_ppc64el.deb ... 232s Unpacking libpcre2-dev:ppc64el (10.42-4ubuntu3) ... 232s Selecting previously unselected package libpkgconf3:ppc64el. 232s Preparing to unpack .../44-libpkgconf3_1.8.1-4_ppc64el.deb ... 232s Unpacking libpkgconf3:ppc64el (1.8.1-4) ... 232s Selecting previously unselected package zlib1g-dev:ppc64el. 232s Preparing to unpack .../45-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 232s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 232s Selecting previously unselected package libpng-dev:ppc64el. 232s Preparing to unpack .../46-libpng-dev_1.6.46-4_ppc64el.deb ... 232s Unpacking libpng-dev:ppc64el (1.6.46-4) ... 232s Selecting previously unselected package libreadline-dev:ppc64el. 232s Preparing to unpack .../47-libreadline-dev_8.2-6_ppc64el.deb ... 232s Unpacking libreadline-dev:ppc64el (8.2-6) ... 232s Selecting previously unselected package liblzma-dev:ppc64el. 232s Preparing to unpack .../48-liblzma-dev_5.6.3-1_ppc64el.deb ... 232s Unpacking liblzma-dev:ppc64el (5.6.3-1) ... 232s Selecting previously unselected package pkgconf-bin. 232s Preparing to unpack .../49-pkgconf-bin_1.8.1-4_ppc64el.deb ... 232s Unpacking pkgconf-bin (1.8.1-4) ... 232s Selecting previously unselected package pkgconf:ppc64el. 232s Preparing to unpack .../50-pkgconf_1.8.1-4_ppc64el.deb ... 232s Unpacking pkgconf:ppc64el (1.8.1-4) ... 232s Selecting previously unselected package libtirpc-dev:ppc64el. 232s Preparing to unpack .../51-libtirpc-dev_1.3.4+ds-1.3_ppc64el.deb ... 232s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1.3) ... 232s Selecting previously unselected package r-base-dev. 232s Preparing to unpack .../52-r-base-dev_4.4.2-1build1_all.deb ... 232s Unpacking r-base-dev (4.4.2-1build1) ... 232s Selecting previously unselected package pkg-r-autopkgtest. 232s Preparing to unpack .../53-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 232s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 232s Setting up libjpeg-turbo8-dev:ppc64el (2.1.5-3ubuntu2) ... 232s Setting up libncurses-dev:ppc64el (6.5+20250125-2) ... 232s Setting up libreadline-dev:ppc64el (8.2-6) ... 232s Setting up libpcre2-16-0:ppc64el (10.42-4ubuntu3) ... 232s Setting up libpcre2-32-0:ppc64el (10.42-4ubuntu3) ... 232s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.3) ... 232s Setting up libpkgconf3:ppc64el (1.8.1-4) ... 232s Setting up libquadmath0:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up libmpc3:ppc64el (1.3.1-1build2) ... 232s Setting up icu-devtools (76.1-1ubuntu2) ... 232s Setting up pkgconf-bin (1.8.1-4) ... 232s Setting up liblzma-dev:ppc64el (5.6.3-1) ... 232s Setting up libubsan1:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 232s Setting up libpcre2-posix3:ppc64el (10.42-4ubuntu3) ... 232s Setting up libasan8:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up libtsan2:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up libjpeg8-dev:ppc64el (8c-2ubuntu11) ... 232s Setting up libisl23:ppc64el (0.27-1) ... 232s Setting up libdeflate-dev:ppc64el (1.23-1) ... 232s Setting up libicu-dev:ppc64el (76.1-1ubuntu2) ... 232s Setting up libcc1-0:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up liblsan0:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up libblas-dev:ppc64el (3.12.1-2) ... 232s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode 232s Setting up dctrl-tools (2.24-3build3) ... 232s Setting up libitm1:ppc64el (15-20250213-1ubuntu1) ... 232s Setting up libbz2-dev:ppc64el (1.0.8-6) ... 232s Setting up libpcre2-dev:ppc64el (10.42-4ubuntu3) ... 232s Setting up libpng-dev:ppc64el (1.6.46-4) ... 232s Setting up libjpeg-dev:ppc64el (8c-2ubuntu11) ... 232s Setting up pkgconf:ppc64el (1.8.1-4) ... 232s Setting up liblapack-dev:ppc64el (3.12.1-2) ... 232s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode 232s Setting up cpp-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 232s Setting up cpp-14 (14.2.0-17ubuntu1) ... 232s Setting up libgcc-14-dev:ppc64el (14.2.0-17ubuntu1) ... 232s Setting up libstdc++-14-dev:ppc64el (14.2.0-17ubuntu1) ... 232s Setting up cpp-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Setting up gcc-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 232s Setting up libgfortran-14-dev:ppc64el (14.2.0-17ubuntu1) ... 232s Setting up g++-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 232s Setting up gcc-14 (14.2.0-17ubuntu1) ... 232s Setting up gcc-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Setting up cpp (4:14.2.0-1ubuntu1) ... 232s Setting up g++-14 (14.2.0-17ubuntu1) ... 232s Setting up gfortran-14-powerpc64le-linux-gnu (14.2.0-17ubuntu1) ... 232s Setting up gfortran-14 (14.2.0-17ubuntu1) ... 232s Setting up g++-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Setting up gcc (4:14.2.0-1ubuntu1) ... 232s Setting up gfortran-powerpc64le-linux-gnu (4:14.2.0-1ubuntu1) ... 232s Setting up g++ (4:14.2.0-1ubuntu1) ... 232s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 232s Setting up build-essential (12.10ubuntu1) ... 232s Setting up gfortran (4:14.2.0-1ubuntu1) ... 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 232s 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 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 232s 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 232s Setting up r-base-dev (4.4.2-1build1) ... 232s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 232s Processing triggers for libc-bin (2.40-4ubuntu1) ... 232s Processing triggers for man-db (2.13.0-1) ... 234s Processing triggers for install-info (7.1.1-1) ... 234s autopkgtest [07:34:50]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 234s autopkgtest [07:34:50]: test pkg-r-autopkgtest: [----------------------- 235s Test: Try to load the R library vegan 235s 235s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 235s Copyright (C) 2024 The R Foundation for Statistical Computing 235s Platform: powerpc64le-unknown-linux-gnu 235s 235s R is free software and comes with ABSOLUTELY NO WARRANTY. 235s You are welcome to redistribute it under certain conditions. 235s Type 'license()' or 'licence()' for distribution details. 235s 235s R is a collaborative project with many contributors. 235s Type 'contributors()' for more information and 235s 'citation()' on how to cite R or R packages in publications. 235s 235s Type 'demo()' for some demos, 'help()' for on-line help, or 235s 'help.start()' for an HTML browser interface to help. 235s Type 'q()' to quit R. 235s 235s > library('vegan') 235s Loading required package: permute 235s Loading required package: lattice 236s > 236s > 236s Other tests are currently unsupported! 236s They will be progressively added. 236s autopkgtest [07:34:52]: test pkg-r-autopkgtest: -----------------------] 237s pkg-r-autopkgtest PASS 237s autopkgtest [07:34:53]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 237s autopkgtest [07:34:53]: @@@@@@@@@@@@@@@@@@@@ summary 237s run-unit-test FAIL non-zero exit status 1 237s pkg-r-autopkgtest PASS 253s nova [W] Using flock in prodstack6-ppc64el 253s flock: timeout while waiting to get lock 253s Creating nova instance adt-plucky-ppc64el-r-cran-vegan-20250219-073056-juju-7f2275-prod-proposed-migration-environment-15-903d55fa-516b-4ee9-9058-c3fc4ed172cf from image adt/ubuntu-plucky-ppc64el-server-20250218.img (UUID 9318aa34-3d3c-43c5-86d2-aaf9390f2f5d)... 253s nova [W] Timed out waiting for 89b26097-3939-4f69-927b-70e5682fbce4 to get deleted.