0s autopkgtest [00:49:39]: starting date and time: 2025-03-04 00:49:39+0000 0s autopkgtest [00:49:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [00:49:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f56vfe6e/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-12.secgroup --name adt-plucky-s390x-r-cran-vegan-20250304-004939-juju-7f2275-prod-proposed-migration-environment-20-1733588a-5550-49cb-97f5-9cf173e66902 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 89s autopkgtest [00:51:08]: testbed dpkg architecture: s390x 90s autopkgtest [00:51:09]: testbed apt version: 2.9.31ubuntu1 90s autopkgtest [00:51:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 90s autopkgtest [00:51:09]: testbed release detected to be: None 91s autopkgtest [00:51:10]: updating testbed package index (apt update) 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 91s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 91s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 91s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 92s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [51.1 kB] 92s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [472 kB] 92s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [18.4 kB] 92s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [2420 B] 92s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [95.0 kB] 92s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [417 kB] 92s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [6756 B] 92s Fetched 1173 kB in 1s (1346 kB/s) 92s Reading package lists... 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade... 93s Calculating upgrade... 94s The following packages will be upgraded: 94s wireless-regdb 94s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 7290 B of archives. 94s After this operation, 1024 B of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x wireless-regdb all 2024.10.07-0ubuntu2 [7290 B] 94s Fetched 7290 B in 0s (49.4 kB/s) 94s (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 ... 81195 files and directories currently installed.) 94s Preparing to unpack .../wireless-regdb_2024.10.07-0ubuntu2_all.deb ... 94s Unpacking wireless-regdb (2024.10.07-0ubuntu2) over (2024.10.07-0ubuntu1) ... 94s Setting up wireless-regdb (2024.10.07-0ubuntu2) ... 94s Processing triggers for man-db (2.13.0-1) ... 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Solving dependencies... 95s The following packages will be REMOVED: 95s linux-image-6.11.0-8-generic* 95s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 95s After this operation, 10.5 MB disk space will be freed. 95s (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 ... 81195 files and directories currently installed.) 95s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 95s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 95s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 95s /etc/kernel/postrm.d/initramfs-tools: 95s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 95s /etc/kernel/postrm.d/zz-zipl: 95s Using config file '/etc/zipl.conf' 95s Building bootmap in '/boot' 95s Adding IPL section 'ubuntu' (default) 95s Preparing boot device for LD-IPL: vda (0000). 95s Done. 95s (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 ... 81191 files and directories currently installed.) 95s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 95s rmdir: failed to remove '/lib/modules/6.11.0-8-generic': Directory not empty 95s autopkgtest [00:51:14]: upgrading testbed (apt dist-upgrade and autopurge) 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 96s Entering ResolveByKeep 96s 96s Calculating upgrade... 96s The following packages were automatically installed and are no longer required: 96s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 96s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 96s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 96s linux-tools-6.11.0-8-generic 96s Use 'sudo apt autoremove' to remove them. 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 97s Solving dependencies... 97s The following packages will be REMOVED: 97s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 97s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 97s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 97s linux-tools-6.11.0-8-generic* 97s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 97s After this operation, 167 MB disk space will be freed. 97s (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 ... 81191 files and directories currently installed.) 97s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 97s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 97s Removing libpython3.12t64:s390x (3.12.9-1) ... 97s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 98s Removing libnsl2:s390x (1.3.0-3build3) ... 98s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 98s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 98s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 99s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 99s Processing triggers for libc-bin (2.40-4ubuntu1) ... 99s (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 ... 56091 files and directories currently installed.) 99s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 99s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 99s autopkgtest [00:51:18]: rebooting testbed after setup commands that affected boot 112s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 119s autopkgtest [00:51:38]: testbed running kernel: Linux 6.12.0-16-generic #16-Ubuntu SMP Fri Feb 14 14:10:01 UTC 2025 121s autopkgtest [00:51:40]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (dsc) [2204 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (tar) [1205 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-8+dfsg-1 (diff) [6312 B] 123s gpgv: Signature made Sun Sep 1 23:45:51 2024 UTC 123s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 123s gpgv: issuer "plessy@debian.org" 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-8+dfsg-1.dsc: no acceptable signature found 123s autopkgtest [00:51:42]: testing package r-cran-vegan version 2.6-8+dfsg-1 124s autopkgtest [00:51:43]: build not needed 126s autopkgtest [00:51:45]: test run-unit-test: preparing testbed 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 127s The following NEW packages will be installed: 127s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 127s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 127s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 127s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 127s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 127s liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 127s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 127s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 127s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 127s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 127s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 127s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 127s x11-common xdg-utils zip 127s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 67.6 MB of archives. 127s After this operation, 160 MB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 127s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 128s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 128s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 128s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 128s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 128s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 128s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 128s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 128s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 128s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 128s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 128s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 128s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 128s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 128s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250213-1ubuntu1 [620 kB] 128s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250213-1ubuntu1 [151 kB] 128s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 128s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 128s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 128s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 128s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 128s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 128s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 128s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 128s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 128s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 128s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 128s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 128s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 128s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.1-1 [253 kB] 128s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.1-1 [50.3 kB] 128s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.1-1 [28.3 kB] 128s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 128s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 128s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 128s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 128s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 128s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 128s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 128s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 128s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 128s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 128s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 128s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 128s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB] 128s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 128s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 128s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 128s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.2-1build1 [28.6 MB] 129s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cluster s390x 2.1.8-1 [577 kB] 129s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-commonmark s390x 1.9.2-2 [142 kB] 129s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-evaluate all 1.0.3-1 [114 kB] 129s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xfun s390x 0.50+dfsg-1 [568 kB] 129s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-highr all 0.11+dfsg-1 [38.5 kB] 129s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-yaml s390x 2.3.10-1 [113 kB] 129s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 129s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-knitr all 1.49+dfsg-1 [859 kB] 129s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB] 130s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-markdown all 1.13-1 [162 kB] 130s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x r-cran-mass s390x 7.3-65-1 [1114 kB] 130s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-2-1 [4441 kB] 130s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB] 130s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 130s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-permute all 0.9-7-1 [228 kB] 130s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vegan s390x 2.6-8+dfsg-1 [3143 kB] 130s Preconfiguring packages ... 130s Fetched 67.6 MB in 3s (21.3 MB/s) 130s Selecting previously unselected package libfreetype6:s390x. 131s (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 ... 56089 files and directories currently installed.) 131s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 131s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 131s Selecting previously unselected package fonts-dejavu-mono. 131s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 131s Unpacking fonts-dejavu-mono (2.37-8) ... 131s Selecting previously unselected package fonts-dejavu-core. 131s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 131s Unpacking fonts-dejavu-core (2.37-8) ... 131s Selecting previously unselected package fontconfig-config. 131s Preparing to unpack .../03-fontconfig-config_2.15.0-2ubuntu1_s390x.deb ... 131s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 131s Selecting previously unselected package libfontconfig1:s390x. 131s Preparing to unpack .../04-libfontconfig1_2.15.0-2ubuntu1_s390x.deb ... 131s Unpacking libfontconfig1:s390x (2.15.0-2ubuntu1) ... 131s Selecting previously unselected package fontconfig. 131s Preparing to unpack .../05-fontconfig_2.15.0-2ubuntu1_s390x.deb ... 131s Unpacking fontconfig (2.15.0-2ubuntu1) ... 131s Selecting previously unselected package fonts-glyphicons-halflings. 131s Preparing to unpack .../06-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 131s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 131s Selecting previously unselected package fonts-mathjax. 131s Preparing to unpack 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libsharpyuv0:s390x (1.5.0-0.1) ... 133s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 133s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 133s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 133s Setting up libdatrie1:s390x (0.2.13-3build1) ... 133s Setting up libxcb-render0:s390x (1.17.0-2) ... 133s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 133s Setting up unzip (6.0-28ubuntu6) ... 133s Setting up x11-common (1:7.7+23ubuntu3) ... 133s Setting up libdeflate0:s390x (1.23-1) ... 133s Setting up libxcb-shm0:s390x (1.17.0-2) ... 133s Setting up libgomp1:s390x (15-20250213-1ubuntu1) ... 133s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 133s Setting up zip (3.0-14ubuntu2) ... 133s Setting up libblas3:s390x (3.12.1-2) ... 133s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 133s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 133s Setting up 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update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 133s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 133s Setting up libpaper-utils (2.2.5-0.3) ... 133s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ... 133s Setting up libthai0:s390x (0.1.29-2build1) ... 133s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 133s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ... 133s Setting up libsm6:s390x (2:1.2.4-1) ... 133s Setting up fontconfig (2.15.0-2ubuntu1) ... 135s Regenerating fonts cache... done. 135s Setting up libxft2:s390x (2.3.6-1build1) ... 135s Setting up libtk8.6:s390x (8.6.16-1) ... 135s Setting up libpango-1.0-0:s390x (1.56.1-1) ... 135s Setting up libcairo2:s390x (1.18.2-2) ... 135s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ... 135s Setting up libpangoft2-1.0-0:s390x (1.56.1-1) ... 135s Setting up libpangocairo-1.0-0:s390x (1.56.1-1) ... 135s Setting up r-base-core (4.4.2-1build1) ... 135s Creating config file /etc/R/Renviron with new version 135s Setting up r-cran-lattice (0.22-6-1) ... 135s Setting up r-cran-nlme (3.1.167-1) ... 135s Setting up r-cran-cluster (2.1.8-1) ... 135s Setting up r-cran-commonmark (1.9.2-2) ... 135s Setting up r-cran-permute (0.9-7-1) ... 135s Setting up r-cran-xfun (0.50+dfsg-1) ... 135s Setting up r-cran-yaml (2.3.10-1) ... 135s Setting up r-cran-evaluate (1.0.3-1) ... 135s Setting up r-cran-highr (0.11+dfsg-1) ... 135s Setting up r-cran-mass (7.3-65-1) ... 135s Setting up r-cran-markdown (1.13-1) ... 135s Setting up r-cran-matrix (1.7-2-1) ... 135s Setting up r-cran-knitr (1.49+dfsg-1) ... 135s Setting up r-cran-mgcv (1.9-1-1) ... 135s Setting up r-cran-vegan (2.6-8+dfsg-1) ... 135s Processing triggers for libc-bin (2.40-4ubuntu1) ... 135s Processing triggers for man-db (2.13.0-1) ... 136s Processing triggers for install-info (7.1.1-1) ... 137s autopkgtest [00:51:56]: test run-unit-test: [----------------------- 137s 137s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 137s Copyright (C) 2024 The R Foundation for Statistical Computing 137s Platform: s390x-ibm-linux-gnu 137s 137s R is free software and comes with ABSOLUTELY NO WARRANTY. 137s You are welcome to redistribute it under certain conditions. 137s Type 'license()' or 'licence()' for distribution details. 137s 137s R is a collaborative project with many contributors. 137s Type 'contributors()' for more information and 137s 'citation()' on how to cite R or R packages in publications. 137s 137s Type 'demo()' for some demos, 'help()' for on-line help, or 137s 'help.start()' for an HTML browser interface to help. 137s Type 'q()' to quit R. 137s 137s > Stangle("decision-vegan.Rnw") 137s Writing to file decision-vegan.R 137s > source("decision-vegan.R", echo=TRUE) 137s 137s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 137s 137s > options(SweaveHooks = list(fig = figset)) 137s 137s > options(prompt = "> ", continue = " ") 137s 137s > options(width = 55) 137s 137s > require(vegan) 137s Loading required package: vegan 137s Loading required package: permute 137s Loading required package: lattice 138s This is vegan 2.6-8 138s 138s > data(sipoo) 138s 138s > mod <- nestedtemp(sipoo) 138s 138s > plot(mod, "i") 138s 138s > x <- mod$c["Falcsubb"] 138s 138s > y <- 1 - mod$r["Svartholm"] 138s 138s > points(x, y, pch = 16, cex = 1.5) 138s 138s > abline(x + y, -1, lty = 2) 138s 138s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 138s 138s > cross <- function(x, a, p) f(x, p) - a + x 138s 138s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 138s 138s > arrows(x, y, r, f(r, mod$p), lwd = 4) 138s 138s > library(vegan) 138s 138s > data(varespec) 138s 138s > data(varechem) 138s 138s > orig <- cca(varespec ~ Al + K, varechem) 138s 138s > plot(orig, dis = c("lc", "bp")) 138s 138s > plot(orig, dis = c("lc", "bp")) 138s 138s > i <- sample(nrow(varespec)) 138s 138s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 138s 138s > plot(shuff, dis = c("lc", "bp")) 138s 138s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 138s + dis = "lc"))) 138s 138s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 138s + dis = "lc"))) 138s 138s > tmp1 <- rda(varespec ~ Al + K, varechem) 138s 138s > i <- sample(nrow(varespec)) 138s 138s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 138s 138s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 138s + dis = "lc"))) 138s 138s > orig 138s Call: cca(formula = varespec ~ Al + K, data = 138s varechem) 138s 138s -- Model Summary -- 138s 138s Inertia Proportion Rank 138s Total 2.0832 1.0000 138s Constrained 0.4760 0.2285 2 138s Unconstrained 1.6072 0.7715 21 138s 138s Inertia is scaled Chi-square 138s 138s -- Eigenvalues -- 138s 138s Eigenvalues for constrained axes: 138s CCA1 CCA2 138s 0.3608 0.1152 138s 138s Eigenvalues for unconstrained axes: 138s CA1 CA2 CA3 CA4 CA5 CA6 CA7 138s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 138s CA8 138s 0.0757 138s (Showing 8 of 21 unconstrained eigenvalues) 138s 138s 138s > shuff 138s Call: cca(formula = varespec[i, ] ~ Al + K, data = 138s varechem) 138s 138s -- Model Summary -- 138s 138s Inertia Proportion Rank 138s Total 2.08320 1.00000 138s Constrained 0.19298 0.09264 2 138s Unconstrained 1.89022 0.90736 21 138s 138s Inertia is scaled Chi-square 138s 138s -- Eigenvalues -- 138s 138s Eigenvalues for constrained axes: 138s CCA1 CCA2 138s 0.12962 0.06336 138s 138s Eigenvalues for unconstrained axes: 138s CA1 CA2 CA3 CA4 CA5 CA6 CA7 138s 0.4683 0.3111 0.2264 0.1818 0.1588 0.1206 0.1048 138s CA8 138s 0.0888 138s (Showing 8 of 21 unconstrained eigenvalues) 138s 138s 138s > plot(procrustes(orig, shuff)) 138s 138s > tmp1 <- rda(varespec ~ ., varechem) 138s 138s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 138s 138s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 138s + scores(tmp2, dis = "lc", choi = 1:14)) 138s 138s > max(residuals(proc)) 138s [1] 3.199856e-14 138s 138s > data(dune) 138s 138s > data(dune.env) 138s 138s > orig <- cca(dune ~ Moisture, dune.env) 138s 138s > plot(orig, dis = "lc") 138s 138s > plot(orig, display = "wa", type = "points") 138s 138s > ordispider(orig, col = "red") 138s 138s > text(orig, dis = "cn", col = "blue") 138s 138s > plot(orig, display = "wa", type = "points") 138s 138s > ordispider(orig, col = "red") 138s 138s > text(orig, dis = "cn", col = "blue") 138s > 138s 138s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 138s Copyright (C) 2024 The R Foundation for Statistical Computing 138s Platform: s390x-ibm-linux-gnu 138s 138s R is free software and comes with ABSOLUTELY NO WARRANTY. 138s You are welcome to redistribute it under certain conditions. 138s Type 'license()' or 'licence()' for distribution details. 138s 138s R is a collaborative project with many contributors. 138s Type 'contributors()' for more information and 138s 'citation()' on how to cite R or R packages in publications. 138s 138s Type 'demo()' for some demos, 'help()' for on-line help, or 138s 'help.start()' for an HTML browser interface to help. 138s Type 'q()' to quit R. 138s 139s > Stangle("diversity-vegan.Rnw") 139s Writing to file diversity-vegan.R 139s > source("diversity-vegan.R", echo=TRUE) 139s 139s > par(mfrow = c(1, 1)) 139s 139s > options(width = 55) 139s 139s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 139s 139s > options(SweaveHooks = list(fig = figset)) 139s 139s > options(prompt = "> ", continue = " ") 139s 139s > library(vegan) 139s Loading required package: permute 139s Loading required package: lattice 140s This is vegan 2.6-8 140s 140s > data(BCI) 140s 140s > H <- diversity(BCI) 140s 140s > J <- H/log(specnumber(BCI)) 140s 140s > k <- sample(nrow(BCI), 6) 140s 140s > R <- renyi(BCI[k, ]) 140s 140s > print(plot(R)) 140s 140s > alpha <- fisher.alpha(BCI) 140s 140s > quantile(rowSums(BCI)) 140s 0% 25% 50% 75% 100% 140s 340.0 409.0 428.0 443.5 601.0 140s 140s > Srar <- rarefy(BCI, min(rowSums(BCI))) 140s 140s > S2 <- rarefy(BCI, 2) 140s 140s > all(rank(Srar) == rank(S2)) 140s [1] FALSE 140s 140s > range(diversity(BCI, "simp") - (S2 - 1)) 140s [1] -0.002868298 -0.001330663 140s 140s > data(dune) 140s 140s > data(dune.taxon) 140s 140s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 140s 140s > mod <- taxondive(dune, taxdis) 140s 140s > plot(mod) 140s forced matching of 'tree' labels and 'comm' names 140s 140s > tr <- hclust(taxdis, "aver") 140s 140s > mod <- treedive(dune, tr) 140s 140s > k <- sample(nrow(BCI), 1) 140s 140s > fish <- fisherfit(BCI[k, ]) 140s 140s > fish 140s 140s Fisher log series model 140s No. of species: 99 140s Fisher alpha: 41.58728 140s 140s 140s > plot(fish) 140s 140s > prestondistr(BCI[k, ]) 140s 140s Preston lognormal model 140s Method: maximized likelihood to log2 abundances 140s No. of species: 99 140s 140s mode width S0 140s 0.6542113 1.7831283 26.9058898 140s 140s Frequencies by Octave 140s 0 1 2 3 4 140s Observed 21.50000 32.50000 18.50000 12.00000 10.500000 140s Fitted 25.15461 26.40471 20.23741 11.32501 4.627347 140s 5 6 140s Observed 3.000000 1.0000000 140s Fitted 1.380497 0.3007107 140s 140s 140s > rad <- radfit(BCI[k, ]) 140s 140s > rad 140s 140s RAD models, family poisson 140s No. of species 99, total abundance 408 140s 140s par1 par2 par3 Deviance AIC 140s Null 73.661 348.773 140s Preemption 0.043432 63.706 340.818 140s Lognormal 0.79548 1.1324 25.022 304.133 140s Zipf 0.1318 -0.82742 33.156 312.268 140s Mandelbrot 1.3923 -1.4237 6.3196 13.572 294.683 140s BIC 140s Null 348.773 140s Preemption 343.413 140s Lognormal 309.324 140s Zipf 317.458 140s Mandelbrot 302.469 140s 140s > print(radlattice(rad)) 140s 140s > sac <- specaccum(BCI) 140s 140s > plot(sac, ci.type = "polygon", ci.col = "yellow") 140s 140s > sac <- specaccum(BCI) 140s 140s > plot(sac, ci.type = "polygon", ci.col = "yellow") 140s 140s > ncol(BCI)/mean(specnumber(BCI)) - 1 140s [1] 1.478519 140s 140s > beta <- vegdist(BCI, binary = TRUE) 140s 140s > mean(beta) 140s [1] 0.3399075 140s 140s > betadiver(help = TRUE) 140s 1 "w" = (b+c)/(2*a+b+c) 140s 2 "-1" = (b+c)/(2*a+b+c) 140s 3 "c" = (b+c)/2 140s 4 "wb" = b+c 140s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 140s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 140s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 140s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 140s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 140s (2*a+b+c))-1 140s 8 "t" = (b+c)/(2*a+b+c) 140s 9 "me" = (b+c)/(2*a+b+c) 140s 10 "j" = a/(a+b+c) 140s 11 "sor" = 2*a/(2*a+b+c) 140s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 140s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 140s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 140s 15 "cc" = (b+c)/(a+b+c) 140s 16 "g" = (b+c)/(a+b+c) 140s 17 "-3" = pmin.int(b,c)/(a+b+c) 140s 18 "l" = (b+c)/2 140s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 140s 20 "hk" = (b+c)/(2*a+b+c) 140s 21 "rlb" = a/(a+c) 140s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 140s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 140s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 140s 140s > z <- betadiver(BCI, "z") 140s 140s > quantile(z) 140s 0% 25% 50% 75% 100% 140s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 140s 140s > data(dune) 140s 140s > data(dune.env) 140s 140s > z <- betadiver(dune, "z") 140s 140s > mod <- with(dune.env, betadisper(z, Management)) 140s 140s > mod 140s 140s Homogeneity of multivariate dispersions 140s 140s Call: betadisper(d = z, group = Management) 140s 140s No. of Positive Eigenvalues: 12 140s No. of Negative Eigenvalues: 7 140s 140s Average distance to median: 140s BF HF NM SF 140s 0.2532 0.2512 0.4406 0.3635 140s 140s Eigenvalues for PCoA axes: 140s (Showing 8 of 19 eigenvalues) 140s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 140s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 140s PCoA7 PCoA8 140s 0.16128 0.08099 140s 140s > boxplot(mod) 140s 140s > specpool(BCI) 140s Species chao chao.se jack1 jack1.se jack2 140s All 225 236.3732 6.54361 245.58 5.650522 247.8722 140s boot boot.se n 140s All 235.6862 3.468888 50 140s 140s > s <- sample(nrow(BCI), 25) 140s 140s > specpool(BCI[s, ]) 140s Species chao chao.se jack1 jack1.se jack2 140s All 207 228.16 11.67651 229.08 6.505136 239.66 140s boot boot.se n 140s All 217.5357 3.86163 25 140s 140s > estimateR(BCI[k, ]) 140s 21 140s S.obs 99.000000 140s S.chao1 138.260870 140s se.chao1 15.815704 140s S.ACE 161.934635 140s se.ACE 7.588099 140s 140s > veiledspec(prestondistr(BCI[k, ])) 140s Extrapolated Observed Veiled 140s 120.25963 99.00000 21.25963 140s 140s > veiledspec(BCI[k, ]) 140s Extrapolated Observed Veiled 140s 134.54945 99.00000 35.54945 140s 140s > smo <- beals(BCI) 140s 140s > j <- which(colnames(BCI) == "Ceiba.pentandra") 140s 140s > plot(beals(BCI, species = j, include = FALSE), BCI[, 140s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 140s 140s > j <- which(colnames(BCI) == "Ceiba.pentandra") 140s 140s > plot(beals(BCI, species = j, include = FALSE), BCI[, 140s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 140s Warning messages: 140s 1: In cor(x > 0) : the standard deviation is zero 140s 2: In cor(x > 0) : the standard deviation is zero 140s 3: In betadisper(z, Management) : 140s some squared distances are negative and changed to zero 140s > 140s 140s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 140s Copyright (C) 2024 The R Foundation for Statistical Computing 140s Platform: s390x-ibm-linux-gnu 140s 140s R is free software and comes with ABSOLUTELY NO WARRANTY. 140s You are welcome to redistribute it under certain conditions. 140s Type 'license()' or 'licence()' for distribution details. 140s 140s R is a collaborative project with many contributors. 140s Type 'contributors()' for more information and 140s 'citation()' on how to cite R or R packages in publications. 140s 140s Type 'demo()' for some demos, 'help()' for on-line help, or 140s 'help.start()' for an HTML browser interface to help. 140s Type 'q()' to quit R. 140s 140s > Stangle("intro-vegan.Rnw") 140s Writing to file intro-vegan.R 140s > source("intro-vegan.R", echo=TRUE) 140s 140s > par(mfrow = c(1, 1)) 140s 140s > options(width = 72) 140s 140s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 140s 140s > options(SweaveHooks = list(fig = figset)) 140s 140s > options(prompt = "> ", continue = " ") 140s 140s > library(vegan) 140s Loading required package: permute 140s Loading required package: lattice 141s This is vegan 2.6-8 141s 141s > data(dune) 141s 141s > ord <- decorana(dune) 141s 141s > ord 141s 141s Call: 141s decorana(veg = dune) 141s 141s Detrended correspondence analysis with 26 segments. 141s Rescaling of axes with 4 iterations. 141s Total inertia (scaled Chi-square): 2.1153 141s 141s DCA1 DCA2 DCA3 DCA4 141s Eigenvalues 0.5117 0.3036 0.12125 0.14267 141s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 141s Decorana values 0.5360 0.2869 0.08136 0.04814 141s Axis lengths 3.7004 3.1166 1.30055 1.47888 141s 141s 141s > ord <- metaMDS(dune, trace = FALSE) 141s 141s > ord 141s 141s Call: 141s metaMDS(comm = dune, trace = FALSE) 141s 141s global Multidimensional Scaling using monoMDS 141s 141s Data: dune 141s Distance: bray 141s 141s Dimensions: 2 141s Stress: 0.1183186 141s Stress type 1, weak ties 141s Best solution was repeated 3 times in 20 tries 141s The best solution was from try 7 (random start) 141s Scaling: centring, PC rotation, halfchange scaling 141s Species: expanded scores based on ‘dune’ 141s 141s 141s > plot(ord) 141s 141s > plot(ord) 141s 141s > plot(ord, type = "n") 141s 141s > points(ord, display = "sites", cex = 0.8, pch = 21, 141s + col = "red", bg = "yellow") 141s 141s > text(ord, display = "species", cex = 0.7, col = "blue") 141s 141s > plot(ord, type = "n") 141s 141s > points(ord, display = "sites", cex = 0.8, pch = 21, 141s + col = "red", bg = "yellow") 141s 141s > text(ord, display = "species", cex = 0.7, col = "blue") 141s 141s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 141s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 141s + col = "blue") 141s 141s > data(dune.env) 141s 141s > attach(dune.env) 141s 141s > plot(ord, disp = "sites", type = "n") 141s 141s > ordihull(ord, Management, col = 1:4, lwd = 3) 141s 141s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 141s + lwd = 3) 141s 141s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 141s 141s > ordispider(ord, Management, col = 1:4, label = TRUE) 141s 141s > points(ord, disp = "sites", pch = 21, col = "red", 141s + bg = "yellow", cex = 1.3) 141s 141s > plot(ord, disp = "sites", type = "n") 141s 141s > ordihull(ord, Management, col = 1:4, lwd = 3) 141s 141s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 141s + lwd = 3) 141s 141s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 141s 141s > ordispider(ord, Management, col = 1:4, label = TRUE) 141s 141s > points(ord, disp = "sites", pch = 21, col = "red", 141s + bg = "yellow", cex = 1.3) 141s 141s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 141s + perm = 999) 141s 141s > ord.fit 141s 141s ***VECTORS 141s 141s NMDS1 NMDS2 r2 Pr(>r) 141s A1 0.96474 0.26322 0.3649 0.02 * 141s --- 141s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 141s Permutation: free 141s Number of permutations: 999 141s 141s ***FACTORS: 141s 141s Centroids: 141s NMDS1 NMDS2 141s ManagementBF -0.4534 -0.0102 141s ManagementHF -0.2636 -0.1282 141s ManagementNM 0.2958 0.5790 141s ManagementSF 0.1506 -0.4670 141s 141s Goodness of fit: 141s r2 Pr(>r) 141s Management 0.4134 0.009 ** 141s --- 141s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 141s Permutation: free 141s Number of permutations: 999 141s 141s 141s 141s > plot(ord, dis = "site") 141s 141s > plot(ord.fit) 141s 141s > ordisurf(ord, A1, add = TRUE) 142s 142s Family: gaussian 142s Link function: identity 142s 142s Formula: 142s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 142s 142s Estimated degrees of freedom: 142s 1.59 total = 2.59 142s 142s REML score: 41.58727 142s 142s > plot(ord, dis = "site") 142s 142s > plot(ord.fit) 142s 142s > ordisurf(ord, A1, add = TRUE) 142s 142s Family: gaussian 142s Link function: identity 142s 142s Formula: 142s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 142s 142s Estimated degrees of freedom: 142s 1.59 total = 2.59 142s 142s REML score: 41.58727 142s 142s > ord <- cca(dune ~ A1 + Management, data = dune.env) 142s 142s > ord 142s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 142s 142s -- Model Summary -- 142s 142s Inertia Proportion Rank 142s Total 2.1153 1.0000 142s Constrained 0.7798 0.3686 4 142s Unconstrained 1.3355 0.6314 15 142s 142s Inertia is scaled Chi-square 142s 142s -- Eigenvalues -- 142s 142s Eigenvalues for constrained axes: 142s CCA1 CCA2 CCA3 CCA4 142s 0.3187 0.2372 0.1322 0.0917 142s 142s Eigenvalues for unconstrained axes: 142s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 142s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 142s CA11 CA12 CA13 CA14 CA15 142s 0.0317 0.0178 0.0116 0.0087 0.0047 142s 142s 142s > plot(ord) 142s 142s > plot(ord) 142s 142s > cca(dune ~ ., data = dune.env) 142s 142s Some constraints or conditions were aliased because they were 142s redundant. This can happen if terms are linearly dependent (collinear): 142s ‘Manure^4’ 142s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 142s Manure, data = dune.env) 142s 142s -- Model Summary -- 142s 142s Inertia Proportion Rank 142s Total 2.1153 1.0000 142s Constrained 1.5032 0.7106 12 142s Unconstrained 0.6121 0.2894 7 142s 142s Inertia is scaled Chi-square 142s 142s -- Note -- 142s 142s Some constraints or conditions were aliased because they were 142s redundant. This can happen if terms are linearly dependent 142s (collinear): ‘Manure^4’ 142s 142s -- Eigenvalues -- 142s 142s Eigenvalues for constrained axes: 142s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 142s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 142s CCA11 CCA12 142s 0.0228 0.0108 142s 142s Eigenvalues for unconstrained axes: 142s CA1 CA2 CA3 CA4 CA5 CA6 CA7 142s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 142s 142s 142s > anova(ord) 142s Permutation test for cca under reduced model 142s Permutation: free 142s Number of permutations: 999 142s 142s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 142s Df ChiSquare F Pr(>F) 142s Model 4 0.77978 2.1896 0.001 *** 142s Residual 15 1.33549 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > anova(ord, by = "term", permutations = 199) 142s Permutation test for cca under reduced model 142s Terms added sequentially (first to last) 142s Permutation: free 142s Number of permutations: 199 142s 142s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 142s Df ChiSquare F Pr(>F) 142s A1 1 0.22476 2.5245 0.010 ** 142s Management 3 0.55502 2.0780 0.005 ** 142s Residual 15 1.33549 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > anova(ord, by = "mar", permutations = 199) 142s Permutation test for cca under reduced model 142s Marginal effects of terms 142s Permutation: free 142s Number of permutations: 199 142s 142s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 142s Df ChiSquare F Pr(>F) 142s A1 1 0.17594 1.9761 0.06 . 142s Management 3 0.55502 2.0780 0.01 ** 142s Residual 15 1.33549 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > anova(ord, by = "axis", permutations = 499) 142s Permutation test for cca under reduced model 142s Forward tests for axes 142s Permutation: free 142s Number of permutations: 499 142s 142s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 142s Df ChiSquare F Pr(>F) 142s CCA1 1 0.31875 3.5801 0.012 * 142s CCA2 1 0.23718 2.6640 0.134 142s CCA3 1 0.13217 1.4845 0.810 142s CCA4 1 0.09168 1.0297 1.000 142s Residual 15 1.33549 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 142s + data = dune.env) 142s 142s > ord 142s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 142s data = dune.env) 142s 142s -- Model Summary -- 142s 142s Inertia Proportion Rank 142s Total 2.1153 1.0000 142s Conditional 0.6283 0.2970 3 142s Constrained 0.5109 0.2415 4 142s Unconstrained 0.9761 0.4615 12 142s 142s Inertia is scaled Chi-square 142s 142s -- Eigenvalues -- 142s 142s Eigenvalues for constrained axes: 142s CCA1 CCA2 CCA3 CCA4 142s 0.24932 0.12090 0.08160 0.05904 142s 142s Eigenvalues for unconstrained axes: 142s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 142s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 142s CA10 CA11 CA12 142s 0.02102 0.01254 0.00928 142s 142s 142s > anova(ord, by = "term", permutations = 499) 142s Permutation test for cca under reduced model 142s Terms added sequentially (first to last) 142s Permutation: free 142s Number of permutations: 499 142s 142s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 142s Df ChiSquare F Pr(>F) 142s A1 1 0.11543 1.4190 1.000 142s Management 3 0.39543 1.6205 0.002 ** 142s Residual 12 0.97610 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 142s 142s > anova(ord, by = "term", permutations = how) 142s Permutation test for cca under reduced model 142s Terms added sequentially (first to last) 142s Plots: dune.env$Moisture, plot permutation: none 142s Permutation: free 142s Number of permutations: 499 142s 142s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 142s Df ChiSquare F Pr(>F) 142s A1 1 0.11543 1.4190 1.000 142s Management 3 0.39543 1.6205 0.002 ** 142s Residual 12 0.97610 142s --- 142s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 142s 142s > detach(dune.env) 142s > 142s 142s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 142s Copyright (C) 2024 The R Foundation for Statistical Computing 142s Platform: s390x-ibm-linux-gnu 142s 142s R is free software and comes with ABSOLUTELY NO WARRANTY. 142s You are welcome to redistribute it under certain conditions. 142s Type 'license()' or 'licence()' for distribution details. 142s 142s R is a collaborative project with many contributors. 142s Type 'contributors()' for more information and 142s 'citation()' on how to cite R or R packages in publications. 142s 142s Type 'demo()' for some demos, 'help()' for on-line help, or 142s 'help.start()' for an HTML browser interface to help. 142s Type 'q()' to quit R. 142s 142s > Stangle("partitioning.Rnw") 142s Writing to file partitioning.R 142s > source("partitioning.R", echo=TRUE) 142s 142s > par(mfrow = c(1, 1)) 142s 142s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 142s 142s > options(SweaveHooks = list(fig = figset)) 142s 142s > library(vegan) 142s Loading required package: permute 142s Loading required package: lattice 143s This is vegan 2.6-8 143s 143s > labs <- paste("Table", 1:4) 143s 143s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 143s 143s > showvarparts(2, bg = cls, Xnames = labs) 143s 143s > showvarparts(3, bg = cls, Xnames = labs) 143s 143s > showvarparts(4, bg = cls, Xnames = labs) 143s > 150s Test cca-object-tests passed 151s Test oecosimu-tests passed 155s Test vegan-tests passed 155s autopkgtest [00:52:14]: test run-unit-test: -----------------------] 155s autopkgtest [00:52:14]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 155s run-unit-test PASS 156s autopkgtest [00:52:15]: test pkg-r-autopkgtest: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 156s The following NEW packages will be installed: 156s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 156s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 156s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 156s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 156s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 156s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 156s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3 156s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 156s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 156s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 157s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 157s Need to get 82.3 MB of archives. 157s After this operation, 279 MB of additional disk space will be used. 157s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB] 158s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B] 158s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 158s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 158s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250213-1ubuntu1 [49.2 kB] 158s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250213-1ubuntu1 [31.2 kB] 158s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250213-1ubuntu1 [2970 kB] 158s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250213-1ubuntu1 [1213 kB] 158s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB] 158s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB] 158s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB] 158s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 158s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 158s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB] 158s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB] 159s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB] 159s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 159s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 159s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 159s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 159s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB] 159s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB] 159s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB] 159s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 159s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 159s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 159s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 159s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 159s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 159s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 160s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 160s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 160s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 160s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 160s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-1 [407 kB] 160s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB] 160s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.45-1 [245 kB] 160s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B] 160s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.45-1 [899 kB] 160s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 160s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 160s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB] 160s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 160s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.3-1 [183 kB] 160s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 160s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 160s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 160s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.2-1build1 [4342 B] 160s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 161s Fetched 82.3 MB in 4s (21.2 MB/s) 161s Selecting previously unselected package libisl23:s390x. 161s (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 ... 64063 files and directories currently installed.) 161s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 161s Unpacking libisl23:s390x (0.27-1) ... 161s Selecting previously unselected package libmpc3:s390x. 161s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 161s Unpacking libmpc3:s390x (1.3.1-1build2) ... 161s Selecting previously unselected package cpp-14-s390x-linux-gnu. 161s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package cpp-14. 161s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package cpp-s390x-linux-gnu. 161s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 161s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 161s Selecting previously unselected package cpp. 161s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 161s Unpacking cpp (4:14.2.0-1ubuntu1) ... 161s Selecting previously unselected package libcc1-0:s390x. 161s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_s390x.deb ... 161s Unpacking libcc1-0:s390x (15-20250213-1ubuntu1) ... 161s Selecting previously unselected package libitm1:s390x. 161s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_s390x.deb ... 161s Unpacking libitm1:s390x (15-20250213-1ubuntu1) ... 161s Selecting previously unselected package libasan8:s390x. 161s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_s390x.deb ... 161s Unpacking libasan8:s390x (15-20250213-1ubuntu1) ... 161s Selecting previously unselected package libubsan1:s390x. 161s Preparing to unpack .../09-libubsan1_15-20250213-1ubuntu1_s390x.deb ... 161s Unpacking libubsan1:s390x (15-20250213-1ubuntu1) ... 161s Selecting previously unselected package libgcc-14-dev:s390x. 161s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package gcc-14-s390x-linux-gnu. 161s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package gcc-14. 161s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package gcc-s390x-linux-gnu. 161s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 161s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 161s Selecting previously unselected package gcc. 161s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 161s Unpacking gcc (4:14.2.0-1ubuntu1) ... 161s Selecting previously unselected package libstdc++-14-dev:s390x. 161s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 161s Selecting previously unselected package g++-14-s390x-linux-gnu. 161s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 161s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 162s Selecting previously unselected package g++-14. 162s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu3_s390x.deb ... 162s Unpacking g++-14 (14.2.0-17ubuntu3) ... 162s Selecting previously unselected package g++-s390x-linux-gnu. 162s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 162s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 162s Selecting previously unselected package g++. 162s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 162s Unpacking g++ (4:14.2.0-1ubuntu1) ... 162s Selecting previously unselected package build-essential. 162s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 162s Unpacking build-essential (12.10ubuntu1) ... 162s Selecting previously unselected package dctrl-tools. 162s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 162s Unpacking dctrl-tools (2.24-3build3) ... 162s Selecting previously unselected package libgfortran-14-dev:s390x. 162s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu3_s390x.deb ... 162s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 162s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 162s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu3_s390x.deb ... 162s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 162s Selecting previously unselected package gfortran-14. 162s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu3_s390x.deb ... 162s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 162s Selecting previously unselected package gfortran-s390x-linux-gnu. 162s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 162s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 162s Selecting previously unselected package gfortran. 162s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 162s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 162s Selecting previously unselected package icu-devtools. 162s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 162s Unpacking icu-devtools (76.1-1ubuntu2) ... 162s Selecting previously unselected package libblas-dev:s390x. 162s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 162s Unpacking libblas-dev:s390x (3.12.1-2) ... 162s Selecting previously unselected package libbz2-dev:s390x. 162s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 162s Unpacking libbz2-dev:s390x (1.0.8-6) ... 162s Selecting previously unselected package libdeflate-dev:s390x. 162s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 162s Unpacking libdeflate-dev:s390x (1.23-1) ... 162s Selecting previously unselected package libicu-dev:s390x. 162s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 162s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 162s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 162s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 162s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 162s Selecting previously unselected package libjpeg8-dev:s390x. 162s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 162s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 162s Selecting previously unselected package libjpeg-dev:s390x. 162s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 162s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 162s Selecting previously unselected package liblapack-dev:s390x. 162s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ... 162s Unpacking liblapack-dev:s390x (3.12.1-2) ... 162s Selecting previously unselected package libncurses-dev:s390x. 162s Preparing to unpack .../36-libncurses-dev_6.5+20250216-1_s390x.deb ... 162s Unpacking libncurses-dev:s390x (6.5+20250216-1) ... 162s Selecting previously unselected package libpcre2-16-0:s390x. 162s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ... 162s Unpacking libpcre2-16-0:s390x (10.45-1) ... 162s Selecting previously unselected package libpcre2-32-0:s390x. 162s Preparing to unpack .../38-libpcre2-32-0_10.45-1_s390x.deb ... 162s Unpacking libpcre2-32-0:s390x (10.45-1) ... 162s Selecting previously unselected package libpcre2-posix3:s390x. 162s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ... 162s Unpacking libpcre2-posix3:s390x (10.45-1) ... 162s Selecting previously unselected package libpcre2-dev:s390x. 162s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ... 162s Unpacking libpcre2-dev:s390x (10.45-1) ... 162s Selecting previously unselected package libpkgconf3:s390x. 162s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ... 162s Unpacking libpkgconf3:s390x (1.8.1-4) ... 162s Selecting previously unselected package zlib1g-dev:s390x. 162s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 162s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 162s Selecting previously unselected package libpng-dev:s390x. 162s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ... 162s Unpacking libpng-dev:s390x (1.6.47-1) ... 162s Selecting previously unselected package libreadline-dev:s390x. 162s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ... 162s Unpacking libreadline-dev:s390x (8.2-6) ... 162s Selecting previously unselected package liblzma-dev:s390x. 162s Preparing to unpack .../45-liblzma-dev_5.6.3-1_s390x.deb ... 162s Unpacking liblzma-dev:s390x (5.6.3-1) ... 162s Selecting previously unselected package pkgconf-bin. 162s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ... 162s Unpacking pkgconf-bin (1.8.1-4) ... 162s Selecting previously unselected package pkgconf:s390x. 162s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ... 162s Unpacking pkgconf:s390x (1.8.1-4) ... 162s Selecting previously unselected package libtirpc-dev:s390x. 162s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 162s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 162s Selecting previously unselected package r-base-dev. 162s Preparing to unpack .../49-r-base-dev_4.4.2-1build1_all.deb ... 162s Unpacking r-base-dev (4.4.2-1build1) ... 162s Selecting previously unselected package pkg-r-autopkgtest. 162s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 162s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 162s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 162s Setting up libncurses-dev:s390x (6.5+20250216-1) ... 162s Setting up libreadline-dev:s390x (8.2-6) ... 162s Setting up libpcre2-16-0:s390x (10.45-1) ... 162s Setting up libpcre2-32-0:s390x (10.45-1) ... 162s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 162s Setting up libpkgconf3:s390x (1.8.1-4) ... 162s Setting up libmpc3:s390x (1.3.1-1build2) ... 162s Setting up icu-devtools (76.1-1ubuntu2) ... 162s Setting up pkgconf-bin (1.8.1-4) ... 163s Setting up liblzma-dev:s390x (5.6.3-1) ... 163s Setting up libubsan1:s390x (15-20250213-1ubuntu1) ... 163s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 163s Setting up libpcre2-posix3:s390x (10.45-1) ... 163s Setting up libasan8:s390x (15-20250213-1ubuntu1) ... 163s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 163s Setting up libisl23:s390x (0.27-1) ... 163s Setting up libdeflate-dev:s390x (1.23-1) ... 163s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 163s Setting up libcc1-0:s390x (15-20250213-1ubuntu1) ... 163s Setting up libblas-dev:s390x (3.12.1-2) ... 163s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode 163s Setting up dctrl-tools (2.24-3build3) ... 163s Setting up libitm1:s390x (15-20250213-1ubuntu1) ... 163s Setting up libbz2-dev:s390x (1.0.8-6) ... 163s Setting up libpcre2-dev:s390x (10.45-1) ... 163s Setting up libpng-dev:s390x (1.6.47-1) ... 163s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 163s Setting up pkgconf:s390x (1.8.1-4) ... 163s Setting up liblapack-dev:s390x (3.12.1-2) ... 163s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode 163s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 163s Setting up cpp-14 (14.2.0-17ubuntu3) ... 163s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ... 163s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ... 163s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu3) ... 163s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 163s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 163s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 163s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 163s Setting up cpp (4:14.2.0-1ubuntu1) ... 163s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ... 163s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 163s Setting up gcc-14 (14.2.0-17ubuntu3) ... 163s Setting up g++-14 (14.2.0-17ubuntu3) ... 163s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 163s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 163s Setting up gcc (4:14.2.0-1ubuntu1) ... 163s Setting up g++ (4:14.2.0-1ubuntu1) ... 163s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 163s Setting up build-essential (12.10ubuntu1) ... 163s Setting up gfortran (4:14.2.0-1ubuntu1) ... 163s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 163s 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 163s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 163s 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 163s Setting up r-base-dev (4.4.2-1build1) ... 163s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 163s Processing triggers for libc-bin (2.40-4ubuntu1) ... 163s Processing triggers for man-db (2.13.0-1) ... 163s Processing triggers for install-info (7.1.1-1) ... 164s autopkgtest [00:52:23]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 164s autopkgtest [00:52:23]: test pkg-r-autopkgtest: [----------------------- 164s Test: Try to load the R library vegan 164s 164s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 164s Copyright (C) 2024 The R Foundation for Statistical Computing 164s Platform: s390x-ibm-linux-gnu 164s 164s R is free software and comes with ABSOLUTELY NO WARRANTY. 164s You are welcome to redistribute it under certain conditions. 164s Type 'license()' or 'licence()' for distribution details. 164s 164s R is a collaborative project with many contributors. 164s Type 'contributors()' for more information and 164s 'citation()' on how to cite R or R packages in publications. 164s 164s Type 'demo()' for some demos, 'help()' for on-line help, or 164s 'help.start()' for an HTML browser interface to help. 164s Type 'q()' to quit R. 164s 164s > library('vegan') 164s Loading required package: permute 164s Loading required package: lattice 165s This is vegan 2.6-8 165s > 165s > 165s Other tests are currently unsupported! 165s They will be progressively added. 165s autopkgtest [00:52:24]: test pkg-r-autopkgtest: -----------------------] 166s autopkgtest [00:52:25]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 166s pkg-r-autopkgtest PASS 166s autopkgtest [00:52:25]: @@@@@@@@@@@@@@@@@@@@ summary 166s run-unit-test PASS 166s pkg-r-autopkgtest PASS 184s nova [W] Using flock in prodstack6-s390x 184s Creating nova instance adt-plucky-s390x-r-cran-vegan-20250304-004939-juju-7f2275-prod-proposed-migration-environment-20-1733588a-5550-49cb-97f5-9cf173e66902 from image adt/ubuntu-plucky-s390x-server-20250303.img (UUID 30050491-04c6-4de1-b7e1-55057a678529)... 184s nova [W] Timed out waiting for b4b2c716-b634-4cf9-a88b-d1caf20bcb5d to get deleted.