0s autopkgtest [18:33:33]: starting date and time: 2025-03-15 18:33:33+0000
0s autopkgtest [18:33:33]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
0s autopkgtest [18:33:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.an9pja_w/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-9.secgroup --name adt-plucky-s390x-r-cran-vegan-20250315-183333-juju-7f2275-prod-proposed-migration-environment-2-1059e52a-f01f-41a0-a15b-1017c0f89e51 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/
130s autopkgtest [18:35:43]: testbed dpkg architecture: s390x
130s autopkgtest [18:35:43]: testbed apt version: 2.9.33
131s autopkgtest [18:35:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup
131s autopkgtest [18:35:44]: testbed release detected to be: None
131s autopkgtest [18:35:44]: updating testbed package index (apt update)
132s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
132s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
132s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB]
132s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB]
132s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB]
133s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB]
133s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B]
133s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
133s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB]
133s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB]
133s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B]
133s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B]
133s Fetched 1073 kB in 1s (745 kB/s)
134s Reading package lists...
134s Reading package lists...
134s Building dependency tree...
134s Reading state information...
135s Calculating upgrade...
135s Calculating upgrade...
135s The following packages were automatically installed and are no longer required:
135s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
135s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
135s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
135s linux-tools-6.11.0-8-generic
135s Use 'sudo apt autoremove' to remove them.
135s The following packages will be upgraded:
135s pinentry-curses python3-jinja2 strace
135s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
135s Need to get 652 kB of archives.
135s After this operation, 27.6 kB of additional disk space will be used.
135s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
135s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB]
136s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
136s Fetched 652 kB in 1s (800 kB/s)
136s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
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(Reading database ... 35%
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(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 ... 81428 files and directories currently installed.)
136s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
136s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
136s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ...
136s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
136s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
136s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
136s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
136s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
136s Setting up strace (6.13+ds-1ubuntu1) ...
136s Processing triggers for man-db (2.13.0-1) ...
137s Reading package lists...
137s Building dependency tree...
137s Reading state information...
137s Solving dependencies...
137s The following packages will be REMOVED:
137s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
137s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
137s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
137s linux-tools-6.11.0-8-generic*
137s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
137s After this operation, 167 MB disk space will be freed.
137s (Reading database ...
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(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 ... 81428 files and directories currently installed.)
137s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
137s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
137s Removing libpython3.12t64:s390x (3.12.9-1) ...
137s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
137s Removing libnsl2:s390x (1.3.0-3build3) ...
137s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
137s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
137s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
138s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
138s Processing triggers for libc-bin (2.41-1ubuntu1) ...
138s (Reading database ...
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(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 ... 56328 files and directories currently installed.)
138s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
138s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
138s autopkgtest [18:35:51]: upgrading testbed (apt dist-upgrade and autopurge)
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
139s Starting 2 pkgProblemResolver with broken count: 0
139s Done
139s Entering ResolveByKeep
139s
139s Calculating upgrade...
139s The following packages will be upgraded:
139s libc-bin libc-dev-bin libc6 libc6-dev locales
140s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
140s Need to get 9512 kB of archives.
140s After this operation, 8192 B of additional disk space will be used.
140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
141s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
141s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
144s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
144s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
148s Preconfiguring packages ...
148s Fetched 9512 kB in 8s (1159 kB/s)
148s (Reading database ...
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(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 ... 56326 files and directories currently installed.)
148s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
148s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
148s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
148s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Setting up libc6:s390x (2.41-1ubuntu2) ...
148s (Reading database ...
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(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 ... 56326 files and directories currently installed.)
148s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
148s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Setting up libc-bin (2.41-1ubuntu2) ...
148s (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(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 ... 56326 files and directories currently installed.)
148s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
148s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
148s Setting up locales (2.41-1ubuntu2) ...
149s Generating locales (this might take a while)...
150s en_US.UTF-8... done
150s Generation complete.
150s Setting up libc-dev-bin (2.41-1ubuntu2) ...
150s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
150s Processing triggers for man-db (2.13.0-1) ...
150s Processing triggers for systemd (257.3-1ubuntu3) ...
151s Reading package lists...
151s Building dependency tree...
151s Reading state information...
151s Starting pkgProblemResolver with broken count: 0
151s Starting 2 pkgProblemResolver with broken count: 0
151s Done
152s Solving dependencies...
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
152s autopkgtest [18:36:05]: rebooting testbed after setup commands that affected boot
171s autopkgtest [18:36:24]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
174s autopkgtest [18:36:27]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan
176s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (dsc) [2293 B]
176s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (tar) [1207 kB]
176s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (diff) [6736 B]
176s gpgv: Signature made Sun Mar 9 19:53:35 2025 UTC
176s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4
176s gpgv: Can't check signature: No public key
176s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1ubuntu2.dsc: no acceptable signature found
177s autopkgtest [18:36:30]: testing package r-cran-vegan version 2.6-10+dfsg-1ubuntu2
177s autopkgtest [18:36:30]: build not needed
180s autopkgtest [18:36:33]: test run-unit-test: preparing testbed
180s Reading package lists...
181s Building dependency tree...
181s Reading state information...
181s Starting pkgProblemResolver with broken count: 0
181s Starting 2 pkgProblemResolver with broken count: 0
181s Done
181s The following NEW packages will be installed:
181s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
181s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1
181s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3
181s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap
181s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax
181s liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
181s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6
181s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0
181s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core
181s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr
181s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv
181s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip
181s x11-common xdg-utils zip
181s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded.
181s Need to get 67.6 MB of archives.
181s After this operation, 160 MB of additional disk space will be used.
181s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB]
182s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB]
182s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB]
183s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB]
183s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB]
183s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB]
183s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB]
183s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
185s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB]
185s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB]
185s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB]
185s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B]
185s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB]
185s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB]
186s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB]
186s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB]
186s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB]
186s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250222-0ubuntu1 [152 kB]
186s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB]
186s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB]
187s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB]
187s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB]
187s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB]
187s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B]
187s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB]
187s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB]
188s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
188s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB]
188s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB]
191s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB]
191s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB]
191s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.2-1 [253 kB]
191s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.2-1 [50.2 kB]
191s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.2-1 [28.2 kB]
191s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB]
191s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB]
191s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB]
191s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB]
191s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB]
192s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB]
192s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB]
193s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB]
193s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB]
193s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B]
193s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB]
193s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB]
194s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB]
194s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB]
194s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB]
194s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
194s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.3-1 [28.6 MB]
217s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cluster s390x 2.1.8-1 [577 kB]
218s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-commonmark s390x 1.9.2-2 [142 kB]
218s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-evaluate all 1.0.3-1 [114 kB]
218s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xfun s390x 0.51+dfsg-1 [574 kB]
219s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-highr all 0.11+dfsg-1 [38.5 kB]
219s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-yaml s390x 2.3.10-1 [113 kB]
219s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
224s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-knitr all 1.49+dfsg-1 [859 kB]
224s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB]
225s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-markdown all 1.13-1 [162 kB]
225s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB]
226s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-3-1 [4449 kB]
230s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB]
231s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB]
234s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-permute all 0.9-7-1 [228 kB]
234s Get:67 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-vegan s390x 2.6-10+dfsg-1ubuntu2 [3149 kB]
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238s Selecting previously unselected package liblapack3:s390x.
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239s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ...
239s Setting up libpixman-1-0:s390x (0.44.0-3) ...
239s Setting up libsharpyuv0:s390x (1.5.0-0.1) ...
239s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
239s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
239s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ...
239s Setting up libdatrie1:s390x (0.2.13-3build1) ...
239s Setting up libxcb-render0:s390x (1.17.0-2) ...
239s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ...
239s Setting up unzip (6.0-28ubuntu6) ...
239s Setting up x11-common (1:7.7+23ubuntu3) ...
239s Setting up libdeflate0:s390x (1.23-1) ...
239s Setting up libxcb-shm0:s390x (1.17.0-2) ...
239s Setting up libgomp1:s390x (15-20250222-0ubuntu1) ...
239s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ...
239s Setting up zip (3.0-14ubuntu2) ...
239s Setting up libblas3:s390x (3.12.1-2) ...
239s 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
239s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ...
239s Setting up fonts-dejavu-mono (2.37-8) ...
239s Setting up libtcl8.6:s390x (8.6.16+dfsg-1) ...
239s Setting up fonts-dejavu-core (2.37-8) ...
239s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ...
239s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ...
239s Setting up libwebp7:s390x (1.5.0-0.1) ...
239s Setting up libjs-highlight.js (9.18.5+dfsg1-2) ...
239s Setting up libharfbuzz0b:s390x (10.2.0-1) ...
239s Setting up libthai-data (0.1.29-2build1) ...
239s Setting up libxss1:s390x (1:1.2.3-1build3) ...
239s Setting up libpaper2:s390x (2.2.5-0.3) ...
239s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
239s Setting up node-normalize.css (8.0.1-5) ...
239s Setting up xdg-utils (1.2.1-2ubuntu1) ...
239s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
239s Setting up libjs-bootstrap (3.4.1+dfsg-3) ...
239s Setting up libjpeg8:s390x (8c-2ubuntu11) ...
239s Setting up libice6:s390x (2:1.1.1-1) ...
239s Setting up liblapack3:s390x (3.12.1-2) ...
239s 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
239s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
239s Setting up libpaper-utils (2.2.5-0.3) ...
239s Setting up libjs-jquery-datatables (1.11.5+dfsg-2) ...
239s Setting up libthai0:s390x (0.1.29-2build1) ...
239s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ...
239s Setting up libfontconfig1:s390x (2.15.0-2ubuntu1) ...
239s Setting up libsm6:s390x (2:1.2.4-1) ...
239s Setting up fontconfig (2.15.0-2ubuntu1) ...
241s Regenerating fonts cache... done.
241s Setting up libxft2:s390x (2.3.6-1build1) ...
241s Setting up libtk8.6:s390x (8.6.16-1) ...
241s Setting up libpango-1.0-0:s390x (1.56.2-1) ...
241s Setting up libcairo2:s390x (1.18.2-2) ...
241s Setting up libxt6t64:s390x (1:1.2.1-1.2build1) ...
241s Setting up libpangoft2-1.0-0:s390x (1.56.2-1) ...
241s Setting up libpangocairo-1.0-0:s390x (1.56.2-1) ...
241s Setting up r-base-core (4.4.3-1) ...
242s Creating config file /etc/R/Renviron with new version
242s Setting up r-cran-lattice (0.22-6-1) ...
242s Setting up r-cran-nlme (3.1.167-1) ...
242s Setting up r-cran-cluster (2.1.8-1) ...
242s Setting up r-cran-commonmark (1.9.2-2) ...
242s Setting up r-cran-permute (0.9-7-1) ...
242s Setting up r-cran-xfun (0.51+dfsg-1) ...
242s Setting up r-cran-yaml (2.3.10-1) ...
242s Setting up r-cran-evaluate (1.0.3-1) ...
242s Setting up r-cran-highr (0.11+dfsg-1) ...
242s Setting up r-cran-mass (7.3-64-1) ...
242s Setting up r-cran-markdown (1.13-1) ...
242s Setting up r-cran-matrix (1.7-3-1) ...
242s Setting up r-cran-knitr (1.49+dfsg-1) ...
242s Setting up r-cran-mgcv (1.9-1-1) ...
242s Setting up r-cran-vegan (2.6-10+dfsg-1ubuntu2) ...
242s Processing triggers for libc-bin (2.41-1ubuntu2) ...
242s Processing triggers for man-db (2.13.0-1) ...
242s Processing triggers for install-info (7.1.1-1) ...
243s autopkgtest [18:37:36]: test run-unit-test: [-----------------------
244s
244s R version 4.4.3 (2025-02-28) -- "Trophy Case"
244s Copyright (C) 2025 The R Foundation for Statistical Computing
244s Platform: s390x-ibm-linux-gnu
244s
244s R is free software and comes with ABSOLUTELY NO WARRANTY.
244s You are welcome to redistribute it under certain conditions.
244s Type 'license()' or 'licence()' for distribution details.
244s
244s R is a collaborative project with many contributors.
244s Type 'contributors()' for more information and
244s 'citation()' on how to cite R or R packages in publications.
244s
244s Type 'demo()' for some demos, 'help()' for on-line help, or
244s 'help.start()' for an HTML browser interface to help.
244s Type 'q()' to quit R.
244s
244s > Stangle("decision-vegan.Rnw")
244s Writing to file decision-vegan.R
244s > source("decision-vegan.R", echo=TRUE)
244s
244s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1)
244s
244s > options(SweaveHooks = list(fig = figset))
244s
244s > options(prompt = "> ", continue = " ")
244s
244s > options(width = 55)
244s
244s > require(vegan)
244s Loading required package: vegan
244s Loading required package: permute
244s Loading required package: lattice
244s
244s > data(sipoo)
244s
244s > mod <- nestedtemp(sipoo)
244s
244s > plot(mod, "i")
245s
245s > x <- mod$c["Falcsubb"]
245s
245s > y <- 1 - mod$r["Svartholm"]
245s
245s > points(x, y, pch = 16, cex = 1.5)
245s
245s > abline(x + y, -1, lty = 2)
245s
245s > f <- function(x, p) (1 - (1 - x)^p)^(1/p)
245s
245s > cross <- function(x, a, p) f(x, p) - a + x
245s
245s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root
245s
245s > arrows(x, y, r, f(r, mod$p), lwd = 4)
245s
245s > library(vegan)
245s
245s > data(varespec)
245s
245s > data(varechem)
245s
245s > orig <- cca(varespec ~ Al + K, varechem)
245s
245s > plot(orig, dis = c("lc", "bp"))
245s
245s > plot(orig, dis = c("lc", "bp"))
245s
245s > i <- sample(nrow(varespec))
245s
245s > shuff <- cca(varespec[i, ] ~ Al + K, varechem)
245s
245s > plot(shuff, dis = c("lc", "bp"))
245s
245s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff,
245s + dis = "lc")))
245s
245s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff,
245s + dis = "lc")))
245s
245s > tmp1 <- rda(varespec ~ Al + K, varechem)
245s
245s > i <- sample(nrow(varespec))
245s
245s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem)
245s
245s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2,
245s + dis = "lc")))
245s
245s > orig
245s Call: cca(formula = varespec ~ Al + K, data =
245s varechem)
245s
245s -- Model Summary --
245s
245s Inertia Proportion Rank
245s Total 2.0832 1.0000
245s Constrained 0.4760 0.2285 2
245s Unconstrained 1.6072 0.7715 21
245s
245s Inertia is scaled Chi-square
245s
245s -- Eigenvalues --
245s
245s Eigenvalues for constrained axes:
245s CCA1 CCA2
245s 0.3608 0.1152
245s
245s Eigenvalues for unconstrained axes:
245s CA1 CA2 CA3 CA4 CA5 CA6 CA7
245s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836
245s CA8
245s 0.0757
245s (Showing 8 of 21 unconstrained eigenvalues)
245s
245s
245s > shuff
245s Call: cca(formula = varespec[i, ] ~ Al + K, data =
245s varechem)
245s
245s -- Model Summary --
245s
245s Inertia Proportion Rank
245s Total 2.08320 1.00000
245s Constrained 0.17100 0.08209 2
245s Unconstrained 1.91220 0.91791 21
245s
245s Inertia is scaled Chi-square
245s
245s -- Eigenvalues --
245s
245s Eigenvalues for constrained axes:
245s CCA1 CCA2
245s 0.10022 0.07078
245s
245s Eigenvalues for unconstrained axes:
245s CA1 CA2 CA3 CA4 CA5 CA6 CA7
245s 0.5138 0.3317 0.2321 0.1837 0.1444 0.1160 0.0879
245s CA8
245s 0.0812
245s (Showing 8 of 21 unconstrained eigenvalues)
245s
245s
245s > plot(procrustes(orig, shuff))
245s
245s > tmp1 <- rda(varespec ~ ., varechem)
245s
245s > tmp2 <- rda(varespec[i, ] ~ ., varechem)
245s
245s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14),
245s + scores(tmp2, dis = "lc", choi = 1:14))
245s
245s > max(residuals(proc))
245s [1] 2.723285e-14
245s
245s > data(dune)
245s
245s > data(dune.env)
245s
245s > orig <- cca(dune ~ Moisture, dune.env)
245s
245s > plot(orig, dis = "lc")
245s
245s > plot(orig, display = "wa", type = "points")
245s
245s > ordispider(orig, col = "red")
245s
245s > text(orig, dis = "cn", col = "blue")
245s
245s > plot(orig, display = "wa", type = "points")
245s
245s > ordispider(orig, col = "red")
245s
245s > text(orig, dis = "cn", col = "blue")
245s >
245s
245s R version 4.4.3 (2025-02-28) -- "Trophy Case"
245s Copyright (C) 2025 The R Foundation for Statistical Computing
245s Platform: s390x-ibm-linux-gnu
245s
245s R is free software and comes with ABSOLUTELY NO WARRANTY.
245s You are welcome to redistribute it under certain conditions.
245s Type 'license()' or 'licence()' for distribution details.
245s
245s R is a collaborative project with many contributors.
245s Type 'contributors()' for more information and
245s 'citation()' on how to cite R or R packages in publications.
245s
245s Type 'demo()' for some demos, 'help()' for on-line help, or
245s 'help.start()' for an HTML browser interface to help.
245s Type 'q()' to quit R.
245s
245s > Stangle("diversity-vegan.Rnw")
245s Writing to file diversity-vegan.R
245s > source("diversity-vegan.R", echo=TRUE)
245s
245s > par(mfrow = c(1, 1))
245s
245s > options(width = 55)
245s
245s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1)
245s
245s > options(SweaveHooks = list(fig = figset))
245s
245s > options(prompt = "> ", continue = " ")
245s
245s > library(vegan)
245s Loading required package: permute
245s Loading required package: lattice
246s
246s > data(BCI)
246s
246s > H <- diversity(BCI)
246s
246s > J <- H/log(specnumber(BCI))
246s
246s > k <- sample(nrow(BCI), 6)
246s
246s > R <- renyi(BCI[k, ])
246s
246s > print(plot(R))
246s
246s > alpha <- fisher.alpha(BCI)
246s
246s > quantile(rowSums(BCI))
246s 0% 25% 50% 75% 100%
246s 340.0 409.0 428.0 443.5 601.0
246s
246s > Srar <- rarefy(BCI, min(rowSums(BCI)))
246s
246s > S2 <- rarefy(BCI, 2)
246s
246s > all(rank(Srar) == rank(S2))
246s [1] FALSE
246s
246s > range(diversity(BCI, "simp") - (S2 - 1))
246s [1] -0.002868298 -0.001330663
246s
246s > data(dune)
246s
246s > data(dune.taxon)
246s
246s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE)
246s
246s > mod <- taxondive(dune, taxdis)
246s forced matching of 'tree' labels and 'comm' names
246s
246s > plot(mod)
246s
246s > tr <- hclust(taxdis, "aver")
246s
246s > mod <- treedive(dune, tr)
246s
246s > k <- sample(nrow(BCI), 1)
246s
246s > fish <- fisherfit(BCI[k, ])
246s
246s > fish
246s
246s Fisher log series model
246s No. of species: 81
246s Fisher alpha: 29.02041
246s
246s
246s > plot(fish)
246s
246s > prestondistr(BCI[k, ])
246s
246s Preston lognormal model
246s Method: maximized likelihood to log2 abundances
246s No. of species: 81
246s
246s mode width S0
246s 0.5985323 2.0883063 19.8892888
246s
246s Frequencies by Octave
246s 0 1 2 3 4
246s Observed 17.00000 24.00000 15.00000 10.00000 9.000000
246s Fitted 19.08892 19.52513 15.87891 10.26744 5.278594
246s 5 6
246s Observed 3.500000 2.5000000
246s Fitted 2.157689 0.7012518
246s
246s
246s > rad <- radfit(BCI[k, ])
246s
246s > rad
246s
246s RAD models, family poisson
246s No. of species 81, total abundance 444
246s
246s par1 par2 par3 Deviance
246s Null 114.1829
246s Preemption 0.062873 82.1220
246s Lognormal 0.89266 1.301 24.4013
246s Zipf 0.17917 -0.94243 32.6148
246s Mandelbrot 1.4107 -1.508 4.0101 7.7853
246s AIC BIC
246s Null 349.0742 349.0742
246s Preemption 319.0133 321.4078
246s Lognormal 263.2927 268.0816
246s Zipf 271.5062 276.2951
246s Mandelbrot 248.6766 255.8600
246s
246s > print(radlattice(rad))
246s
246s > sac <- specaccum(BCI)
246s
246s > plot(sac, ci.type = "polygon", ci.col = "yellow")
246s
246s > sac <- specaccum(BCI)
246s
246s > plot(sac, ci.type = "polygon", ci.col = "yellow")
246s
246s > ncol(BCI)/mean(specnumber(BCI)) - 1
246s [1] 1.478519
246s
246s > beta <- vegdist(BCI, binary = TRUE)
246s
246s > mean(beta)
246s [1] 0.3399075
246s
246s > betadiver(help = TRUE)
246s 1 "w" = (b+c)/(2*a+b+c)
246s 2 "-1" = (b+c)/(2*a+b+c)
246s 3 "c" = (b+c)/2
246s 4 "wb" = b+c
246s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c)
246s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) -
246s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c)
246s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c)
246s - ((a+b)*log(a+b) + (a+c)*log(a+c)) /
246s (2*a+b+c))-1
246s 8 "t" = (b+c)/(2*a+b+c)
246s 9 "me" = (b+c)/(2*a+b+c)
246s 10 "j" = a/(a+b+c)
246s 11 "sor" = 2*a/(2*a+b+c)
246s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c)
246s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a)
246s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c))
246s 15 "cc" = (b+c)/(a+b+c)
246s 16 "g" = (b+c)/(a+b+c)
246s 17 "-3" = pmin.int(b,c)/(a+b+c)
246s 18 "l" = (b+c)/2
246s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1)
246s 20 "hk" = (b+c)/(2*a+b+c)
246s 21 "rlb" = a/(a+c)
246s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a)
246s 23 "gl" = 2*abs(b-c)/(2*a+b+c)
246s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2)
246s
246s > z <- betadiver(BCI, "z")
246s
246s > quantile(z)
246s 0% 25% 50% 75% 100%
246s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091
246s
246s > data(dune)
246s
246s > data(dune.env)
246s
246s > z <- betadiver(dune, "z")
246s
246s > mod <- with(dune.env, betadisper(z, Management))
246s
246s > mod
246s
246s Homogeneity of multivariate dispersions
246s
246s Call: betadisper(d = z, group = Management)
246s
246s No. of Positive Eigenvalues: 12
246s No. of Negative Eigenvalues: 7
246s
246s Average distance to median:
246s BF HF NM SF
246s 0.2532 0.2512 0.4406 0.3635
246s
246s Eigenvalues for PCoA axes:
246s (Showing 8 of 19 eigenvalues)
246s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6
246s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445
246s PCoA7 PCoA8
246s 0.16128 0.08099
246s
246s > boxplot(mod)
246s
246s > specpool(BCI)
246s Species chao chao.se jack1 jack1.se jack2
246s All 225 236.3732 6.54361 245.58 5.650522 247.8722
246s boot boot.se n
246s All 235.6862 3.468888 50
246s
246s > s <- sample(nrow(BCI), 25)
246s
246s > specpool(BCI[s, ])
246s Species chao chao.se jack1 jack1.se jack2
246s All 203 213.83 6.546217 221.24 5.387987 224.6133
246s boot boot.se n
246s All 212.6463 3.601798 25
246s
246s > estimateR(BCI[k, ])
246s 45
246s S.obs 81.000000
246s S.chao1 118.400000
246s se.chao1 17.143725
246s S.ACE 129.701001
246s se.ACE 6.249946
246s
246s > veiledspec(prestondistr(BCI[k, ]))
246s Extrapolated Observed Veiled
246s 104.11262 81.00000 23.11262
246s
246s > veiledspec(BCI[k, ])
246s Extrapolated Observed Veiled
246s 127.42578 81.00000 46.42578
246s
246s > smo <- beals(BCI)
246s
246s > j <- which(colnames(BCI) == "Ceiba.pentandra")
246s
246s > plot(beals(BCI, species = j, include = FALSE), BCI[,
246s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence")
246s
246s > j <- which(colnames(BCI) == "Ceiba.pentandra")
246s
246s > plot(beals(BCI, species = j, include = FALSE), BCI[,
246s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence")
246s Warning messages:
246s 1: In cor(x > 0) : the standard deviation is zero
246s 2: In cor(x > 0) : the standard deviation is zero
246s 3: In betadisper(z, Management) :
246s some squared distances are negative and changed to zero
246s >
246s
246s R version 4.4.3 (2025-02-28) -- "Trophy Case"
246s Copyright (C) 2025 The R Foundation for Statistical Computing
246s Platform: s390x-ibm-linux-gnu
246s
246s R is free software and comes with ABSOLUTELY NO WARRANTY.
246s You are welcome to redistribute it under certain conditions.
246s Type 'license()' or 'licence()' for distribution details.
246s
246s R is a collaborative project with many contributors.
246s Type 'contributors()' for more information and
246s 'citation()' on how to cite R or R packages in publications.
246s
246s Type 'demo()' for some demos, 'help()' for on-line help, or
246s 'help.start()' for an HTML browser interface to help.
246s Type 'q()' to quit R.
246s
246s > Stangle("intro-vegan.Rnw")
246s Writing to file intro-vegan.R
246s > source("intro-vegan.R", echo=TRUE)
246s
246s > par(mfrow = c(1, 1))
246s
246s > options(width = 72)
246s
246s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1)
246s
246s > options(SweaveHooks = list(fig = figset))
246s
246s > options(prompt = "> ", continue = " ")
246s
246s > library(vegan)
246s Loading required package: permute
246s Loading required package: lattice
247s
247s > data(dune)
247s
247s > ord <- decorana(dune)
247s
247s > ord
247s
247s Call:
247s decorana(veg = dune)
247s
247s Detrended correspondence analysis with 26 segments.
247s Rescaling of axes with 4 iterations.
247s Total inertia (scaled Chi-square): 2.1153
247s
247s DCA1 DCA2 DCA3 DCA4
247s Eigenvalues 0.5117 0.3036 0.12125 0.14267
247s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984
247s Decorana values 0.5360 0.2869 0.08136 0.04814
247s Axis lengths 3.7004 3.1166 1.30055 1.47888
247s
247s
247s > ord <- metaMDS(dune, trace = FALSE)
247s
247s > ord
247s
247s Call:
247s metaMDS(comm = dune, trace = FALSE)
247s
247s global Multidimensional Scaling using monoMDS
247s
247s Data: dune
247s Distance: bray
247s
247s Dimensions: 2
247s Stress: 0.1183186
247s Stress type 1, weak ties
247s Best solution was repeated 1 time in 20 tries
247s The best solution was from try 19 (random start)
247s Scaling: centring, PC rotation, halfchange scaling
247s Species: expanded scores based on ‘dune’
247s
247s
247s > plot(ord)
247s
247s > plot(ord)
247s
247s > plot(ord, type = "n")
247s
247s > points(ord, display = "sites", cex = 0.8, pch = 21,
247s + col = "red", bg = "yellow")
247s
247s > text(ord, display = "species", cex = 0.7, col = "blue")
247s
247s > plot(ord, type = "n")
247s
247s > points(ord, display = "sites", cex = 0.8, pch = 21,
247s + col = "red", bg = "yellow")
247s
247s > text(ord, display = "species", cex = 0.7, col = "blue")
247s
247s > text(points(plot(ord, type = "n"), "sites", cex = 0.8,
247s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7,
247s + col = "blue")
247s
247s > data(dune.env)
247s
247s > attach(dune.env)
247s
247s > plot(ord, disp = "sites", type = "n")
247s
247s > ordihull(ord, Management, col = 1:4, lwd = 3)
247s
247s > ordiellipse(ord, Management, col = 1:4, kind = "ehull",
247s + lwd = 3)
247s
247s > ordiellipse(ord, Management, col = 1:4, draw = "polygon")
247s
247s > ordispider(ord, Management, col = 1:4, label = TRUE)
247s
247s > points(ord, disp = "sites", pch = 21, col = "red",
247s + bg = "yellow", cex = 1.3)
247s
247s > plot(ord, disp = "sites", type = "n")
247s
247s > ordihull(ord, Management, col = 1:4, lwd = 3)
247s
247s > ordiellipse(ord, Management, col = 1:4, kind = "ehull",
247s + lwd = 3)
247s
247s > ordiellipse(ord, Management, col = 1:4, draw = "polygon")
247s
247s > ordispider(ord, Management, col = 1:4, label = TRUE)
247s
247s > points(ord, disp = "sites", pch = 21, col = "red",
247s + bg = "yellow", cex = 1.3)
247s
247s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env,
247s + perm = 999)
247s
247s > ord.fit
247s
247s ***VECTORS
247s
247s NMDS1 NMDS2 r2 Pr(>r)
247s A1 0.96474 0.26321 0.3649 0.015 *
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s Permutation: free
247s Number of permutations: 999
247s
247s ***FACTORS:
247s
247s Centroids:
247s NMDS1 NMDS2
247s ManagementBF -0.4534 -0.0102
247s ManagementHF -0.2636 -0.1282
247s ManagementNM 0.2958 0.5790
247s ManagementSF 0.1506 -0.4670
247s
247s Goodness of fit:
247s r2 Pr(>r)
247s Management 0.4134 0.01 **
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s Permutation: free
247s Number of permutations: 999
247s
247s
247s
247s > plot(ord, dis = "site")
247s
247s > plot(ord.fit)
247s
247s > ordisurf(ord, A1, add = TRUE)
247s
247s Family: gaussian
247s Link function: identity
247s
247s Formula:
247s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
247s
247s Estimated degrees of freedom:
247s 1.59 total = 2.59
247s
247s REML score: 41.58728
247s
247s > plot(ord, dis = "site")
247s
247s > plot(ord.fit)
247s
247s > ordisurf(ord, A1, add = TRUE)
247s
247s Family: gaussian
247s Link function: identity
247s
247s Formula:
247s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE)
247s
247s Estimated degrees of freedom:
247s 1.59 total = 2.59
247s
247s REML score: 41.58728
247s
247s > ord <- cca(dune ~ A1 + Management, data = dune.env)
247s
247s > ord
247s Call: cca(formula = dune ~ A1 + Management, data = dune.env)
247s
247s -- Model Summary --
247s
247s Inertia Proportion Rank
247s Total 2.1153 1.0000
247s Constrained 0.7798 0.3686 4
247s Unconstrained 1.3355 0.6314 15
247s
247s Inertia is scaled Chi-square
247s
247s -- Eigenvalues --
247s
247s Eigenvalues for constrained axes:
247s CCA1 CCA2 CCA3 CCA4
247s 0.3187 0.2372 0.1322 0.0917
247s
247s Eigenvalues for unconstrained axes:
247s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10
247s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415
247s CA11 CA12 CA13 CA14 CA15
247s 0.0317 0.0178 0.0116 0.0087 0.0047
247s
247s
247s > plot(ord)
247s
247s > plot(ord)
247s
247s > cca(dune ~ ., data = dune.env)
247s
247s Some constraints or conditions were aliased because they were
247s redundant. This can happen if terms are linearly dependent (collinear):
247s ‘Manure^4’
247s Call: cca(formula = dune ~ A1 + Moisture + Management + Use +
247s Manure, data = dune.env)
247s
247s -- Model Summary --
247s
247s Inertia Proportion Rank
247s Total 2.1153 1.0000
247s Constrained 1.5032 0.7106 12
247s Unconstrained 0.6121 0.2894 7
247s
247s Inertia is scaled Chi-square
247s
247s -- Note --
247s
247s Some constraints or conditions were aliased because they were
247s redundant. This can happen if terms are linearly dependent
247s (collinear): ‘Manure^4’
247s
247s -- Eigenvalues --
247s
247s Eigenvalues for constrained axes:
247s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10
247s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260
247s CCA11 CCA12
247s 0.0228 0.0108
247s
247s Eigenvalues for unconstrained axes:
247s CA1 CA2 CA3 CA4 CA5 CA6 CA7
247s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798
247s
247s
247s > anova(ord)
247s Permutation test for cca under reduced model
247s Permutation: free
247s Number of permutations: 999
247s
247s Model: cca(formula = dune ~ A1 + Management, data = dune.env)
247s Df ChiSquare F Pr(>F)
247s Model 4 0.77978 2.1896 0.001 ***
247s Residual 15 1.33549
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s
247s > anova(ord, by = "term", permutations = 199)
247s Permutation test for cca under reduced model
247s Terms added sequentially (first to last)
247s Permutation: free
247s Number of permutations: 199
247s
247s Model: cca(formula = dune ~ A1 + Management, data = dune.env)
247s Df ChiSquare F Pr(>F)
247s A1 1 0.22476 2.5245 0.010 **
247s Management 3 0.55502 2.0780 0.005 **
247s Residual 15 1.33549
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s
247s > anova(ord, by = "mar", permutations = 199)
247s Permutation test for cca under reduced model
247s Marginal effects of terms
247s Permutation: free
247s Number of permutations: 199
247s
247s Model: cca(formula = dune ~ A1 + Management, data = dune.env)
247s Df ChiSquare F Pr(>F)
247s A1 1 0.17594 1.9761 0.035 *
247s Management 3 0.55502 2.0780 0.005 **
247s Residual 15 1.33549
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s
247s > anova(ord, by = "axis", permutations = 499)
247s Permutation test for cca under reduced model
247s Forward tests for axes
247s Permutation: free
247s Number of permutations: 499
247s
247s Model: cca(formula = dune ~ A1 + Management, data = dune.env)
247s Df ChiSquare F Pr(>F)
247s CCA1 1 0.31875 3.5801 0.018 *
247s CCA2 1 0.23718 2.6640 0.146
247s CCA3 1 0.13217 1.4845 0.858
247s CCA4 1 0.09168 1.0297 1.000
247s Residual 15 1.33549
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s
247s > ord <- cca(dune ~ A1 + Management + Condition(Moisture),
247s + data = dune.env)
247s
247s > ord
247s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture),
247s data = dune.env)
247s
247s -- Model Summary --
247s
247s Inertia Proportion Rank
247s Total 2.1153 1.0000
247s Conditional 0.6283 0.2970 3
247s Constrained 0.5109 0.2415 4
247s Unconstrained 0.9761 0.4615 12
247s
247s Inertia is scaled Chi-square
247s
247s -- Eigenvalues --
247s
247s Eigenvalues for constrained axes:
247s CCA1 CCA2 CCA3 CCA4
247s 0.24932 0.12090 0.08160 0.05904
247s
247s Eigenvalues for unconstrained axes:
247s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9
247s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106
247s CA10 CA11 CA12
247s 0.02102 0.01254 0.00928
247s
247s
247s > anova(ord, by = "term", permutations = 499)
247s Permutation test for cca under reduced model
247s Terms added sequentially (first to last)
247s Permutation: free
247s Number of permutations: 499
247s
247s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env)
247s Df ChiSquare F Pr(>F)
247s A1 1 0.11543 1.4190 1.000
247s Management 3 0.39543 1.6205 0.002 **
247s Residual 12 0.97610
247s ---
247s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
247s
247s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture))
247s
247s > anova(ord, by = "term", permutations = how)
248s Permutation test for cca under reduced model
248s Terms added sequentially (first to last)
248s Plots: dune.env$Moisture, plot permutation: none
248s Permutation: free
248s Number of permutations: 499
248s
248s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env)
248s Df ChiSquare F Pr(>F)
248s A1 1 0.11543 1.4190 1.000
248s Management 3 0.39543 1.6205 0.002 **
248s Residual 12 0.97610
248s ---
248s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
248s
248s > detach(dune.env)
248s >
248s
248s R version 4.4.3 (2025-02-28) -- "Trophy Case"
248s Copyright (C) 2025 The R Foundation for Statistical Computing
248s Platform: s390x-ibm-linux-gnu
248s
248s R is free software and comes with ABSOLUTELY NO WARRANTY.
248s You are welcome to redistribute it under certain conditions.
248s Type 'license()' or 'licence()' for distribution details.
248s
248s R is a collaborative project with many contributors.
248s Type 'contributors()' for more information and
248s 'citation()' on how to cite R or R packages in publications.
248s
248s Type 'demo()' for some demos, 'help()' for on-line help, or
248s 'help.start()' for an HTML browser interface to help.
248s Type 'q()' to quit R.
248s
248s > Stangle("partitioning.Rnw")
248s Writing to file partitioning.R
248s > source("partitioning.R", echo=TRUE)
248s
248s > par(mfrow = c(1, 1))
248s Loading required package: permute
248s
248s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1)
248s
248s > options(SweaveHooks = list(fig = figset))
248s
248s > library(vegan)
248s Loading required package: lattice
249s
249s > labs <- paste("Table", 1:4)
249s
249s > cls <- c("hotpink", "skyblue", "orange", "limegreen")
249s
249s > showvarparts(2, bg = cls, Xnames = labs)
249s
249s > showvarparts(3, bg = cls, Xnames = labs)
249s
249s > showvarparts(4, bg = cls, Xnames = labs)
249s >
255s Test cca-object-tests passed
256s Test oecosimu-tests passed
259s Test vegan-tests passed
259s autopkgtest [18:37:52]: test run-unit-test: -----------------------]
260s autopkgtest [18:37:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
260s run-unit-test PASS
260s autopkgtest [18:37:53]: test pkg-r-autopkgtest: preparing testbed
261s Reading package lists...
261s Building dependency tree...
261s Reading state information...
261s Starting pkgProblemResolver with broken count: 0
261s Starting 2 pkgProblemResolver with broken count: 0
261s Done
261s The following NEW packages will be installed:
261s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu
261s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14
261s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14
261s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8
261s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev
261s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev
261s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3
261s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
261s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev
261s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev
261s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded.
261s Need to get 82.3 MB of archives.
261s After this operation, 279 MB of additional disk space will be used.
261s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB]
262s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB]
262s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [9572 kB]
272s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu3 [1028 B]
272s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B]
272s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB]
272s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250222-0ubuntu1 [49.2 kB]
272s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250222-0ubuntu1 [31.2 kB]
272s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250222-0ubuntu1 [2970 kB]
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277s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu3 [1037 kB]
278s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [18.7 MB]
299s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu3 [526 kB]
299s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B]
299s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B]
299s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu3 [2611 kB]
302s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [11.0 MB]
312s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu3 [21.8 kB]
312s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B]
312s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B]
312s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B]
312s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB]
312s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu3 [654 kB]
313s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu3 [10.3 MB]
322s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu3 [13.6 kB]
322s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B]
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322s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB]
322s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB]
322s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB]
322s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB]
330s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB]
331s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B]
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331s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB]
335s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250216-2 [407 kB]
335s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.45-1 [259 kB]
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335s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.45-1 [7080 B]
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336s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB]
336s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB]
336s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.47-1 [278 kB]
337s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB]
337s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.4-1 [183 kB]
337s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB]
337s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB]
337s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB]
337s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.3-1 [4176 B]
337s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
337s Fetched 82.3 MB in 1min 16s (1087 kB/s)
337s Selecting previously unselected package libisl23:s390x.
337s (Reading database ...
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339s Preparing to unpack .../36-libncurses-dev_6.5+20250216-2_s390x.deb ...
339s Unpacking libncurses-dev:s390x (6.5+20250216-2) ...
339s Selecting previously unselected package libpcre2-16-0:s390x.
339s Preparing to unpack .../37-libpcre2-16-0_10.45-1_s390x.deb ...
339s Unpacking libpcre2-16-0:s390x (10.45-1) ...
339s Selecting previously unselected package libpcre2-32-0:s390x.
339s Preparing to unpack .../38-libpcre2-32-0_10.45-1_s390x.deb ...
339s Unpacking libpcre2-32-0:s390x (10.45-1) ...
339s Selecting previously unselected package libpcre2-posix3:s390x.
339s Preparing to unpack .../39-libpcre2-posix3_10.45-1_s390x.deb ...
339s Unpacking libpcre2-posix3:s390x (10.45-1) ...
339s Selecting previously unselected package libpcre2-dev:s390x.
339s Preparing to unpack .../40-libpcre2-dev_10.45-1_s390x.deb ...
339s Unpacking libpcre2-dev:s390x (10.45-1) ...
339s Selecting previously unselected package libpkgconf3:s390x.
339s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ...
339s Unpacking libpkgconf3:s390x (1.8.1-4) ...
339s Selecting previously unselected package zlib1g-dev:s390x.
339s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ...
339s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
339s Selecting previously unselected package libpng-dev:s390x.
339s Preparing to unpack .../43-libpng-dev_1.6.47-1_s390x.deb ...
339s Unpacking libpng-dev:s390x (1.6.47-1) ...
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339s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ...
339s Setting up libncurses-dev:s390x (6.5+20250216-2) ...
339s Setting up libreadline-dev:s390x (8.2-6) ...
339s Setting up libpcre2-16-0:s390x (10.45-1) ...
339s Setting up libpcre2-32-0:s390x (10.45-1) ...
339s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ...
339s Setting up libpkgconf3:s390x (1.8.1-4) ...
339s Setting up libmpc3:s390x (1.3.1-1build2) ...
339s Setting up icu-devtools (76.1-1ubuntu2) ...
339s Setting up pkgconf-bin (1.8.1-4) ...
339s Setting up liblzma-dev:s390x (5.6.4-1) ...
339s Setting up libubsan1:s390x (15-20250222-0ubuntu1) ...
339s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
339s Setting up libpcre2-posix3:s390x (10.45-1) ...
339s Setting up libasan8:s390x (15-20250222-0ubuntu1) ...
339s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ...
339s Setting up libisl23:s390x (0.27-1) ...
339s Setting up libdeflate-dev:s390x (1.23-1) ...
339s Setting up libicu-dev:s390x (76.1-1ubuntu2) ...
339s Setting up libcc1-0:s390x (15-20250222-0ubuntu1) ...
339s Setting up libblas-dev:s390x (3.12.1-2) ...
339s 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
339s Setting up dctrl-tools (2.24-3build3) ...
339s Setting up libitm1:s390x (15-20250222-0ubuntu1) ...
339s Setting up libbz2-dev:s390x (1.0.8-6) ...
339s Setting up libpcre2-dev:s390x (10.45-1) ...
339s Setting up libpng-dev:s390x (1.6.47-1) ...
339s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ...
339s Setting up pkgconf:s390x (1.8.1-4) ...
339s Setting up liblapack-dev:s390x (3.12.1-2) ...
339s 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
339s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
339s Setting up cpp-14 (14.2.0-17ubuntu3) ...
339s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu3) ...
339s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu3) ...
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339s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
339s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
339s Setting up cpp (4:14.2.0-1ubuntu1) ...
339s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu3) ...
339s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
339s Setting up gcc-14 (14.2.0-17ubuntu3) ...
339s Setting up g++-14 (14.2.0-17ubuntu3) ...
339s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
339s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ...
339s Setting up gcc (4:14.2.0-1ubuntu1) ...
339s Setting up g++ (4:14.2.0-1ubuntu1) ...
339s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
339s Setting up build-essential (12.10ubuntu1) ...
339s Setting up gfortran (4:14.2.0-1ubuntu1) ...
339s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
339s 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
339s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
339s 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
339s Setting up r-base-dev (4.4.3-1) ...
339s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
339s Processing triggers for libc-bin (2.41-1ubuntu2) ...
339s Processing triggers for man-db (2.13.0-1) ...
340s Processing triggers for install-info (7.1.1-1) ...
341s autopkgtest [18:39:14]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
341s autopkgtest [18:39:14]: test pkg-r-autopkgtest: [-----------------------
341s Test: Try to load the R library vegan
341s
341s R version 4.4.3 (2025-02-28) -- "Trophy Case"
341s Copyright (C) 2025 The R Foundation for Statistical Computing
341s Platform: s390x-ibm-linux-gnu
341s
341s R is free software and comes with ABSOLUTELY NO WARRANTY.
341s You are welcome to redistribute it under certain conditions.
341s Type 'license()' or 'licence()' for distribution details.
341s
341s R is a collaborative project with many contributors.
341s Type 'contributors()' for more information and
341s 'citation()' on how to cite R or R packages in publications.
341s
341s Type 'demo()' for some demos, 'help()' for on-line help, or
341s 'help.start()' for an HTML browser interface to help.
341s Type 'q()' to quit R.
341s
341s > library('vegan')
341s Loading required package: permute
341s Loading required package: lattice
342s >
342s >
342s Other tests are currently unsupported!
342s They will be progressively added.
342s autopkgtest [18:39:15]: test pkg-r-autopkgtest: -----------------------]
342s pkg-r-autopkgtest PASS
342s autopkgtest [18:39:15]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - -
343s autopkgtest [18:39:16]: @@@@@@@@@@@@@@@@@@@@ summary
343s run-unit-test PASS
343s pkg-r-autopkgtest PASS
362s nova [W] Using flock in prodstack6-s390x
362s Creating nova instance adt-plucky-s390x-r-cran-vegan-20250315-183333-juju-7f2275-prod-proposed-migration-environment-2-1059e52a-f01f-41a0-a15b-1017c0f89e51 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
362s nova [W] Timed out waiting for 0a7b7987-6712-455a-8ce6-b522865c59ad to get deleted.