0s autopkgtest [04:36:50]: starting date and time: 2025-02-19 04:36:50+0000 0s autopkgtest [04:36:50]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [04:36:50]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vra9qe2n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-vegan --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-vegan/2.6-10+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-32.secgroup --name adt-plucky-s390x-r-cran-vegan-20250219-043649-juju-7f2275-prod-proposed-migration-environment-20-a69c807f-ddc7-4e8f-bfdd-f03303e46aa2 --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/ 128s autopkgtest [04:38:58]: testbed dpkg architecture: s390x 128s autopkgtest [04:38:58]: testbed apt version: 2.9.29 128s autopkgtest [04:38:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 128s autopkgtest [04:38:58]: testbed release detected to be: None 129s autopkgtest [04:38:59]: updating testbed package index (apt update) 129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 130s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 130s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 130s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 130s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 130s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 130s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.2 kB] 130s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [770 kB] 130s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [93.9 kB] 130s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 130s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [648 kB] 130s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [5836 B] 130s Fetched 1723 kB in 1s (1732 kB/s) 131s Reading package lists... 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Calculating upgrade... 132s The following packages were automatically installed and are no longer required: 132s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 132s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 132s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 132s linux-tools-6.11.0-8-generic 132s Use 'sudo apt autoremove' to remove them. 132s The following NEW packages will be installed: 132s libapt-pkg7.0 132s The following packages will be upgraded: 132s apt apt-utils dhcpcd-base rsyslog s390-tools s390-tools-data 132s s390-tools-signed 132s 7 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 8909 kB of archives. 132s After this operation, 3624 kB of additional disk space will be used. 132s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libapt-pkg7.0 s390x 2.9.30 [1103 kB] 133s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x apt s390x 2.9.30 [1418 kB] 133s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x apt-utils s390x 2.9.30 [214 kB] 133s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x dhcpcd-base s390x 1:10.1.0-7 [219 kB] 133s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x rsyslog s390x 8.2412.0-2ubuntu1 [536 kB] 133s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x s390-tools-data all 2.37.0-0ubuntu2 [20.4 kB] 133s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x s390-tools s390x 2.37.0-0ubuntu2 [5385 kB] 133s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x s390-tools-signed all 2.37.0-0ubuntu2 [12.4 kB] 133s Fetched 8909 kB in 1s (8095 kB/s) 133s Selecting previously unselected package libapt-pkg7.0:s390x. 133s (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 ... 80980 files and directories currently installed.) 133s Preparing to unpack .../libapt-pkg7.0_2.9.30_s390x.deb ... 133s Unpacking libapt-pkg7.0:s390x (2.9.30) ... 133s Setting up libapt-pkg7.0:s390x (2.9.30) ... 133s (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 ... 81029 files and directories currently installed.) 133s Preparing to unpack .../archives/apt_2.9.30_s390x.deb ... 133s Unpacking apt (2.9.30) over (2.9.29) ... 134s Setting up apt (2.9.30) ... 134s (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 ... 81029 files and directories currently installed.) 134s Preparing to unpack .../0-apt-utils_2.9.30_s390x.deb ... 134s Unpacking apt-utils (2.9.30) over (2.9.29) ... 134s Preparing to unpack .../1-dhcpcd-base_1%3a10.1.0-7_s390x.deb ... 134s Unpacking dhcpcd-base (1:10.1.0-7) over (1:10.1.0-6) ... 134s Preparing to unpack .../2-rsyslog_8.2412.0-2ubuntu1_s390x.deb ... 134s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 134s Preparing to unpack .../3-s390-tools-data_2.37.0-0ubuntu2_all.deb ... 134s Unpacking s390-tools-data (2.37.0-0ubuntu2) over (2.37.0-0ubuntu1) ... 134s Preparing to unpack .../4-s390-tools_2.37.0-0ubuntu2_s390x.deb ... 134s Unpacking s390-tools (2.37.0-0ubuntu2) over (2.37.0-0ubuntu1) ... 134s Preparing to unpack .../5-s390-tools-signed_2.37.0-0ubuntu2_all.deb ... 134s Unpacking s390-tools-signed (2.37.0-0ubuntu2) over (2.37.0-0ubuntu1) ... 134s Setting up apt-utils (2.9.30) ... 134s Setting up rsyslog (8.2412.0-2ubuntu1) ... 134s info: The user `syslog' is already a member of `adm'. 135s Setting up s390-tools-signed (2.37.0-0ubuntu2) ... 135s Setting up dhcpcd-base (1:10.1.0-7) ... 135s Setting up s390-tools-data (2.37.0-0ubuntu2) ... 135s Setting up s390-tools (2.37.0-0ubuntu2) ... 136s Processing triggers for libc-bin (2.40-4ubuntu1) ... 136s Processing triggers for man-db (2.13.0-1) ... 137s Processing triggers for initramfs-tools (0.145ubuntu2) ... 137s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 137s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 141s Using config file '/etc/zipl.conf' 142s Building bootmap in '/boot' 142s Adding IPL section 'ubuntu' (default) 142s Preparing boot device for LD-IPL: vda (0000). 142s Done. 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 143s The following packages will be REMOVED: 143s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 143s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 143s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 143s linux-tools-6.11.0-8-generic* 143s 0 upgraded, 0 newly installed, 9 to remove and 0 not upgraded. 143s After this operation, 167 MB disk space will be freed. 143s (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 ... 81030 files and directories currently installed.) 143s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 143s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 143s Removing libpython3.12t64:s390x (3.12.9-1) ... 143s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 143s Removing libnsl2:s390x (1.3.0-3build3) ... 143s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 143s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 143s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 144s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 144s Processing triggers for libc-bin (2.40-4ubuntu1) ... 144s (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 ... 55930 files and directories currently installed.) 144s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 144s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 144s autopkgtest [04:39:14]: upgrading testbed (apt dist-upgrade and autopurge) 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 145s Starting 2 pkgProblemResolver with broken count: 0 145s Done 145s Entering ResolveByKeep 145s 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s autopkgtest [04:39:16]: rebooting testbed after setup commands that affected boot 167s autopkgtest [04:39:37]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 15:05:57 UTC 2025 169s autopkgtest [04:39:39]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 171s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (dsc) [2211 B] 171s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (tar) [1207 kB] 171s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe r-cran-vegan 2.6-10+dfsg-1 (diff) [6328 B] 172s gpgv: Signature made Sun Feb 2 23:43:24 2025 UTC 172s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 172s gpgv: issuer "plessy@debian.org" 172s gpgv: Can't check signature: No public key 172s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1.dsc: no acceptable signature found 172s autopkgtest [04:39:42]: testing package r-cran-vegan version 2.6-10+dfsg-1 174s autopkgtest [04:39:44]: build not needed 177s autopkgtest [04:39:47]: test run-unit-test: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s The following NEW packages will be installed: 178s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 178s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 178s libdeflate0 libfontconfig1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 178s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 178s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 178s liblapack3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 178s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 178s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 178s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 178s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 178s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 178s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 178s x11-common xdg-utils zip 178s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 67.6 MB of archives. 178s After this operation, 160 MB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 178s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 179s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 179s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-2ubuntu1 [37.5 kB] 179s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-2ubuntu1 [150 kB] 179s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig s390x 2.15.0-2ubuntu1 [191 kB] 179s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 179s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 179s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 179s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 179s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 179s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 179s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 179s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 179s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libdatrie1 s390x 0.2.13-3build1 [20.6 kB] 179s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 179s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250213-1ubuntu1 [620 kB] 179s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 15-20250213-1ubuntu1 [151 kB] 179s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 179s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 179s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 179s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libice6 s390x 2:1.1.1-1 [45.4 kB] 179s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 179s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 179s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 179s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 179s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 179s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 179s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 179s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libthai-data all 0.1.29-2build1 [158 kB] 179s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libthai0 s390x 0.1.29-2build1 [20.7 kB] 179s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libpango-1.0-0 s390x 1.56.1-1 [253 kB] 179s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libpangoft2-1.0-0 s390x 1.56.1-1 [50.3 kB] 179s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libpangocairo-1.0-0 s390x 1.56.1-1 [28.3 kB] 179s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper2 s390x 2.2.5-0.3 [17.2 kB] 179s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libpaper-utils s390x 2.2.5-0.3 [15.3 kB] 179s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 179s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libsm6 s390x 2:1.2.4-1 [18.4 kB] 179s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libtcl8.6 s390x 8.6.16+dfsg-1 [1034 kB] 179s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 179s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 179s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 179s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] 179s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] 179s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libtk8.6 s390x 8.6.16-1 [830 kB] 179s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x libxt6t64 s390x 1:1.2.1-1.2build1 [184 kB] 179s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x node-normalize.css all 8.0.1-5 [10.8 kB] 179s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x zip s390x 3.0-14ubuntu2 [187 kB] 179s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x unzip s390x 6.0-28ubuntu6 [186 kB] 179s Get:50 http://ftpmaster.internal/ubuntu plucky/main s390x xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 179s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-core s390x 4.4.2-1build1 [28.6 MB] 180s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-cluster s390x 2.1.8-1 [577 kB] 180s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-commonmark s390x 1.9.2-2 [142 kB] 180s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-evaluate all 1.0.3-1 [114 kB] 180s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-xfun s390x 0.50+dfsg-1 [568 kB] 180s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-highr all 0.11+dfsg-1 [38.5 kB] 180s Get:57 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-yaml s390x 2.3.10-1 [113 kB] 180s Get:58 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 180s Get:59 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-knitr all 1.49+dfsg-1 [859 kB] 180s Get:60 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-lattice s390x 0.22-6-1 [1340 kB] 180s Get:61 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-markdown all 1.13-1 [162 kB] 180s Get:62 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mass s390x 7.3-64-1 [1113 kB] 180s Get:63 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-matrix s390x 1.7-2-1 [4441 kB] 180s Get:64 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-nlme s390x 3.1.167-1 [2323 kB] 181s Get:65 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-mgcv s390x 1.9-1-1 [3348 kB] 181s Get:66 http://ftpmaster.internal/ubuntu plucky/universe s390x r-cran-permute all 0.9-7-1 [228 kB] 181s Get:67 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x r-cran-vegan s390x 2.6-10+dfsg-1 [3149 kB] 181s Preconfiguring packages ... 181s Fetched 67.6 MB in 3s (23.3 MB/s) 181s Selecting previously unselected package libfreetype6:s390x. 181s (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 ... 55928 files and directories currently installed.) 181s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 181s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 181s Selecting previously unselected package fonts-dejavu-mono. 181s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 181s Unpacking fonts-dejavu-mono (2.37-8) ... 181s Selecting previously unselected package fonts-dejavu-core. 181s Preparing to unpack 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... 186s Setting up r-base-core (4.4.2-1build1) ... 186s Creating config file /etc/R/Renviron with new version 186s Setting up r-cran-lattice (0.22-6-1) ... 186s Setting up r-cran-nlme (3.1.167-1) ... 186s Setting up r-cran-cluster (2.1.8-1) ... 186s Setting up r-cran-commonmark (1.9.2-2) ... 186s Setting up r-cran-permute (0.9-7-1) ... 186s Setting up r-cran-xfun (0.50+dfsg-1) ... 186s Setting up r-cran-yaml (2.3.10-1) ... 186s Setting up r-cran-evaluate (1.0.3-1) ... 186s Setting up r-cran-highr (0.11+dfsg-1) ... 186s Setting up r-cran-mass (7.3-64-1) ... 186s Setting up r-cran-markdown (1.13-1) ... 186s Setting up r-cran-matrix (1.7-2-1) ... 186s Setting up r-cran-knitr (1.49+dfsg-1) ... 186s Setting up r-cran-mgcv (1.9-1-1) ... 186s Setting up r-cran-vegan (2.6-10+dfsg-1) ... 186s Processing triggers for libc-bin (2.40-4ubuntu1) ... 186s Processing triggers for man-db (2.13.0-1) ... 187s Processing triggers for install-info (7.1.1-1) ... 188s autopkgtest [04:39:58]: test run-unit-test: [----------------------- 189s 189s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 189s Copyright (C) 2024 The R Foundation for Statistical Computing 189s Platform: s390x-ibm-linux-gnu 189s 189s R is free software and comes with ABSOLUTELY NO WARRANTY. 189s You are welcome to redistribute it under certain conditions. 189s Type 'license()' or 'licence()' for distribution details. 189s 189s R is a collaborative project with many contributors. 189s Type 'contributors()' for more information and 189s 'citation()' on how to cite R or R packages in publications. 189s 189s Type 'demo()' for some demos, 'help()' for on-line help, or 189s 'help.start()' for an HTML browser interface to help. 189s Type 'q()' to quit R. 189s 189s > Stangle("decision-vegan.Rnw") 189s Writing to file decision-vegan.R 189s > source("decision-vegan.R", echo=TRUE) 189s 189s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 189s 189s > options(SweaveHooks = list(fig = figset)) 189s 189s > options(prompt = "> ", continue = " ") 189s 189s > options(width = 55) 189s 189s > require(vegan) 189s Loading required package: vegan 189s Loading required package: permute 189s Loading required package: lattice 190s 190s > data(sipoo) 190s 190s > mod <- nestedtemp(sipoo) 190s 190s > plot(mod, "i") 190s 190s > x <- mod$c["Falcsubb"] 190s 190s > y <- 1 - mod$r["Svartholm"] 190s 190s > points(x, y, pch = 16, cex = 1.5) 190s 190s > abline(x + y, -1, lty = 2) 190s 190s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 190s 190s > cross <- function(x, a, p) f(x, p) - a + x 190s 190s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 190s 190s > arrows(x, y, r, f(r, mod$p), lwd = 4) 190s 190s > library(vegan) 190s 190s > data(varespec) 190s 190s > data(varechem) 190s 190s > orig <- cca(varespec ~ Al + K, varechem) 190s 190s > plot(orig, dis = c("lc", "bp")) 190s 190s > plot(orig, dis = c("lc", "bp")) 190s 190s > i <- sample(nrow(varespec)) 190s 190s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 190s 190s > plot(shuff, dis = c("lc", "bp")) 190s 190s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 190s + dis = "lc"))) 190s 190s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 190s + dis = "lc"))) 190s 190s > tmp1 <- rda(varespec ~ Al + K, varechem) 190s 190s > i <- sample(nrow(varespec)) 190s 190s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 190s 190s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 190s + dis = "lc"))) 190s 190s > orig 190s Call: cca(formula = varespec ~ Al + K, data = 190s varechem) 190s 190s -- Model Summary -- 190s 190s Inertia Proportion Rank 190s Total 2.0832 1.0000 190s Constrained 0.4760 0.2285 2 190s Unconstrained 1.6072 0.7715 21 190s 190s Inertia is scaled Chi-square 190s 190s -- Eigenvalues -- 190s 190s Eigenvalues for constrained axes: 190s CCA1 CCA2 190s 0.3608 0.1152 190s 190s Eigenvalues for unconstrained axes: 190s CA1 CA2 CA3 CA4 CA5 CA6 CA7 190s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 190s CA8 190s 0.0757 190s (Showing 8 of 21 unconstrained eigenvalues) 190s 190s 190s > shuff 190s Call: cca(formula = varespec[i, ] ~ Al + K, data = 190s varechem) 190s 190s -- Model Summary -- 190s 190s Inertia Proportion Rank 190s Total 2.08320 1.00000 190s Constrained 0.13807 0.06628 2 190s Unconstrained 1.94513 0.93372 21 190s 190s Inertia is scaled Chi-square 190s 190s -- Eigenvalues -- 190s 190s Eigenvalues for constrained axes: 190s CCA1 CCA2 190s 0.10822 0.02985 190s 190s Eigenvalues for unconstrained axes: 190s CA1 CA2 CA3 CA4 CA5 CA6 CA7 190s 0.4926 0.3427 0.2125 0.1929 0.1530 0.1211 0.1089 190s CA8 190s 0.0872 190s (Showing 8 of 21 unconstrained eigenvalues) 190s 190s 190s > plot(procrustes(orig, shuff)) 190s 190s > tmp1 <- rda(varespec ~ ., varechem) 190s 190s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 190s 190s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 190s + scores(tmp2, dis = "lc", choi = 1:14)) 190s 190s > max(residuals(proc)) 190s [1] 3.174699e-14 190s 190s > data(dune) 190s 190s > data(dune.env) 190s 190s > orig <- cca(dune ~ Moisture, dune.env) 190s 190s > plot(orig, dis = "lc") 190s 190s > plot(orig, display = "wa", type = "points") 190s 190s > ordispider(orig, col = "red") 190s 190s > text(orig, dis = "cn", col = "blue") 190s 190s > plot(orig, display = "wa", type = "points") 190s 190s > ordispider(orig, col = "red") 190s 190s > text(orig, dis = "cn", col = "blue") 190s > 191s 191s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 191s Copyright (C) 2024 The R Foundation for Statistical Computing 191s Platform: s390x-ibm-linux-gnu 191s 191s R is free software and comes with ABSOLUTELY NO WARRANTY. 191s You are welcome to redistribute it under certain conditions. 191s Type 'license()' or 'licence()' for distribution details. 191s 191s R is a collaborative project with many contributors. 191s Type 'contributors()' for more information and 191s 'citation()' on how to cite R or R packages in publications. 191s 191s Type 'demo()' for some demos, 'help()' for on-line help, or 191s 'help.start()' for an HTML browser interface to help. 191s Type 'q()' to quit R. 191s 191s > Stangle("diversity-vegan.Rnw") 191s Writing to file diversity-vegan.R 191s > source("diversity-vegan.R", echo=TRUE) 191s 191s > par(mfrow = c(1, 1)) 191s 191s > options(width = 55) 191s 191s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 191s 191s > options(SweaveHooks = list(fig = figset)) 191s 191s > options(prompt = "> ", continue = " ")Loading required package: permute 191s 191s 191s > library(vegan) 191s Loading required package: lattice 192s 192s > data(BCI) 192s 192s > H <- diversity(BCI) 192s 192s > J <- H/log(specnumber(BCI)) 192s 192s > k <- sample(nrow(BCI), 6) 192s 192s > R <- renyi(BCI[k, ]) 192s 192s > print(plot(R)) 192s 192s > alpha <- fisher.alpha(BCI) 192s 192s > quantile(rowSums(BCI)) 192s 0% 25% 50% 75% 100% 192s 340.0 409.0 428.0 443.5 601.0 192s 192s > Srar <- rarefy(BCI, min(rowSums(BCI))) 192s 192s > S2 <- rarefy(BCI, 2) 192s 192s > all(rank(Srar) == rank(S2)) 192s [1] FALSE 192s 192s > range(diversity(BCI, "simp") - (S2 - 1)) 192s [1] -0.002868298 -0.001330663 192s 192s > data(dune) 192s 192s > data(dune.taxon) 192s 192s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 192s 192s > mod <- taxondive(dune, taxdis) 192s 192s > plot(mod) 192s 192s > tr <- hclust(taxdis, "aver") 192s 192s > mod <- treedive(dune, tr) 192s 192s > k <- sample(nrow(BCI), 1) 192s 192s > fish <- fisherfit(BCI[k, ]) 192s forced matching of 'tree' labels and 'comm' names 192s 192s > fish 192s 192s Fisher log series model 192s No. of species: 84 192s Fisher alpha: 30.99091 192s 192s 192s > plot(fish) 192s 192s > prestondistr(BCI[k, ]) 192s 192s Preston lognormal model 192s Method: maximized likelihood to log2 abundances 192s No. of species: 84 192s 192s mode width S0 192s 1.082775 1.824562 21.034404 192s 192s Frequencies by Octave 192s 0 1 2 3 4 192s Observed 15.50000 22.00000 15.5000 15.50000 9.500000 192s Fitted 17.63828 21.01277 18.5376 12.11063 5.858995 192s 5 6 192s Observed 5.00000 1.0000000 192s Fitted 2.09905 0.5568849 192s 192s 192s > rad <- radfit(BCI[k, ]) 192s 192s > rad 192s 192s RAD models, family poisson 192s No. of species 84, total abundance 435 192s 192s par1 par2 par3 Deviance 192s Null 46.7795 192s Preemption 0.051075 29.5066 192s Lognormal 1.0585 1.1021 18.8511 192s Zipf 0.13279 -0.80984 48.4277 192s Mandelbrot 19.857 -2.034 14.519 4.7586 192s AIC BIC 192s Null 296.7328 296.7328 192s Preemption 281.4600 283.8908 192s Lognormal 272.8045 277.6661 192s Zipf 302.3811 307.2427 192s Mandelbrot 260.7120 268.0044 192s 192s > print(radlattice(rad)) 192s 192s > sac <- specaccum(BCI) 192s 192s > plot(sac, ci.type = "polygon", ci.col = "yellow") 192s 192s > sac <- specaccum(BCI) 192s 192s > plot(sac, ci.type = "polygon", ci.col = "yellow") 192s 192s > ncol(BCI)/mean(specnumber(BCI)) - 1 192s [1] 1.478519 192s 192s > beta <- vegdist(BCI, binary = TRUE) 192s 192s > mean(beta) 192s [1] 0.3399075 192s 192s > betadiver(help = TRUE) 192s 1 "w" = (b+c)/(2*a+b+c) 192s 2 "-1" = (b+c)/(2*a+b+c) 192s 3 "c" = (b+c)/2 192s 4 "wb" = b+c 192s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 192s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 192s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 192s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 192s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 192s (2*a+b+c))-1 192s 8 "t" = (b+c)/(2*a+b+c) 192s 9 "me" = (b+c)/(2*a+b+c) 192s 10 "j" = a/(a+b+c) 192s 11 "sor" = 2*a/(2*a+b+c) 192s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 192s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 192s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 192s 15 "cc" = (b+c)/(a+b+c) 192s 16 "g" = (b+c)/(a+b+c) 192s 17 "-3" = pmin.int(b,c)/(a+b+c) 192s 18 "l" = (b+c)/2 192s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 192s 20 "hk" = (b+c)/(2*a+b+c) 192s 21 "rlb" = a/(a+c) 192s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 192s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 192s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 192s 192s > z <- betadiver(BCI, "z") 192s 192s > quantile(z) 192s 0% 25% 50% 75% 100% 192s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 192s 192s > data(dune) 192s 192s > data(dune.env) 192s 192s > z <- betadiver(dune, "z") 192s 192s > mod <- with(dune.env, betadisper(z, Management)) 192s 192s > mod 192s 192s Homogeneity of multivariate dispersions 192s 192s Call: betadisper(d = z, group = Management) 192s 192s No. of Positive Eigenvalues: 12 192s No. of Negative Eigenvalues: 7 192s 192s Average distance to median: 192s BF HF NM SF 192s 0.2532 0.2512 0.4406 0.3635 192s 192s Eigenvalues for PCoA axes: 192s (Showing 8 of 19 eigenvalues) 192s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 192s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 192s PCoA7 PCoA8 192s 0.16128 0.08099 192s 192s > boxplot(mod) 192s 192s > specpool(BCI) 192s Species chao chao.se jack1 jack1.se jack2 192s All 225 236.3732 6.54361 245.58 5.650522 247.8722 192s boot boot.se n 192s All 235.6862 3.468888 50 192s 192s > s <- sample(nrow(BCI), 25) 192s 192s > specpool(BCI[s, ]) 192s Species chao chao.se jack1 jack1.se jack2 192s All 208 225.28 9.257905 231.04 6.427939 239.0133 192s boot boot.se n 192s All 219.2044 3.81239 25 192s 192s > estimateR(BCI[k, ]) 192s 2 192s S.obs 84.000000 192s S.chao1 117.214286 192s se.chao1 15.918953 192s S.ACE 117.317307 192s se.ACE 5.571998 192s 192s > veiledspec(prestondistr(BCI[k, ])) 192s Extrapolated Observed Veiled 192s 96.20084 84.00000 12.20084 192s 192s > veiledspec(BCI[k, ]) 192s Extrapolated Observed Veiled 192s 103.14426 84.00000 19.14426 192s 192s > smo <- beals(BCI) 193s 193s > j <- which(colnames(BCI) == "Ceiba.pentandra") 193s 193s > plot(beals(BCI, species = j, include = FALSE), BCI[, 193s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 193s 193s > j <- which(colnames(BCI) == "Ceiba.pentandra") 193s 193s > plot(beals(BCI, species = j, include = FALSE), BCI[, 193s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 193s Warning messages: 193s 1: In cor(x > 0) : the standard deviation is zero 193s 2: In cor(x > 0) : the standard deviation is zero 193s 3: In betadisper(z, Management) : 193s some squared distances are negative and changed to zero 193s > 193s 193s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 193s Copyright (C) 2024 The R Foundation for Statistical Computing 193s Platform: s390x-ibm-linux-gnu 193s 193s R is free software and comes with ABSOLUTELY NO WARRANTY. 193s You are welcome to redistribute it under certain conditions. 193s Type 'license()' or 'licence()' for distribution details. 193s 193s R is a collaborative project with many contributors. 193s Type 'contributors()' for more information and 193s 'citation()' on how to cite R or R packages in publications. 193s 193s Type 'demo()' for some demos, 'help()' for on-line help, or 193s 'help.start()' for an HTML browser interface to help. 193s Type 'q()' to quit R. 193s 193s > Stangle("intro-vegan.Rnw") 193s Writing to file intro-vegan.R 193s > source("intro-vegan.R", echo=TRUE) 193s 193s > par(mfrow = c(1, 1)) 193s 193s > options(width = 72) 193s 193s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 193s 193s > options(SweaveHooks = list(fig = figset)) 193s 193s > options(prompt = "> ", continue = " ") 193s 193s > library(vegan) 193s Loading required package: permute 193s Loading required package: lattice 194s 194s > data(dune) 194s 194s > ord <- decorana(dune) 194s 194s > ord 194s 194s Call: 194s decorana(veg = dune) 194s 194s Detrended correspondence analysis with 26 segments. 194s Rescaling of axes with 4 iterations. 194s Total inertia (scaled Chi-square): 2.1153 194s 194s DCA1 DCA2 DCA3 DCA4 194s Eigenvalues 0.5117 0.3036 0.12125 0.14267 194s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 194s Decorana values 0.5360 0.2869 0.08136 0.04814 194s Axis lengths 3.7004 3.1166 1.30055 1.47888 194s 194s 194s > ord <- metaMDS(dune, trace = FALSE) 194s 194s > ord 194s 194s Call: 194s metaMDS(comm = dune, trace = FALSE) 194s 194s global Multidimensional Scaling using monoMDS 194s 194s Data: dune 194s Distance: bray 194s 194s Dimensions: 2 194s Stress: 0.1183186 194s Stress type 1, weak ties 194s Best solution was repeated 5 times in 20 tries 194s The best solution was from try 7 (random start) 194s Scaling: centring, PC rotation, halfchange scaling 194s Species: expanded scores based on ‘dune’ 194s 194s 194s > plot(ord) 194s 194s > plot(ord) 194s 194s > plot(ord, type = "n") 194s 194s > points(ord, display = "sites", cex = 0.8, pch = 21, 194s + col = "red", bg = "yellow") 194s 194s > text(ord, display = "species", cex = 0.7, col = "blue") 194s 194s > plot(ord, type = "n") 194s 194s > points(ord, display = "sites", cex = 0.8, pch = 21, 194s + col = "red", bg = "yellow") 194s 194s > text(ord, display = "species", cex = 0.7, col = "blue") 194s 194s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 194s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 194s + col = "blue") 194s 194s > data(dune.env) 194s 194s > attach(dune.env) 194s 194s > plot(ord, disp = "sites", type = "n") 194s 194s > ordihull(ord, Management, col = 1:4, lwd = 3) 194s 194s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 194s + lwd = 3) 194s 194s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 194s 194s > ordispider(ord, Management, col = 1:4, label = TRUE) 194s 194s > points(ord, disp = "sites", pch = 21, col = "red", 194s + bg = "yellow", cex = 1.3) 194s 194s > plot(ord, disp = "sites", type = "n") 194s 194s > ordihull(ord, Management, col = 1:4, lwd = 3) 194s 194s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 194s + lwd = 3) 194s 194s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 194s 194s > ordispider(ord, Management, col = 1:4, label = TRUE) 194s 194s > points(ord, disp = "sites", pch = 21, col = "red", 194s + bg = "yellow", cex = 1.3) 194s 194s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 194s + perm = 999) 195s 195s > ord.fit 195s 195s ***VECTORS 195s 195s NMDS1 NMDS2 r2 Pr(>r) 195s A1 0.96474 0.26322 0.3649 0.015 * 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s Permutation: free 195s Number of permutations: 999 195s 195s ***FACTORS: 195s 195s Centroids: 195s NMDS1 NMDS2 195s ManagementBF -0.4534 -0.0102 195s ManagementHF -0.2636 -0.1282 195s ManagementNM 0.2958 0.5790 195s ManagementSF 0.1506 -0.4670 195s 195s Goodness of fit: 195s r2 Pr(>r) 195s Management 0.4134 0.005 ** 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s Permutation: free 195s Number of permutations: 999 195s 195s 195s 195s > plot(ord, dis = "site") 195s 195s > plot(ord.fit) 195s 195s > ordisurf(ord, A1, add = TRUE) 195s 195s Family: gaussian 195s Link function: identity 195s 195s Formula: 195s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 195s 195s Estimated degrees of freedom: 195s 1.59 total = 2.59 195s 195s REML score: 41.58727 195s 195s > plot(ord, dis = "site") 195s 195s > plot(ord.fit) 195s 195s > ordisurf(ord, A1, add = TRUE) 195s 195s Family: gaussian 195s Link function: identity 195s 195s Formula: 195s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 195s 195s Estimated degrees of freedom: 195s 1.59 total = 2.59 195s 195s REML score: 41.58727 195s 195s > ord <- cca(dune ~ A1 + Management, data = dune.env) 195s 195s > ord 195s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 195s 195s -- Model Summary -- 195s 195s Inertia Proportion Rank 195s Total 2.1153 1.0000 195s Constrained 0.7798 0.3686 4 195s Unconstrained 1.3355 0.6314 15 195s 195s Inertia is scaled Chi-square 195s 195s -- Eigenvalues -- 195s 195s Eigenvalues for constrained axes: 195s CCA1 CCA2 CCA3 CCA4 195s 0.3187 0.2372 0.1322 0.0917 195s 195s Eigenvalues for unconstrained axes: 195s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 195s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 195s CA11 CA12 CA13 CA14 CA15 195s 0.0317 0.0178 0.0116 0.0087 0.0047 195s 195s 195s > plot(ord) 195s 195s > plot(ord) 195s 195s > cca(dune ~ ., data = dune.env) 195s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 195s Manure, data = dune.env) 195s 195s -- Model Summary -- 195s 195s Inertia Proportion Rank 195s Total 2.1153 1.0000 195s Constrained 1.5032 0.7106 12 195s Unconstrained 0.6121 0.2894 7 195s 195s Inertia is scaled Chi-square 195s 195s -- Note -- 195s 195s Some constraints or conditions were aliased because they were 195s redundant. This can happen if terms are linearly dependent 195s (collinear): ‘Manure^4’ 195s 195s -- Eigenvalues -- 195s 195s Eigenvalues for constrained axes: 195s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 195s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 195s CCA11 CCA12 195s 0.0228 0.0108 195s 195s Eigenvalues for unconstrained axes: 195s CA1 CA2 CA3 CA4 CA5 CA6 CA7 195s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 195s 195s 195s > anova(ord) 195s 195s Some constraints or conditions were aliased because they were 195s redundant. This can happen if terms are linearly dependent (collinear): 195s ‘Manure^4’ 195s Permutation test for cca under reduced model 195s Permutation: free 195s Number of permutations: 999 195s 195s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 195s Df ChiSquare F Pr(>F) 195s Model 4 0.77978 2.1896 0.001 *** 195s Residual 15 1.33549 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > anova(ord, by = "term", permutations = 199) 195s Permutation test for cca under reduced model 195s Terms added sequentially (first to last) 195s Permutation: free 195s Number of permutations: 199 195s 195s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 195s Df ChiSquare F Pr(>F) 195s A1 1 0.22476 2.5245 0.005 ** 195s Management 3 0.55502 2.0780 0.005 ** 195s Residual 15 1.33549 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > anova(ord, by = "mar", permutations = 199) 195s Permutation test for cca under reduced model 195s Marginal effects of terms 195s Permutation: free 195s Number of permutations: 199 195s 195s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 195s Df ChiSquare F Pr(>F) 195s A1 1 0.17594 1.9761 0.030 * 195s Management 3 0.55502 2.0780 0.015 * 195s Residual 15 1.33549 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > anova(ord, by = "axis", permutations = 499) 195s Permutation test for cca under reduced model 195s Forward tests for axes 195s Permutation: free 195s Number of permutations: 499 195s 195s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 195s Df ChiSquare F Pr(>F) 195s CCA1 1 0.31875 3.5801 0.016 * 195s CCA2 1 0.23718 2.6640 0.108 195s CCA3 1 0.13217 1.4845 0.872 195s CCA4 1 0.09168 1.0297 1.000 195s Residual 15 1.33549 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 195s + data = dune.env) 195s 195s > ord 195s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 195s data = dune.env) 195s 195s -- Model Summary -- 195s 195s Inertia Proportion Rank 195s Total 2.1153 1.0000 195s Conditional 0.6283 0.2970 3 195s Constrained 0.5109 0.2415 4 195s Unconstrained 0.9761 0.4615 12 195s 195s Inertia is scaled Chi-square 195s 195s -- Eigenvalues -- 195s 195s Eigenvalues for constrained axes: 195s CCA1 CCA2 CCA3 CCA4 195s 0.24932 0.12090 0.08160 0.05904 195s 195s Eigenvalues for unconstrained axes: 195s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 195s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 195s CA10 CA11 CA12 195s 0.02102 0.01254 0.00928 195s 195s 195s > anova(ord, by = "term", permutations = 499) 195s Permutation test for cca under reduced model 195s Terms added sequentially (first to last) 195s Permutation: free 195s Number of permutations: 499 195s 195s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 195s Df ChiSquare F Pr(>F) 195s A1 1 0.11543 1.4190 1.000 195s Management 3 0.39543 1.6205 0.002 ** 195s Residual 12 0.97610 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 195s 195s > anova(ord, by = "term", permutations = how) 195s Permutation test for cca under reduced model 195s Terms added sequentially (first to last) 195s Plots: dune.env$Moisture, plot permutation: none 195s Permutation: free 195s Number of permutations: 499 195s 195s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 195s Df ChiSquare F Pr(>F) 195s A1 1 0.11543 1.4190 1.000 195s Management 3 0.39543 1.6205 0.002 ** 195s Residual 12 0.97610 195s --- 195s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 195s 195s > detach(dune.env) 195s > 195s 195s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 195s Copyright (C) 2024 The R Foundation for Statistical Computing 195s Platform: s390x-ibm-linux-gnu 195s 195s R is free software and comes with ABSOLUTELY NO WARRANTY. 195s You are welcome to redistribute it under certain conditions. 195s Type 'license()' or 'licence()' for distribution details. 195s 195s R is a collaborative project with many contributors. 195s Type 'contributors()' for more information and 195s 'citation()' on how to cite R or R packages in publications. 195s 195s Type 'demo()' for some demos, 'help()' for on-line help, or 195s 'help.start()' for an HTML browser interface to help. 195s Type 'q()' to quit R. 195s 196s > Stangle("partitioning.Rnw") 196s Writing to file partitioning.R 196s > source("partitioning.R", echo=TRUE) 196s 196s > par(mfrow = c(1, 1)) 196s 196s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 196s 196s > options(SweaveHooks = list(fig = figset)) 196s 196s > library(vegan) 196s Loading required package: permute 196s Loading required package: lattice 197s 197s > labs <- paste("Table", 1:4) 197s 197s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 197s 197s > showvarparts(2, bg = cls, Xnames = labs) 197s 197s > showvarparts(3, bg = cls, Xnames = labs) 197s 197s > showvarparts(4, bg = cls, Xnames = labs) 197s > 206s --- cca-object-tests.Rout.save_ 2025-02-19 04:40:16.112782084 +0000 206s +++ cca-object-tests.Rout_ 2025-02-19 04:40:16.112782084 +0000 206s @@ -1,4 +1,4 @@ 206s - 206s + 206s 206s R is free software and comes with ABSOLUTELY NO WARRANTY. 206s You are welcome to redistribute it under certain conditions. 206s autopkgtest [04:40:16]: test run-unit-test: -----------------------] 206s run-unit-test FAIL non-zero exit status 1 206s autopkgtest [04:40:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 207s autopkgtest [04:40:17]: test pkg-r-autopkgtest: preparing testbed 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 208s The following NEW packages will be installed: 208s build-essential cpp cpp-14 cpp-14-s390x-linux-gnu cpp-s390x-linux-gnu 208s dctrl-tools g++ g++-14 g++-14-s390x-linux-gnu g++-s390x-linux-gnu gcc gcc-14 208s gcc-14-s390x-linux-gnu gcc-s390x-linux-gnu gfortran gfortran-14 208s gfortran-14-s390x-linux-gnu gfortran-s390x-linux-gnu icu-devtools libasan8 208s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 208s libgfortran-14-dev libicu-dev libisl23 libitm1 libjpeg-dev 208s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblzma-dev libmpc3 208s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 208s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 208s libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev zlib1g-dev 208s 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 82.2 MB of archives. 208s After this operation, 278 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libisl23 s390x 0.27-1 [704 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libmpc3 s390x 1.3.1-1build2 [57.8 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [9571 kB] 209s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-14 s390x 14.2.0-17ubuntu1 [1030 B] 209s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x cpp-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [5556 B] 209s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x cpp s390x 4:14.2.0-1ubuntu1 [22.4 kB] 209s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libcc1-0 s390x 15-20250213-1ubuntu1 [49.2 kB] 209s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libitm1 s390x 15-20250213-1ubuntu1 [31.2 kB] 209s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libasan8 s390x 15-20250213-1ubuntu1 [2970 kB] 209s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libubsan1 s390x 15-20250213-1ubuntu1 [1213 kB] 209s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-14-dev s390x 14.2.0-17ubuntu1 [1037 kB] 209s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [18.7 MB] 210s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14 s390x 14.2.0-17ubuntu1 [526 kB] 210s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1204 B] 210s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x gcc s390x 4:14.2.0-1ubuntu1 [5004 B] 210s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++-14-dev s390x 14.2.0-17ubuntu1 [2611 kB] 210s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [11.0 MB] 211s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x g++-14 s390x 14.2.0-17ubuntu1 [21.8 kB] 211s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x g++-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [956 B] 211s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x g++ s390x 4:14.2.0-1ubuntu1 [1080 B] 211s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x build-essential s390x 12.10ubuntu1 [4930 B] 211s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x dctrl-tools s390x 2.24-3build3 [106 kB] 211s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran-14-dev s390x 14.2.0-17ubuntu1 [654 kB] 212s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14-s390x-linux-gnu s390x 14.2.0-17ubuntu1 [10.3 MB] 213s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-14 s390x 14.2.0-17ubuntu1 [13.6 kB] 213s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran-s390x-linux-gnu s390x 4:14.2.0-1ubuntu1 [1012 B] 213s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x gfortran s390x 4:14.2.0-1ubuntu1 [1160 B] 213s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x icu-devtools s390x 76.1-1ubuntu2 [225 kB] 213s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x libblas-dev s390x 3.12.1-2 [254 kB] 213s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x libbz2-dev s390x 1.0.8-6 [39.1 kB] 213s Get:31 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate-dev s390x 1.23-1 [52.2 kB] 213s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libicu-dev s390x 76.1-1ubuntu2 [12.2 MB] 214s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8-dev s390x 2.1.5-3ubuntu2 [281 kB] 214s Get:34 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] 214s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] 214s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack-dev s390x 3.12.1-2 [5967 kB] 215s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libncurses-dev s390x 6.5+20250125-2 [407 kB] 215s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-16-0 s390x 10.42-4ubuntu3 [236 kB] 215s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-32-0 s390x 10.42-4ubuntu3 [221 kB] 215s Get:40 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-posix3 s390x 10.42-4ubuntu3 [6820 B] 215s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x libpcre2-dev s390x 10.42-4ubuntu3 [815 kB] 215s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libpkgconf3 s390x 1.8.1-4 [31.2 kB] 215s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 215s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x libpng-dev s390x 1.6.46-4 [283 kB] 215s Get:45 http://ftpmaster.internal/ubuntu plucky/main s390x libreadline-dev s390x 8.2-6 [187 kB] 215s Get:46 http://ftpmaster.internal/ubuntu plucky/main s390x liblzma-dev s390x 5.6.3-1 [183 kB] 215s Get:47 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf-bin s390x 1.8.1-4 [21.5 kB] 215s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x pkgconf s390x 1.8.1-4 [16.7 kB] 215s Get:49 http://ftpmaster.internal/ubuntu plucky/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] 215s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x r-base-dev all 4.4.2-1build1 [4342 B] 215s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 215s Fetched 82.2 MB in 7s (11.2 MB/s) 215s Selecting previously unselected package libisl23:s390x. 215s (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 ... 63902 files and directories currently installed.) 215s Preparing to unpack .../00-libisl23_0.27-1_s390x.deb ... 215s Unpacking libisl23:s390x (0.27-1) ... 215s Selecting previously unselected package libmpc3:s390x. 215s Preparing to unpack .../01-libmpc3_1.3.1-1build2_s390x.deb ... 215s Unpacking libmpc3:s390x (1.3.1-1build2) ... 215s Selecting previously unselected package cpp-14-s390x-linux-gnu. 215s Preparing to unpack .../02-cpp-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 215s Unpacking cpp-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 215s Selecting previously unselected package cpp-14. 215s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu1_s390x.deb ... 215s Unpacking cpp-14 (14.2.0-17ubuntu1) ... 215s Selecting previously unselected package cpp-s390x-linux-gnu. 215s Preparing to unpack .../04-cpp-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 215s Unpacking cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 215s Selecting previously unselected package cpp. 215s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_s390x.deb ... 215s Unpacking cpp (4:14.2.0-1ubuntu1) ... 215s Selecting previously unselected package libcc1-0:s390x. 215s Preparing to unpack .../06-libcc1-0_15-20250213-1ubuntu1_s390x.deb ... 215s Unpacking libcc1-0:s390x (15-20250213-1ubuntu1) ... 216s Selecting previously unselected package libitm1:s390x. 216s Preparing to unpack .../07-libitm1_15-20250213-1ubuntu1_s390x.deb ... 216s Unpacking libitm1:s390x (15-20250213-1ubuntu1) ... 216s Selecting previously unselected package libasan8:s390x. 216s Preparing to unpack .../08-libasan8_15-20250213-1ubuntu1_s390x.deb ... 216s Unpacking libasan8:s390x (15-20250213-1ubuntu1) ... 216s Selecting previously unselected package libubsan1:s390x. 216s Preparing to unpack .../09-libubsan1_15-20250213-1ubuntu1_s390x.deb ... 216s Unpacking libubsan1:s390x (15-20250213-1ubuntu1) ... 216s Selecting previously unselected package libgcc-14-dev:s390x. 216s Preparing to unpack .../10-libgcc-14-dev_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking libgcc-14-dev:s390x (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gcc-14-s390x-linux-gnu. 216s Preparing to unpack .../11-gcc-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking gcc-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gcc-14. 216s Preparing to unpack .../12-gcc-14_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking gcc-14 (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gcc-s390x-linux-gnu. 216s Preparing to unpack .../13-gcc-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package gcc. 216s Preparing to unpack .../14-gcc_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking gcc (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package libstdc++-14-dev:s390x. 216s Preparing to unpack .../15-libstdc++-14-dev_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking libstdc++-14-dev:s390x (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package g++-14-s390x-linux-gnu. 216s Preparing to unpack .../16-g++-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking g++-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package g++-14. 216s Preparing to unpack .../17-g++-14_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking g++-14 (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package g++-s390x-linux-gnu. 216s Preparing to unpack .../18-g++-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package g++. 216s Preparing to unpack .../19-g++_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking g++ (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package build-essential. 216s Preparing to unpack .../20-build-essential_12.10ubuntu1_s390x.deb ... 216s Unpacking build-essential (12.10ubuntu1) ... 216s Selecting previously unselected package dctrl-tools. 216s Preparing to unpack .../21-dctrl-tools_2.24-3build3_s390x.deb ... 216s Unpacking dctrl-tools (2.24-3build3) ... 216s Selecting previously unselected package libgfortran-14-dev:s390x. 216s Preparing to unpack .../22-libgfortran-14-dev_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking libgfortran-14-dev:s390x (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gfortran-14-s390x-linux-gnu. 216s Preparing to unpack .../23-gfortran-14-s390x-linux-gnu_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gfortran-14. 216s Preparing to unpack .../24-gfortran-14_14.2.0-17ubuntu1_s390x.deb ... 216s Unpacking gfortran-14 (14.2.0-17ubuntu1) ... 216s Selecting previously unselected package gfortran-s390x-linux-gnu. 216s Preparing to unpack .../25-gfortran-s390x-linux-gnu_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 216s Selecting previously unselected package gfortran. 216s Preparing to unpack .../26-gfortran_4%3a14.2.0-1ubuntu1_s390x.deb ... 216s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 217s Selecting previously unselected package icu-devtools. 217s Preparing to unpack .../27-icu-devtools_76.1-1ubuntu2_s390x.deb ... 217s Unpacking icu-devtools (76.1-1ubuntu2) ... 217s Selecting previously unselected package libblas-dev:s390x. 217s Preparing to unpack .../28-libblas-dev_3.12.1-2_s390x.deb ... 217s Unpacking libblas-dev:s390x (3.12.1-2) ... 217s Selecting previously unselected package libbz2-dev:s390x. 217s Preparing to unpack .../29-libbz2-dev_1.0.8-6_s390x.deb ... 217s Unpacking libbz2-dev:s390x (1.0.8-6) ... 217s Selecting previously unselected package libdeflate-dev:s390x. 217s Preparing to unpack .../30-libdeflate-dev_1.23-1_s390x.deb ... 217s Unpacking libdeflate-dev:s390x (1.23-1) ... 217s Selecting previously unselected package libicu-dev:s390x. 217s Preparing to unpack .../31-libicu-dev_76.1-1ubuntu2_s390x.deb ... 217s Unpacking libicu-dev:s390x (76.1-1ubuntu2) ... 217s Selecting previously unselected package libjpeg-turbo8-dev:s390x. 217s Preparing to unpack .../32-libjpeg-turbo8-dev_2.1.5-3ubuntu2_s390x.deb ... 217s Unpacking libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 217s Selecting previously unselected package libjpeg8-dev:s390x. 217s Preparing to unpack .../33-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... 217s Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... 217s Selecting previously unselected package libjpeg-dev:s390x. 217s Preparing to unpack .../34-libjpeg-dev_8c-2ubuntu11_s390x.deb ... 217s Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... 217s Selecting previously unselected package liblapack-dev:s390x. 217s Preparing to unpack .../35-liblapack-dev_3.12.1-2_s390x.deb ... 217s Unpacking liblapack-dev:s390x (3.12.1-2) ... 217s Selecting previously unselected package libncurses-dev:s390x. 217s Preparing to unpack .../36-libncurses-dev_6.5+20250125-2_s390x.deb ... 217s Unpacking libncurses-dev:s390x (6.5+20250125-2) ... 217s Selecting previously unselected package libpcre2-16-0:s390x. 217s Preparing to unpack .../37-libpcre2-16-0_10.42-4ubuntu3_s390x.deb ... 217s Unpacking libpcre2-16-0:s390x (10.42-4ubuntu3) ... 217s Selecting previously unselected package libpcre2-32-0:s390x. 217s Preparing to unpack .../38-libpcre2-32-0_10.42-4ubuntu3_s390x.deb ... 217s Unpacking libpcre2-32-0:s390x (10.42-4ubuntu3) ... 217s Selecting previously unselected package libpcre2-posix3:s390x. 217s Preparing to unpack .../39-libpcre2-posix3_10.42-4ubuntu3_s390x.deb ... 217s Unpacking libpcre2-posix3:s390x (10.42-4ubuntu3) ... 217s Selecting previously unselected package libpcre2-dev:s390x. 217s Preparing to unpack .../40-libpcre2-dev_10.42-4ubuntu3_s390x.deb ... 217s Unpacking libpcre2-dev:s390x (10.42-4ubuntu3) ... 217s Selecting previously unselected package libpkgconf3:s390x. 217s Preparing to unpack .../41-libpkgconf3_1.8.1-4_s390x.deb ... 217s Unpacking libpkgconf3:s390x (1.8.1-4) ... 217s Selecting previously unselected package zlib1g-dev:s390x. 217s Preparing to unpack .../42-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 217s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 217s Selecting previously unselected package libpng-dev:s390x. 217s Preparing to unpack .../43-libpng-dev_1.6.46-4_s390x.deb ... 217s Unpacking libpng-dev:s390x (1.6.46-4) ... 217s Selecting previously unselected package libreadline-dev:s390x. 217s Preparing to unpack .../44-libreadline-dev_8.2-6_s390x.deb ... 217s Unpacking libreadline-dev:s390x (8.2-6) ... 217s Selecting previously unselected package liblzma-dev:s390x. 217s Preparing to unpack .../45-liblzma-dev_5.6.3-1_s390x.deb ... 217s Unpacking liblzma-dev:s390x (5.6.3-1) ... 217s Selecting previously unselected package pkgconf-bin. 217s Preparing to unpack .../46-pkgconf-bin_1.8.1-4_s390x.deb ... 217s Unpacking pkgconf-bin (1.8.1-4) ... 217s Selecting previously unselected package pkgconf:s390x. 217s Preparing to unpack .../47-pkgconf_1.8.1-4_s390x.deb ... 217s Unpacking pkgconf:s390x (1.8.1-4) ... 217s Selecting previously unselected package libtirpc-dev:s390x. 217s Preparing to unpack .../48-libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... 217s Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) ... 217s Selecting previously unselected package r-base-dev. 217s Preparing to unpack .../49-r-base-dev_4.4.2-1build1_all.deb ... 217s Unpacking r-base-dev (4.4.2-1build1) ... 217s Selecting previously unselected package pkg-r-autopkgtest. 217s Preparing to unpack .../50-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 217s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 217s Setting up libjpeg-turbo8-dev:s390x (2.1.5-3ubuntu2) ... 217s Setting up libncurses-dev:s390x (6.5+20250125-2) ... 217s Setting up libreadline-dev:s390x (8.2-6) ... 217s Setting up libpcre2-16-0:s390x (10.42-4ubuntu3) ... 217s Setting up libpcre2-32-0:s390x (10.42-4ubuntu3) ... 217s Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... 217s Setting up libpkgconf3:s390x (1.8.1-4) ... 217s Setting up libmpc3:s390x (1.3.1-1build2) ... 217s Setting up icu-devtools (76.1-1ubuntu2) ... 217s Setting up pkgconf-bin (1.8.1-4) ... 217s Setting up liblzma-dev:s390x (5.6.3-1) ... 217s Setting up libubsan1:s390x (15-20250213-1ubuntu1) ... 217s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 217s Setting up libpcre2-posix3:s390x (10.42-4ubuntu3) ... 217s Setting up libasan8:s390x (15-20250213-1ubuntu1) ... 217s Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... 217s Setting up libisl23:s390x (0.27-1) ... 217s Setting up libdeflate-dev:s390x (1.23-1) ... 217s Setting up libicu-dev:s390x (76.1-1ubuntu2) ... 217s Setting up libcc1-0:s390x (15-20250213-1ubuntu1) ... 217s Setting up libblas-dev:s390x (3.12.1-2) ... 217s 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 217s Setting up dctrl-tools (2.24-3build3) ... 217s Setting up libitm1:s390x (15-20250213-1ubuntu1) ... 217s Setting up libbz2-dev:s390x (1.0.8-6) ... 217s Setting up libpcre2-dev:s390x (10.42-4ubuntu3) ... 217s Setting up libpng-dev:s390x (1.6.46-4) ... 217s Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... 217s Setting up pkgconf:s390x (1.8.1-4) ... 217s Setting up liblapack-dev:s390x (3.12.1-2) ... 217s 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 217s Setting up cpp-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 217s Setting up cpp-14 (14.2.0-17ubuntu1) ... 217s Setting up libgcc-14-dev:s390x (14.2.0-17ubuntu1) ... 217s Setting up libstdc++-14-dev:s390x (14.2.0-17ubuntu1) ... 217s Setting up libgfortran-14-dev:s390x (14.2.0-17ubuntu1) ... 217s Setting up cpp-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 217s Setting up gcc-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 217s Setting up gcc-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 217s Setting up g++-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 217s Setting up cpp (4:14.2.0-1ubuntu1) ... 217s Setting up gfortran-14-s390x-linux-gnu (14.2.0-17ubuntu1) ... 217s Setting up g++-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 217s Setting up gcc-14 (14.2.0-17ubuntu1) ... 217s Setting up g++-14 (14.2.0-17ubuntu1) ... 217s Setting up gfortran-14 (14.2.0-17ubuntu1) ... 217s Setting up gfortran-s390x-linux-gnu (4:14.2.0-1ubuntu1) ... 217s Setting up gcc (4:14.2.0-1ubuntu1) ... 217s Setting up g++ (4:14.2.0-1ubuntu1) ... 217s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 217s Setting up build-essential (12.10ubuntu1) ... 217s Setting up gfortran (4:14.2.0-1ubuntu1) ... 217s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 217s 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 217s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 217s 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 217s Setting up r-base-dev (4.4.2-1build1) ... 217s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 217s Processing triggers for libc-bin (2.40-4ubuntu1) ... 217s Processing triggers for man-db (2.13.0-1) ... 217s Processing triggers for install-info (7.1.1-1) ... 218s autopkgtest [04:40:28]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 218s autopkgtest [04:40:28]: test pkg-r-autopkgtest: [----------------------- 218s Test: Try to load the R library vegan 218s 218s R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 218s Copyright (C) 2024 The R Foundation for Statistical Computing 218s Platform: s390x-ibm-linux-gnu 218s 218s R is free software and comes with ABSOLUTELY NO WARRANTY. 218s You are welcome to redistribute it under certain conditions. 218s Type 'license()' or 'licence()' for distribution details. 218s 218s R is a collaborative project with many contributors. 218s Type 'contributors()' for more information and 218s 'citation()' on how to cite R or R packages in publications. 218s 218s Type 'demo()' for some demos, 'help()' for on-line help, or 218s 'help.start()' for an HTML browser interface to help. 218s Type 'q()' to quit R. 218s 218s > library('vegan') 218s Loading required package: permute 218s Loading required package: lattice 220s > 220s > 220s Other tests are currently unsupported! 220s They will be progressively added. 220s autopkgtest [04:40:30]: test pkg-r-autopkgtest: -----------------------] 220s pkg-r-autopkgtest PASS 220s autopkgtest [04:40:30]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 221s autopkgtest [04:40:31]: @@@@@@@@@@@@@@@@@@@@ summary 221s run-unit-test FAIL non-zero exit status 1 221s pkg-r-autopkgtest PASS 238s nova [W] Using flock in prodstack6-s390x 238s Creating nova instance adt-plucky-s390x-r-cran-vegan-20250219-043649-juju-7f2275-prod-proposed-migration-environment-20-a69c807f-ddc7-4e8f-bfdd-f03303e46aa2 from image adt/ubuntu-plucky-s390x-server-20250218.img (UUID d4b3949f-1d31-4fe6-9e99-080adec067af)... 238s nova [W] Timed out waiting for 69ee6c7c-06c1-4998-ac98-5ed4f6a3ae90 to get deleted.