0s autopkgtest [16:03:32]: starting date and time: 2025-03-15 16:03:32+0000 0s autopkgtest [16:03:32]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:03:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.620odftz/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-22.secgroup --name adt-plucky-arm64-r-cran-vegan-20250315-160332-juju-7f2275-prod-proposed-migration-environment-2-851a44a9-9786-460a-a809-098cf1a677f0 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 240s autopkgtest [16:07:32]: testbed dpkg architecture: arm64 240s autopkgtest [16:07:32]: testbed apt version: 2.9.33 240s autopkgtest [16:07:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 240s autopkgtest [16:07:32]: testbed release detected to be: None 241s autopkgtest [16:07:33]: updating testbed package index (apt update) 242s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 242s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 242s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 242s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 242s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 243s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 243s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 243s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 243s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 243s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 243s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 243s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 243s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 243s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 244s Fetched 1078 kB in 2s (570 kB/s) 245s Reading package lists... 246s Reading package lists... 246s Building dependency tree... 246s Reading state information... 247s Calculating upgrade... 248s Calculating upgrade... 249s The following packages will be upgraded: 249s pinentry-curses python3-jinja2 strace 249s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 249s Need to get 647 kB of archives. 249s After this operation, 11.3 kB of additional disk space will be used. 249s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 250s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 250s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 250s Fetched 647 kB in 1s (558 kB/s) 250s (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 ... 117701 files and directories currently installed.) 250s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 250s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 251s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 251s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 251s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 251s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 251s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 251s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 251s Setting up strace (6.13+ds-1ubuntu1) ... 251s Processing triggers for man-db (2.13.0-1) ... 252s Reading package lists... 252s Building dependency tree... 252s Reading state information... 252s Solving dependencies... 253s The following packages will be REMOVED: 253s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 253s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 253s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 253s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 253s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 253s After this operation, 267 MB disk space will be freed. 253s (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 ... 117701 files and directories currently installed.) 253s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 253s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 253s Removing libpython3.12t64:arm64 (3.12.9-1) ... 253s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 253s Removing libnsl2:arm64 (1.3.0-3build3) ... 253s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 253s Removing libunwind8:arm64 (1.6.2-3.1) ... 253s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 254s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 255s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 255s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 255s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 255s /etc/kernel/postrm.d/initramfs-tools: 255s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 255s /etc/kernel/postrm.d/zz-flash-kernel: 255s flash-kernel: Kernel 6.11.0-8-generic has been removed. 256s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 256s /etc/kernel/postrm.d/zz-update-grub: 256s Sourcing file `/etc/default/grub' 256s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 256s Generating grub configuration file ... 256s Found linux image: /boot/vmlinuz-6.14.0-10-generic 256s Found initrd image: /boot/initrd.img-6.14.0-10-generic 256s Warning: os-prober will not be executed to detect other bootable partitions. 256s Systems on them will not be added to the GRUB boot configuration. 256s Check GRUB_DISABLE_OS_PROBER documentation entry. 256s Adding boot menu entry for UEFI Firmware Settings ... 256s done 256s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 257s Processing triggers for libc-bin (2.41-1ubuntu1) ... 257s (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 ... 81650 files and directories currently installed.) 257s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 257s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 257s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 257s autopkgtest [16:07:49]: upgrading testbed (apt dist-upgrade and autopurge) 257s Reading package lists... 257s Building dependency tree... 257s Reading state information... 258s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 258s Starting 2 pkgProblemResolver with broken count: 0 258s Done 259s Entering ResolveByKeep 259s 259s Calculating upgrade... 260s The following packages will be upgraded: 260s libc-bin libc-dev-bin libc6 libc6-dev locales 260s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 260s Need to get 9530 kB of archives. 260s After this operation, 0 B of additional disk space will be used. 260s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 262s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 262s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 265s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 266s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 271s Preconfiguring packages ... 271s Fetched 9530 kB in 11s (834 kB/s) 272s (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 ... 81647 files and directories currently installed.) 272s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 272s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 272s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 272s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 272s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 272s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 272s Setting up libc6:arm64 (2.41-1ubuntu2) ... 272s (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 ... 81647 files and directories currently installed.) 272s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 272s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 272s Setting up libc-bin (2.41-1ubuntu2) ... 272s (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 ... 81647 files and directories currently installed.) 272s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 272s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 273s Setting up locales (2.41-1ubuntu2) ... 273s Generating locales (this might take a while)... 276s en_US.UTF-8... done 276s Generation complete. 276s Setting up libc-dev-bin (2.41-1ubuntu2) ... 276s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 277s Processing triggers for man-db (2.13.0-1) ... 277s Processing triggers for systemd (257.3-1ubuntu3) ... 278s Reading package lists... 279s Building dependency tree... 279s Reading state information... 279s Starting pkgProblemResolver with broken count: 0 279s Starting 2 pkgProblemResolver with broken count: 0 279s Done 280s Solving dependencies... 280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s autopkgtest [16:08:12]: rebooting testbed after setup commands that affected boot 303s autopkgtest [16:08:35]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 306s autopkgtest [16:08:38]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 310s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (dsc) [2293 B] 310s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (tar) [1207 kB] 310s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (diff) [6736 B] 310s gpgv: Signature made Sun Mar 9 19:53:35 2025 UTC 310s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 310s gpgv: Can't check signature: No public key 310s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1ubuntu2.dsc: no acceptable signature found 311s autopkgtest [16:08:43]: testing package r-cran-vegan version 2.6-10+dfsg-1ubuntu2 311s autopkgtest [16:08:43]: build not needed 313s autopkgtest [16:08:45]: test run-unit-test: preparing testbed 313s Reading package lists... 314s Building dependency tree... 314s Reading state information... 314s Starting pkgProblemResolver with broken count: 0 314s Starting 2 pkgProblemResolver with broken count: 0 314s Done 315s The following NEW packages will be installed: 315s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 315s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 315s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 315s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 315s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 315s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 315s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 315s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 315s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 315s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 315s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 315s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 315s x11-common xdg-utils zip 315s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 315s Need to get 65.3 MB of archives. 315s After this operation, 158 MB of additional disk space will be used. 315s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 316s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 317s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 317s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 318s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 318s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 318s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 322s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 322s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 323s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 323s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 323s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 323s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 324s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 324s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 324s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 325s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 325s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 325s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 326s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 326s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 326s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 326s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 326s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 326s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 327s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 327s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 327s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 331s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 331s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 332s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 332s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 332s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 332s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 332s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 332s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 332s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 332s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 332s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 334s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 334s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 334s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 334s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 335s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 335s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 336s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 336s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 node-normalize.css all 8.0.1-5 [10.8 kB] 336s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 336s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 337s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 337s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 375s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-cluster arm64 2.1.8-1 [568 kB] 376s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-commonmark arm64 1.9.2-2 [129 kB] 376s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-evaluate all 1.0.3-1 [114 kB] 376s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-xfun arm64 0.51+dfsg-1 [573 kB] 377s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 377s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-yaml arm64 2.3.10-1 [108 kB] 377s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 384s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 385s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 387s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-markdown all 1.13-1 [162 kB] 387s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mass arm64 7.3-64-1 [1110 kB] 388s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 394s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 397s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 401s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-permute all 0.9-7-1 [228 kB] 401s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-vegan arm64 2.6-10+dfsg-1ubuntu2 [3136 kB] 405s Preconfiguring packages ... 406s Fetched 65.3 MB in 1min 30s (726 kB/s) 406s Selecting previously unselected package fonts-dejavu-mono. 406s (Reading database ... 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test run-unit-test: [----------------------- 416s 416s R version 4.4.3 (2025-02-28) -- "Trophy Case" 416s Copyright (C) 2025 The R Foundation for Statistical Computing 416s Platform: aarch64-unknown-linux-gnu 416s 416s R is free software and comes with ABSOLUTELY NO WARRANTY. 416s You are welcome to redistribute it under certain conditions. 416s Type 'license()' or 'licence()' for distribution details. 416s 416s R is a collaborative project with many contributors. 416s Type 'contributors()' for more information and 416s 'citation()' on how to cite R or R packages in publications. 416s 416s Type 'demo()' for some demos, 'help()' for on-line help, or 416s 'help.start()' for an HTML browser interface to help. 416s Type 'q()' to quit R. 416s 416s > Stangle("decision-vegan.Rnw") 416s Writing to file decision-vegan.R 416s > source("decision-vegan.R", echo=TRUE) 416s 416s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 416s 416s > options(SweaveHooks = list(fig = figset)) 416s 416s > options(prompt = "> ", continue = " ") 416s 416s > options(width = 55) 416s 416s > require(vegan) 416s Loading required package: vegan 416s Loading required package: permute 416s Loading required package: lattice 417s 417s > data(sipoo) 417s 417s > mod <- nestedtemp(sipoo) 417s 417s > plot(mod, "i") 417s 417s > x <- mod$c["Falcsubb"] 417s 417s > y <- 1 - mod$r["Svartholm"] 417s 417s > points(x, y, pch = 16, cex = 1.5) 417s 417s > abline(x + y, -1, lty = 2) 417s 417s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 417s 417s > cross <- function(x, a, p) f(x, p) - a + x 417s 417s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 417s 417s > arrows(x, y, r, f(r, mod$p), lwd = 4) 417s 417s > library(vegan) 417s 417s > data(varespec) 417s 417s > data(varechem) 417s 417s > orig <- cca(varespec ~ Al + K, varechem) 417s 417s > plot(orig, dis = c("lc", "bp")) 417s 417s > plot(orig, dis = c("lc", "bp")) 417s 417s > i <- sample(nrow(varespec)) 417s 417s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 417s 417s > plot(shuff, dis = c("lc", "bp")) 417s 417s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 417s + dis = "lc"))) 417s 417s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 417s + dis = "lc"))) 417s 417s > tmp1 <- rda(varespec ~ Al + K, varechem) 417s 417s > i <- sample(nrow(varespec)) 417s 417s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 417s 417s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 417s + dis = "lc"))) 417s 417s > orig 417s Call: cca(formula = varespec ~ Al + K, data = 417s varechem) 417s 417s -- Model Summary -- 417s 417s Inertia Proportion Rank 417s Total 2.0832 1.0000 417s Constrained 0.4760 0.2285 2 417s Unconstrained 1.6072 0.7715 21 417s 417s Inertia is scaled Chi-square 417s 417s -- Eigenvalues -- 417s 417s Eigenvalues for constrained axes: 417s CCA1 CCA2 417s 0.3608 0.1152 417s 417s Eigenvalues for unconstrained axes: 417s CA1 CA2 CA3 CA4 CA5 CA6 CA7 417s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 417s CA8 417s 0.0757 417s (Showing 8 of 21 unconstrained eigenvalues) 417s 417s 417s > shuff 417s Call: cca(formula = varespec[i, ] ~ Al + K, data = 417s varechem) 417s 417s -- Model Summary -- 417s 417s Inertia Proportion Rank 417s Total 2.0832 1.0000 417s Constrained 0.2142 0.1028 2 417s Unconstrained 1.8690 0.8972 21 417s 417s Inertia is scaled Chi-square 417s 417s -- Eigenvalues -- 417s 417s Eigenvalues for constrained axes: 417s CCA1 CCA2 417s 0.14177 0.07245 417s 417s Eigenvalues for unconstrained axes: 417s CA1 CA2 CA3 CA4 CA5 CA6 CA7 417s 0.5051 0.3298 0.1986 0.1727 0.1242 0.1168 0.1034 417s CA8 417s 0.0849 417s (Showing 8 of 21 unconstrained eigenvalues) 417s 417s 417s > plot(procrustes(orig, shuff)) 417s 417s > tmp1 <- rda(varespec ~ ., varechem) 417s 417s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 417s 417s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 417s + scores(tmp2, dis = "lc", choi = 1:14)) 417s 417s > max(residuals(proc)) 417s [1] 2.715473e-14 417s 417s > data(dune) 417s 417s > data(dune.env) 417s 417s > orig <- cca(dune ~ Moisture, dune.env) 417s 417s > plot(orig, dis = "lc") 417s 417s > plot(orig, display = "wa", type = "points") 417s 417s > ordispider(orig, col = "red") 417s 417s > text(orig, dis = "cn", col = "blue") 417s 417s > plot(orig, display = "wa", type = "points") 417s 417s > ordispider(orig, col = "red") 417s 417s > text(orig, dis = "cn", col = "blue") 417s > 417s 417s R version 4.4.3 (2025-02-28) -- "Trophy Case" 417s Copyright (C) 2025 The R Foundation for Statistical Computing 417s Platform: aarch64-unknown-linux-gnu 417s 417s R is free software and comes with ABSOLUTELY NO WARRANTY. 417s You are welcome to redistribute it under certain conditions. 417s Type 'license()' or 'licence()' for distribution details. 417s 417s R is a collaborative project with many contributors. 417s Type 'contributors()' for more information and 417s 'citation()' on how to cite R or R packages in publications. 417s 417s Type 'demo()' for some demos, 'help()' for on-line help, or 417s 'help.start()' for an HTML browser interface to help. 417s Type 'q()' to quit R. 417s 417s > Stangle("diversity-vegan.Rnw") 417s Writing to file diversity-vegan.R 417s > source("diversity-vegan.R", echo=TRUE) 417s 417s > par(mfrow = c(1, 1)) 417s 417s > options(width = 55) 417s 417s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 417s 417s > options(SweaveHooks = list(fig = figset)) 417s 417s > options(prompt = "> ", continue = " ") 417s 417s > library(vegan) 417s Loading required package: permute 417s Loading required package: lattice 418s 418s > data(BCI) 418s 418s > H <- diversity(BCI) 418s 418s > J <- H/log(specnumber(BCI)) 418s 418s > k <- sample(nrow(BCI), 6) 418s 418s > R <- renyi(BCI[k, ]) 418s 418s > print(plot(R)) 419s 419s > alpha <- fisher.alpha(BCI) 419s 419s > quantile(rowSums(BCI)) 419s 0% 25% 50% 75% 100% 419s 340.0 409.0 428.0 443.5 601.0 419s 419s > Srar <- rarefy(BCI, min(rowSums(BCI))) 419s 419s > S2 <- rarefy(BCI, 2) 419s 419s > all(rank(Srar) == rank(S2)) 419s [1] FALSE 419s 419s > range(diversity(BCI, "simp") - (S2 - 1)) 419s [1] -0.002868298 -0.001330663 419s 419s > data(dune) 419s 419s > data(dune.taxon) 419s 419s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 419s 419s > mod <- taxondive(dune, taxdis) 419s 419s > plot(mod) 419s 419s > tr <- hclust(taxdis, "aver") 419s 419s > mod <- treedive(dune, tr) 419s forced matching of 'tree' labels and 'comm' names 419s 419s > k <- sample(nrow(BCI), 1) 419s 419s > fish <- fisherfit(BCI[k, ]) 419s 419s > fish 419s 419s Fisher log series model 419s No. of species: 89 419s Fisher alpha: 38.71442 419s 419s 419s > plot(fish) 419s 419s > prestondistr(BCI[k, ]) 419s 419s Preston lognormal model 419s Method: maximized likelihood to log2 abundances 419s No. of species: 89 419s 419s mode width S0 419s 1.078353 1.421681 26.908896 419s 419s Frequencies by Octave 419s 0 1 2 3 4 419s Observed 14.000 27.50000 25.50000 11.50000 6.500000 419s Fitted 20.182 26.86806 21.80902 10.79355 3.257016 419s 5 6 419s Observed 3.0000000 1.0000000 419s Fitted 0.5992439 0.0672226 419s 419s 419s > rad <- radfit(BCI[k, ]) 419s 419s > rad 419s 419s RAD models, family poisson 419s No. of species 89, total abundance 347 419s 419s par1 par2 par3 Deviance 419s Null 54.2031 419s Preemption 0.042572 61.4592 419s Lognormal 0.82084 1.056 16.9629 419s Zipf 0.12873 -0.80419 11.3023 419s Mandelbrot 0.32478 -1.0534 2.0929 4.6291 419s AIC BIC 419s Null 305.1437 305.1437 419s Preemption 314.3998 316.8884 419s Lognormal 271.9035 276.8808 419s Zipf 266.2429 271.2202 419s Mandelbrot 261.5697 269.0356 419s 419s > print(radlattice(rad)) 419s 419s > sac <- specaccum(BCI) 419s 419s > plot(sac, ci.type = "polygon", ci.col = "yellow") 419s 419s > sac <- specaccum(BCI) 419s 419s > plot(sac, ci.type = "polygon", ci.col = "yellow") 419s 419s > ncol(BCI)/mean(specnumber(BCI)) - 1 419s [1] 1.478519 419s 419s > beta <- vegdist(BCI, binary = TRUE) 419s 419s > mean(beta) 419s [1] 0.3399075 419s 419s > betadiver(help = TRUE) 419s 1 "w" = (b+c)/(2*a+b+c) 419s 2 "-1" = (b+c)/(2*a+b+c) 419s 3 "c" = (b+c)/2 419s 4 "wb" = b+c 419s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 419s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 419s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 419s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 419s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 419s (2*a+b+c))-1 419s 8 "t" = (b+c)/(2*a+b+c) 419s 9 "me" = (b+c)/(2*a+b+c) 419s 10 "j" = a/(a+b+c) 419s 11 "sor" = 2*a/(2*a+b+c) 419s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 419s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 419s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 419s 15 "cc" = (b+c)/(a+b+c) 419s 16 "g" = (b+c)/(a+b+c) 419s 17 "-3" = pmin.int(b,c)/(a+b+c) 419s 18 "l" = (b+c)/2 419s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 419s 20 "hk" = (b+c)/(2*a+b+c) 419s 21 "rlb" = a/(a+c) 419s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 419s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 419s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 419s 419s > z <- betadiver(BCI, "z") 419s 419s > quantile(z) 419s 0% 25% 50% 75% 100% 419s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 419s 419s > data(dune) 419s 419s > data(dune.env) 419s 419s > z <- betadiver(dune, "z") 419s 419s > mod <- with(dune.env, betadisper(z, Management)) 419s 419s > mod 419s 419s Homogeneity of multivariate dispersions 419s 419s Call: betadisper(d = z, group = Management) 419s 419s No. of Positive Eigenvalues: 12 419s No. of Negative Eigenvalues: 7 419s 419s Average distance to median: 419s BF HF NM SF 419s 0.2532 0.2512 0.4406 0.3635 419s 419s Eigenvalues for PCoA axes: 419s (Showing 8 of 19 eigenvalues) 419s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 419s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 419s PCoA7 PCoA8 419s 0.16128 0.08099 419s 419s > boxplot(mod) 419s 419s > specpool(BCI) 419s Species chao chao.se jack1 jack1.se jack2 419s All 225 236.3732 6.54361 245.58 5.650522 247.8722 419s boot boot.se n 419s All 235.6862 3.468888 50 419s 419s > s <- sample(nrow(BCI), 25) 419s 419s > specpool(BCI[s, ]) 419s Species chao chao.se jack1 jack1.se jack2 419s All 201 216.488 8.665684 222.12 6.282929 229.135 419s boot boot.se n 419s All 211.6258 3.792972 25 419s 419s > estimateR(BCI[k, ]) 419s 18 419s S.obs 89.000000 419s S.chao1 102.500000 419s se.chao1 6.839297 419s S.ACE 115.975135 419s se.ACE 5.459537 419s 419s > veiledspec(prestondistr(BCI[k, ])) 419s Extrapolated Observed Veiled 419s 95.893238 89.000000 6.893238 419s 419s > veiledspec(BCI[k, ]) 419s Extrapolated Observed Veiled 419s 100.72986 89.00000 11.72986 419s 419s > smo <- beals(BCI) 419s 419s > j <- which(colnames(BCI) == "Ceiba.pentandra") 419s 419s > plot(beals(BCI, species = j, include = FALSE), BCI[, 419s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 419s 419s > j <- which(colnames(BCI) == "Ceiba.pentandra") 419s 419s > plot(beals(BCI, species = j, include = FALSE), BCI[, 419s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 419s Warning messages: 419s 1: In cor(x > 0) : the standard deviation is zero 419s 2: In cor(x > 0) : the standard deviation is zero 419s 3: In betadisper(z, Management) : 419s some squared distances are negative and changed to zero 419s > 419s 419s R version 4.4.3 (2025-02-28) -- "Trophy Case" 419s Copyright (C) 2025 The R Foundation for Statistical Computing 419s Platform: aarch64-unknown-linux-gnu 419s 419s R is free software and comes with ABSOLUTELY NO WARRANTY. 419s You are welcome to redistribute it under certain conditions. 419s Type 'license()' or 'licence()' for distribution details. 419s 419s R is a collaborative project with many contributors. 419s Type 'contributors()' for more information and 419s 'citation()' on how to cite R or R packages in publications. 419s 419s Type 'demo()' for some demos, 'help()' for on-line help, or 419s 'help.start()' for an HTML browser interface to help. 419s Type 'q()' to quit R. 419s 420s > Stangle("intro-vegan.Rnw") 420s Writing to file intro-vegan.R 420s > source("intro-vegan.R", echo=TRUE) 420s 420s > par(mfrow = c(1, 1)) 420s 420s > options(width = 72) 420s 420s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 420s 420s > options(SweaveHooks = list(fig = figset)) 420s 420s > options(prompt = "> ", continue = " ") 420s 420s > library(vegan) 420s Loading required package: permute 420s Loading required package: lattice 421s 421s > data(dune) 421s 421s > ord <- decorana(dune) 421s 421s > ord 421s 421s Call: 421s decorana(veg = dune) 421s 421s Detrended correspondence analysis with 26 segments. 421s Rescaling of axes with 4 iterations. 421s Total inertia (scaled Chi-square): 2.1153 421s 421s DCA1 DCA2 DCA3 DCA4 421s Eigenvalues 0.5117 0.3036 0.12125 0.14267 421s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 421s Decorana values 0.5360 0.2869 0.08136 0.04814 421s Axis lengths 3.7004 3.1166 1.30055 1.47888 421s 421s 421s > ord <- metaMDS(dune, trace = FALSE) 421s 421s > ord 421s 421s Call: 421s metaMDS(comm = dune, trace = FALSE) 421s 421s global Multidimensional Scaling using monoMDS 421s 421s Data: dune 421s Distance: bray 421s 421s Dimensions: 2 421s Stress: 0.1183186 421s Stress type 1, weak ties 421s Best solution was repeated 5 times in 20 tries 421s The best solution was from try 3 (random start) 421s Scaling: centring, PC rotation, halfchange scaling 421s Species: expanded scores based on ‘dune’ 421s 421s 421s > plot(ord) 421s 421s > plot(ord) 421s 421s > plot(ord, type = "n") 421s 421s > points(ord, display = "sites", cex = 0.8, pch = 21, 421s + col = "red", bg = "yellow") 421s 421s > text(ord, display = "species", cex = 0.7, col = "blue") 421s 421s > plot(ord, type = "n") 421s 421s > points(ord, display = "sites", cex = 0.8, pch = 21, 421s + col = "red", bg = "yellow") 421s 421s > text(ord, display = "species", cex = 0.7, col = "blue") 421s 421s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 421s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 421s + col = "blue") 421s 421s > data(dune.env) 421s 421s > attach(dune.env) 421s 421s > plot(ord, disp = "sites", type = "n") 421s 421s > ordihull(ord, Management, col = 1:4, lwd = 3) 421s 421s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 421s + lwd = 3) 421s 421s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 421s 421s > ordispider(ord, Management, col = 1:4, label = TRUE) 421s 421s > points(ord, disp = "sites", pch = 21, col = "red", 421s + bg = "yellow", cex = 1.3) 421s 421s > plot(ord, disp = "sites", type = "n") 421s 421s > ordihull(ord, Management, col = 1:4, lwd = 3) 421s 421s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 421s + lwd = 3) 421s 421s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 421s 421s > ordispider(ord, Management, col = 1:4, label = TRUE) 421s 421s > points(ord, disp = "sites", pch = 21, col = "red", 421s + bg = "yellow", cex = 1.3) 421s 421s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 421s + perm = 999) 421s 421s > ord.fit 421s 421s ***VECTORS 421s 421s NMDS1 NMDS2 r2 Pr(>r) 421s A1 0.96474 0.26322 0.3649 0.016 * 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s Permutation: free 421s Number of permutations: 999 421s 421s ***FACTORS: 421s 421s Centroids: 421s NMDS1 NMDS2 421s ManagementBF -0.4534 -0.0102 421s ManagementHF -0.2636 -0.1282 421s ManagementNM 0.2958 0.5790 421s ManagementSF 0.1506 -0.4670 421s 421s Goodness of fit: 421s r2 Pr(>r) 421s Management 0.4134 0.009 ** 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s Permutation: free 421s Number of permutations: 999 421s 421s 421s 421s > plot(ord, dis = "site") 421s 421s > plot(ord.fit) 421s 421s > ordisurf(ord, A1, add = TRUE) 421s 421s Family: gaussian 421s Link function: identity 421s 421s Formula: 421s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 421s 421s Estimated degrees of freedom: 421s 1.59 total = 2.59 421s 421s REML score: 41.58727 421s 421s > plot(ord, dis = "site") 421s 421s > plot(ord.fit) 421s 421s > ordisurf(ord, A1, add = TRUE) 421s 421s Family: gaussian 421s Link function: identity 421s 421s Formula: 421s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 421s 421s Estimated degrees of freedom: 421s 1.59 total = 2.59 421s 421s REML score: 41.58727 421s 421s > ord <- cca(dune ~ A1 + Management, data = dune.env) 421s 421s > ord 421s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 421s 421s -- Model Summary -- 421s 421s Inertia Proportion Rank 421s Total 2.1153 1.0000 421s Constrained 0.7798 0.3686 4 421s Unconstrained 1.3355 0.6314 15 421s 421s Inertia is scaled Chi-square 421s 421s -- Eigenvalues -- 421s 421s Eigenvalues for constrained axes: 421s CCA1 CCA2 CCA3 CCA4 421s 0.3187 0.2372 0.1322 0.0917 421s 421s Eigenvalues for unconstrained axes: 421s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 421s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 421s CA11 CA12 CA13 CA14 CA15 421s 0.0317 0.0178 0.0116 0.0087 0.0047 421s 421s 421s > plot(ord) 421s 421s > plot(ord) 421s 421s > cca(dune ~ ., data = dune.env) 421s 421s Some constraints or conditions were aliased because they were 421s redundant. This can happen if terms are linearly dependent (collinear): 421s ‘Manure^4’ 421s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 421s Manure, data = dune.env) 421s 421s -- Model Summary -- 421s 421s Inertia Proportion Rank 421s Total 2.1153 1.0000 421s Constrained 1.5032 0.7106 12 421s Unconstrained 0.6121 0.2894 7 421s 421s Inertia is scaled Chi-square 421s 421s -- Note -- 421s 421s Some constraints or conditions were aliased because they were 421s redundant. This can happen if terms are linearly dependent 421s (collinear): ‘Manure^4’ 421s 421s -- Eigenvalues -- 421s 421s Eigenvalues for constrained axes: 421s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 421s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 421s CCA11 CCA12 421s 0.0228 0.0108 421s 421s Eigenvalues for unconstrained axes: 421s CA1 CA2 CA3 CA4 CA5 CA6 CA7 421s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 421s 421s 421s > anova(ord) 421s Permutation test for cca under reduced model 421s Permutation: free 421s Number of permutations: 999 421s 421s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 421s Df ChiSquare F Pr(>F) 421s Model 4 0.77978 2.1896 0.001 *** 421s Residual 15 1.33549 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > anova(ord, by = "term", permutations = 199) 421s Permutation test for cca under reduced model 421s Terms added sequentially (first to last) 421s Permutation: free 421s Number of permutations: 199 421s 421s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 421s Df ChiSquare F Pr(>F) 421s A1 1 0.22476 2.5245 0.010 ** 421s Management 3 0.55502 2.0780 0.005 ** 421s Residual 15 1.33549 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > anova(ord, by = "mar", permutations = 199) 421s Permutation test for cca under reduced model 421s Marginal effects of terms 421s Permutation: free 421s Number of permutations: 199 421s 421s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 421s Df ChiSquare F Pr(>F) 421s A1 1 0.17594 1.9761 0.05 * 421s Management 3 0.55502 2.0780 0.01 ** 421s Residual 15 1.33549 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > anova(ord, by = "axis", permutations = 499) 421s Permutation test for cca under reduced model 421s Forward tests for axes 421s Permutation: free 421s Number of permutations: 499 421s 421s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 421s Df ChiSquare F Pr(>F) 421s CCA1 1 0.31875 3.5801 0.018 * 421s CCA2 1 0.23718 2.6640 0.148 421s CCA3 1 0.13217 1.4845 0.850 421s CCA4 1 0.09168 1.0297 1.000 421s Residual 15 1.33549 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 421s + data = dune.env) 421s 421s > ord 421s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 421s data = dune.env) 421s 421s -- Model Summary -- 421s 421s Inertia Proportion Rank 421s Total 2.1153 1.0000 421s Conditional 0.6283 0.2970 3 421s Constrained 0.5109 0.2415 4 421s Unconstrained 0.9761 0.4615 12 421s 421s Inertia is scaled Chi-square 421s 421s -- Eigenvalues -- 421s 421s Eigenvalues for constrained axes: 421s CCA1 CCA2 CCA3 CCA4 421s 0.24932 0.12090 0.08160 0.05904 421s 421s Eigenvalues for unconstrained axes: 421s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 421s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 421s CA10 CA11 CA12 421s 0.02102 0.01254 0.00928 421s 421s 421s > anova(ord, by = "term", permutations = 499) 421s Permutation test for cca under reduced model 421s Terms added sequentially (first to last) 421s Permutation: free 421s Number of permutations: 499 421s 421s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 421s Df ChiSquare F Pr(>F) 421s A1 1 0.11543 1.4190 1.000 421s Management 3 0.39543 1.6205 0.002 ** 421s Residual 12 0.97610 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 421s 421s > anova(ord, by = "term", permutations = how) 421s Permutation test for cca under reduced model 421s Terms added sequentially (first to last) 421s Plots: dune.env$Moisture, plot permutation: none 421s Permutation: free 421s Number of permutations: 499 421s 421s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 421s Df ChiSquare F Pr(>F) 421s A1 1 0.11543 1.4190 1.000 421s Management 3 0.39543 1.6205 0.002 ** 421s Residual 12 0.97610 421s --- 421s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 421s 421s > detach(dune.env) 421s > 422s 422s R version 4.4.3 (2025-02-28) -- "Trophy Case" 422s Copyright (C) 2025 The R Foundation for Statistical Computing 422s Platform: aarch64-unknown-linux-gnu 422s 422s R is free software and comes with ABSOLUTELY NO WARRANTY. 422s You are welcome to redistribute it under certain conditions. 422s Type 'license()' or 'licence()' for distribution details. 422s 422s R is a collaborative project with many contributors. 422s Type 'contributors()' for more information and 422s 'citation()' on how to cite R or R packages in publications. 422s 422s Type 'demo()' for some demos, 'help()' for on-line help, or 422s 'help.start()' for an HTML browser interface to help. 422s Type 'q()' to quit R. 422s 422s > Stangle("partitioning.Rnw") 422s Writing to file partitioning.R 422s > source("partitioning.R", echo=TRUE) 422s 422s > par(mfrow = c(1, 1)) 422s 422s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 422s 422s > options(SweaveHooks = list(fig = figset)) 422s 422s > library(vegan) 422s Loading required package: permute 422s Loading required package: lattice 423s 423s > labs <- paste("Table", 1:4) 423s 423s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 423s 423s > showvarparts(2, bg = cls, Xnames = labs) 423s 423s > showvarparts(3, bg = cls, Xnames = labs) 423s 423s > showvarparts(4, bg = cls, Xnames = labs) 423s > 430s Test cca-object-tests passed 432s Test oecosimu-tests passed 435s Test vegan-tests passed 435s autopkgtest [16:10:47]: test run-unit-test: -----------------------] 436s autopkgtest [16:10:48]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 436s run-unit-test PASS 436s autopkgtest [16:10:48]: test pkg-r-autopkgtest: preparing testbed 436s Reading package lists... 437s Building dependency tree... 437s Reading state information... 437s Starting pkgProblemResolver with broken count: 0 437s Starting 2 pkgProblemResolver with broken count: 0 437s Done 438s The following NEW packages will be installed: 438s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 438s dctrl-tools g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 438s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 438s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 438s libasan8 libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 438s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 438s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 438s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 438s libpkgconf3 libpng-dev libreadline-dev libstdc++-14-dev libtirpc-dev 438s libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev 438s zlib1g-dev 438s 0 upgraded, 54 newly installed, 0 to remove and 0 not upgraded. 438s Need to get 92.7 MB of archives. 438s After this operation, 334 MB of additional disk space will be used. 438s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 440s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 440s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 457s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 457s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 457s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 457s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 457s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 457s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 460s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 462s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 466s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 467s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 469s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 472s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 497s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 498s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 498s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 498s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 501s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 515s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 515s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 515s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 515s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 516s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 516s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 516s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 530s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 530s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 530s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 530s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 530s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 530s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 530s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 530s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 545s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 545s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 545s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 545s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 551s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 551s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 551s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 552s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 552s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 552s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 552s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 553s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 554s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 554s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 554s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 554s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 554s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 554s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 554s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 555s Fetched 92.7 MB in 1min 56s (797 kB/s) 555s Selecting previously unselected package libisl23:arm64. 555s (Reading database ... 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libdeflate-dev:arm64. 558s Preparing to unpack .../33-libdeflate-dev_1.23-1_arm64.deb ... 558s Unpacking libdeflate-dev:arm64 (1.23-1) ... 558s Selecting previously unselected package libicu-dev:arm64. 558s Preparing to unpack .../34-libicu-dev_76.1-1ubuntu2_arm64.deb ... 558s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 558s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 558s Preparing to unpack .../35-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 558s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 558s Selecting previously unselected package libjpeg8-dev:arm64. 558s Preparing to unpack .../36-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 558s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 558s Selecting previously unselected package libjpeg-dev:arm64. 558s Preparing to unpack .../37-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 558s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 558s Selecting previously unselected package liblapack-dev:arm64. 558s Preparing to 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auto mode 559s Setting up build-essential (12.10ubuntu1) ... 559s Setting up gfortran (4:14.2.0-1ubuntu1) ... 559s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 559s 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 559s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 559s 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 559s Setting up r-base-dev (4.4.3-1) ... 559s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 559s Processing triggers for libc-bin (2.41-1ubuntu2) ... 559s Processing triggers for man-db (2.13.0-1) ... 560s Processing triggers for install-info (7.1.1-1) ... 561s autopkgtest [16:12:53]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 561s autopkgtest [16:12:53]: test pkg-r-autopkgtest: [----------------------- 562s Test: Try to load the R library vegan 562s 562s R version 4.4.3 (2025-02-28) -- "Trophy Case" 562s Copyright (C) 2025 The R Foundation for Statistical Computing 562s Platform: aarch64-unknown-linux-gnu 562s 562s R is free software and comes with ABSOLUTELY NO WARRANTY. 562s You are welcome to redistribute it under certain conditions. 562s Type 'license()' or 'licence()' for distribution details. 562s 562s R is a collaborative project with many contributors. 562s Type 'contributors()' for more information and 562s 'citation()' on how to cite R or R packages in publications. 562s 562s Type 'demo()' for some demos, 'help()' for on-line help, or 562s 'help.start()' for an HTML browser interface to help. 562s Type 'q()' to quit R. 562s 562s Loading required package: permute 562s > library('vegan') 562s Loading required package: lattice 563s > 563s > 563s Other tests are currently unsupported! 563s They will be progressively added. 563s autopkgtest [16:12:55]: test pkg-r-autopkgtest: -----------------------] 563s autopkgtest [16:12:55]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 563s pkg-r-autopkgtest PASS 564s autopkgtest [16:12:56]: @@@@@@@@@@@@@@@@@@@@ summary 564s run-unit-test PASS 564s pkg-r-autopkgtest PASS 570s nova [W] Using flock in prodstack6-arm64 570s flock: timeout while waiting to get lock 570s Creating nova instance adt-plucky-arm64-r-cran-vegan-20250315-160332-juju-7f2275-prod-proposed-migration-environment-2-851a44a9-9786-460a-a809-098cf1a677f0 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 570s nova [W] Timed out waiting for fe773f24-fded-474b-8d2e-9bdaeb6024a8 to get deleted.