0s autopkgtest [15:57:27]: starting date and time: 2025-03-15 15:57:27+0000 0s autopkgtest [15:57:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:57:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.f_55k6iq/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-spatstat.explore --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-arm64-2.secgroup --name adt-plucky-arm64-r-cran-spatstat.explore-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-b29006cb-5109-49c1-b699-81555d687b84 --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/ 138s autopkgtest [15:59:45]: testbed dpkg architecture: arm64 138s autopkgtest [15:59:45]: testbed apt version: 2.9.33 138s autopkgtest [15:59:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 138s autopkgtest [15:59:45]: testbed release detected to be: None 139s autopkgtest [15:59:46]: updating testbed package index (apt update) 140s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 140s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 140s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 140s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 140s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 141s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 141s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 141s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 141s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 141s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 142s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 142s Fetched 1078 kB in 2s (519 kB/s) 143s Reading package lists... 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s Calculating upgrade... 145s The following packages will be upgraded: 145s pinentry-curses python3-jinja2 strace 145s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 647 kB of archives. 145s After this operation, 11.3 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 146s Fetched 647 kB in 1s (588 kB/s) 147s (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.) 147s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 147s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 147s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 147s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 147s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 147s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 147s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 147s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 147s Setting up strace (6.13+ds-1ubuntu1) ... 147s Processing triggers for man-db (2.13.0-1) ... 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s Solving dependencies... 149s The following packages will be REMOVED: 149s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 149s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 149s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 149s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 149s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 149s After this operation, 267 MB disk space will be freed. 149s (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.) 149s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 149s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 149s Removing libpython3.12t64:arm64 (3.12.9-1) ... 149s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 149s Removing libnsl2:arm64 (1.3.0-3build3) ... 149s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 149s Removing libunwind8:arm64 (1.6.2-3.1) ... 149s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 151s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 151s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 151s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 151s /etc/kernel/postrm.d/initramfs-tools: 151s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 152s /etc/kernel/postrm.d/zz-flash-kernel: 152s flash-kernel: Kernel 6.11.0-8-generic has been removed. 152s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 152s /etc/kernel/postrm.d/zz-update-grub: 152s Sourcing file `/etc/default/grub' 152s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 152s Generating grub configuration file ... 152s Found linux image: /boot/vmlinuz-6.14.0-10-generic 152s Found initrd image: /boot/initrd.img-6.14.0-10-generic 152s Warning: os-prober will not be executed to detect other bootable partitions. 152s Systems on them will not be added to the GRUB boot configuration. 152s Check GRUB_DISABLE_OS_PROBER documentation entry. 152s Adding boot menu entry for UEFI Firmware Settings ... 152s done 152s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 153s Processing triggers for libc-bin (2.41-1ubuntu1) ... 153s (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.) 153s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 153s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 153s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 153s autopkgtest [16:00:00]: upgrading testbed (apt dist-upgrade and autopurge) 153s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 155s Entering ResolveByKeep 155s 155s Calculating upgrade... 156s The following packages will be upgraded: 156s libc-bin libc-dev-bin libc6 libc6-dev locales 156s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 9530 kB of archives. 156s After this operation, 0 B of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 158s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 158s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 162s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 168s Preconfiguring packages ... 168s Fetched 9530 kB in 12s (804 kB/s) 168s (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.) 168s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 168s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 168s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 168s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 169s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc6:arm64 (2.41-1ubuntu2) ... 169s (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.) 169s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 169s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up libc-bin (2.41-1ubuntu2) ... 169s (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.) 169s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 169s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 169s Setting up locales (2.41-1ubuntu2) ... 170s Generating locales (this might take a while)... 173s en_US.UTF-8... done 173s Generation complete. 173s Setting up libc-dev-bin (2.41-1ubuntu2) ... 173s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 173s Processing triggers for man-db (2.13.0-1) ... 174s Processing triggers for systemd (257.3-1ubuntu3) ... 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 176s Starting pkgProblemResolver with broken count: 0 176s Starting 2 pkgProblemResolver with broken count: 0 176s Done 176s Solving dependencies... 177s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 177s autopkgtest [16:00:24]: rebooting testbed after setup commands that affected boot 200s autopkgtest [16:00:47]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 203s autopkgtest [16:00:50]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.explore 206s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.explore 3.3-4-1 (dsc) [2563 B] 206s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.explore 3.3-4-1 (tar) [668 kB] 206s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.explore 3.3-4-1 (diff) [3452 B] 206s gpgv: Signature made Fri Jan 31 07:56:43 2025 UTC 206s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 206s gpgv: issuer "plessy@debian.org" 206s gpgv: Can't check signature: No public key 206s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.explore_3.3-4-1.dsc: no acceptable signature found 206s autopkgtest [16:00:53]: testing package r-cran-spatstat.explore version 3.3-4-1 206s autopkgtest [16:00:53]: build not needed 210s autopkgtest [16:00:57]: test run-unit-test: preparing testbed 210s Reading package lists... 211s Building dependency tree... 211s Reading state information... 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 212s The following NEW packages will be installed: 212s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 212s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 212s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libice6 libjbig0 212s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 212s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 212s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 212s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 212s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 212s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 212s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 212s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 212s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 212s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 212s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 212s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 84.1 MB of archives. 212s After this operation, 139 MB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 213s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 214s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 214s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 214s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 215s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 215s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 215s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 215s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 215s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 215s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 216s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 216s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 216s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 217s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 217s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 217s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 217s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 219s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 220s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 220s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 220s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 220s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 220s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 226s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 226s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 226s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 226s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 227s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 227s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 227s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 227s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 227s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 227s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 227s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 230s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 230s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 230s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 231s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 231s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 231s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 233s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 233s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 233s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 234s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 234s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 276s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 276s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 277s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 277s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gsl arm64 2.1-8-1build1 [485 kB] 278s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 279s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-locfit arm64 1.5-9.12-1 [514 kB] 280s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 284s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 287s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 290s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 290s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 300s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 300s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 301s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 301s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.utils arm64 3.1-2-1 [381 kB] 302s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.data all 3.1-4-1 [4047 kB] 307s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.univar arm64 3.1-1-1build1 [308 kB] 307s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.geom arm64 3.3-5-1 [3929 kB] 312s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.random arm64 3.3-2-1 [1159 kB] 313s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 313s Get:67 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 313s Get:68 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 317s Get:69 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 321s Get:70 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 322s Get:71 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 327s Preconfiguring packages ... 327s Fetched 84.1 MB in 1min 55s (732 kB/s) 327s Selecting previously unselected package fonts-dejavu-mono. 328s (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.) 328s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 328s Unpacking fonts-dejavu-mono (2.37-8) ... 328s Selecting previously unselected package fonts-dejavu-core. 328s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 328s Unpacking fonts-dejavu-core (2.37-8) ... 328s Selecting previously unselected package fontconfig-config. 328s Preparing to unpack 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libxcb-render0:arm64 (1.17.0-2) ... 328s Selecting previously unselected package libxcb-shm0:arm64. 328s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ... 328s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 328s Selecting previously unselected package libxrender1:arm64. 328s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 328s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 328s Selecting previously unselected package libcairo2:arm64. 328s Preparing to unpack .../10-libcairo2_1.18.2-2_arm64.deb ... 328s Unpacking libcairo2:arm64 (1.18.2-2) ... 328s Selecting previously unselected package libdatrie1:arm64. 328s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 328s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 328s Selecting previously unselected package libdeflate0:arm64. 328s Preparing to unpack .../12-libdeflate0_1.23-1_arm64.deb ... 328s Unpacking libdeflate0:arm64 (1.23-1) ... 328s Selecting previously unselected package libgfortran5:arm64. 328s Preparing to unpack .../13-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 328s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 328s Selecting previously unselected package libgomp1:arm64. 328s Preparing to unpack .../14-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 328s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 328s Selecting previously unselected package libgraphite2-3:arm64. 328s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 328s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 328s Selecting previously unselected package libgslcblas0:arm64. 328s Preparing to unpack .../16-libgslcblas0_2.8+dfsg-5_arm64.deb ... 328s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... 329s Selecting previously unselected package libgsl28:arm64. 329s Preparing to unpack .../17-libgsl28_2.8+dfsg-5_arm64.deb ... 329s Unpacking libgsl28:arm64 (2.8+dfsg-5) ... 329s Selecting previously unselected package libharfbuzz0b:arm64. 329s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_arm64.deb ... 329s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 329s Selecting previously unselected package x11-common. 329s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 329s Unpacking x11-common (1:7.7+23ubuntu3) ... 329s Selecting previously unselected package libice6:arm64. 329s Preparing to unpack .../20-libice6_2%3a1.1.1-1_arm64.deb ... 329s Unpacking libice6:arm64 (2:1.1.1-1) ... 329s Selecting previously unselected package libjpeg-turbo8:arm64. 329s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 329s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 329s Selecting previously unselected package libjpeg8:arm64. 329s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ... 329s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 329s Selecting previously unselected package liblapack3:arm64. 329s Preparing to unpack .../23-liblapack3_3.12.1-2_arm64.deb ... 329s Unpacking liblapack3:arm64 (3.12.1-2) 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libpangocairo-1.0-0:arm64. 329s Preparing to unpack .../29-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 329s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 329s Selecting previously unselected package libpaper2:arm64. 329s Preparing to unpack .../30-libpaper2_2.2.5-0.3_arm64.deb ... 329s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 329s Selecting previously unselected package libpaper-utils. 329s Preparing to unpack .../31-libpaper-utils_2.2.5-0.3_arm64.deb ... 329s Unpacking libpaper-utils (2.2.5-0.3) ... 329s Selecting previously unselected package libsharpyuv0:arm64. 329s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_arm64.deb ... 329s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 329s Selecting previously unselected package libsm6:arm64. 329s Preparing to unpack .../33-libsm6_2%3a1.2.4-1_arm64.deb ... 329s Unpacking libsm6:arm64 (2:1.2.4-1) ... 329s Selecting previously unselected package libtcl8.6:arm64. 329s Preparing to unpack .../34-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 329s 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package libtk8.6:arm64. 330s Preparing to unpack .../40-libtk8.6_8.6.16-1_arm64.deb ... 330s Unpacking libtk8.6:arm64 (8.6.16-1) ... 330s Selecting previously unselected package libxt6t64:arm64. 330s Preparing to unpack .../41-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 330s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 330s Selecting previously unselected package zip. 330s Preparing to unpack .../42-zip_3.0-14ubuntu2_arm64.deb ... 330s Unpacking zip (3.0-14ubuntu2) ... 330s Selecting previously unselected package unzip. 330s Preparing to unpack .../43-unzip_6.0-28ubuntu6_arm64.deb ... 330s Unpacking unzip (6.0-28ubuntu6) ... 330s Selecting previously unselected package xdg-utils. 330s Preparing to unpack .../44-xdg-utils_1.2.1-2ubuntu1_all.deb ... 330s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 330s Selecting previously unselected package r-base-core. 330s Preparing to unpack .../45-r-base-core_4.4.3-1_arm64.deb ... 330s Unpacking r-base-core (4.4.3-1) ... 331s Selecting previously unselected package r-cran-abind. 331s Preparing to unpack .../46-r-cran-abind_1.4-8-1_all.deb ... 331s Unpacking r-cran-abind (1.4-8-1) ... 331s Selecting previously unselected package r-cran-deldir. 331s Preparing to unpack .../47-r-cran-deldir_2.0-4-1build1_arm64.deb ... 331s Unpacking r-cran-deldir (2.0-4-1build1) ... 331s Selecting previously unselected package r-cran-goftest. 331s Preparing to unpack .../48-r-cran-goftest_1.2-3-1_arm64.deb ... 331s Unpacking r-cran-goftest (1.2-3-1) ... 331s Selecting previously unselected package r-cran-gsl. 331s Preparing to unpack .../49-r-cran-gsl_2.1-8-1build1_arm64.deb ... 331s Unpacking r-cran-gsl (2.1-8-1build1) ... 331s Selecting previously unselected package r-cran-lattice. 331s Preparing to unpack .../50-r-cran-lattice_0.22-6-1_arm64.deb ... 331s Unpacking r-cran-lattice (0.22-6-1) ... 331s Selecting previously unselected package r-cran-locfit. 331s Preparing to unpack .../51-r-cran-locfit_1.5-9.12-1_arm64.deb ... 331s Unpacking 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unselected package r-cran-spatstat.model. 332s Preparing to unpack .../68-r-cran-spatstat.model_3.3-4-1_arm64.deb ... 332s Unpacking r-cran-spatstat.model (3.3-4-1) ... 332s Selecting previously unselected package r-cran-spatstat.linnet. 332s Preparing to unpack .../69-r-cran-spatstat.linnet_3.2-5-1_arm64.deb ... 332s Unpacking r-cran-spatstat.linnet (3.2-5-1) ... 332s Selecting previously unselected package r-cran-spatstat. 332s Preparing to unpack .../70-r-cran-spatstat_3.3-1-1_arm64.deb ... 332s Unpacking r-cran-spatstat (3.3-1-1) ... 332s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 332s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 332s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 332s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 332s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 332s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 332s Setting up libgslcblas0:arm64 (2.8+dfsg-5) ... 332s Setting up libxcb-render0:arm64 (1.17.0-2) ... 332s Setting up unzip (6.0-28ubuntu6) ... 332s Setting up x11-common (1:7.7+23ubuntu3) ... 333s Setting up libdeflate0:arm64 (1.23-1) ... 333s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 333s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 333s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 333s Setting up zip (3.0-14ubuntu2) ... 333s Setting up libblas3:arm64 (3.12.1-2) ... 333s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 333s Setting up fonts-dejavu-mono (2.37-8) ... 333s Setting up libtcl8.6:arm64 (8.6.16+dfsg-1) ... 333s Setting up fonts-dejavu-core (2.37-8) ... 333s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 333s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 333s Setting up libwebp7:arm64 (1.5.0-0.1) ... 333s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 333s Setting up libthai-data (0.1.29-2build1) ... 333s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 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The R Foundation for Statistical Computing 339s Platform: aarch64-unknown-linux-gnu 339s 339s R is free software and comes with ABSOLUTELY NO WARRANTY. 339s You are welcome to redistribute it under certain conditions. 339s Type 'license()' or 'licence()' for distribution details. 339s 339s R is a collaborative project with many contributors. 339s Type 'contributors()' for more information and 339s 'citation()' on how to cite R or R packages in publications. 339s 339s Type 'demo()' for some demos, 'help()' for on-line help, or 339s 'help.start()' for an HTML browser interface to help. 339s Type 'q()' to quit R. 339s 340s > #' 340s > #' Header for all (concatenated) test files 340s > #' 340s > #' Require spatstat.explore 340s > #' Obtain environment variable controlling tests. 340s > #' 340s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 340s > 340s > require(spatstat.explore) 340s Loading required package: spatstat.explore 340s Loading required package: spatstat.data 341s Loading required package: spatstat.univar 341s spatstat.univar 3.1-1 341s Loading required package: spatstat.geom 341s spatstat.geom 3.3-5 341s Loading required package: spatstat.random 341s spatstat.random 3.3-2 341s Loading required package: nlme 341s spatstat.explore 3.3-4 341s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 341s > ALWAYS <- TRUE 341s > cat(paste("--------- Executing", 341s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 341s + "test code -----------\n")) 341s --------- Executing **RESTRICTED** subset of test code ----------- 341s > ## tests/cdf.test.R 341s > 341s > 341s > local({ 341s + NSIM <- 9 341s + op <- spatstat.options(ndummy.min=16, npixel=32) 341s + AA <- split(ants, un=FALSE) 341s + AC <- AA[["Cataglyphis"]] 341s + AM <- AA[["Messor"]] 341s + DM <- distmap(AM) 341s + if(ALWAYS) { 341s + ## Check cdf.test with strange data 341s + ## Marked point patterns with some marks not represented 341s + ## should produce a warning, rather than a crash: 341s + cdf.test(AC, DM) 341s + } 341s + if(FULLTEST) { 341s + ## should be OK: 341s + cdf.test(unmark(AC), DM) 341s + cdf.test(unmark(AC), DM, "cvm") 341s + cdf.test(unmark(AC), DM, "ad") 341s + ## other code blocks 341s + cdf.test(finpines, "x") 341s + } 341s + }) 341s > 341s > 341s > #' tests/circular.R 341s > #' 341s > #' Circular data and periodic distributions 341s > #' 341s > #' $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 341s > 341s > 341s > local({ 341s + if(ALWAYS) { 341s + a <- pairorient(redwood, 0.05, 0.15, correction="none") 341s + rose(a) 341s + } 341s + if(FULLTEST) { 341s + b <- pairorient(redwood, 0.05, 0.15, correction="best") 341s + rose(b, start="N", clockwise=TRUE) 341s + } 341s + if(ALWAYS) { 341s + #' arcs on the circle 341s + #' (depends on numerical behaviour) 341s + set.seed(19171025) 341s Warning message: 341s In cdf.test.ppp(AC, DM) : 341s Ignoring marks, because some mark values have zero frequency 341s + aa <- replicate(7, runif(1, 0, 2*pi) + c(0, runif(1, 0, pi)), 341s + simplify=FALSE) 341s + bb <- circunion(aa) 341s + 341s + assertsingle <- function(x, a, id) { 341s + y <- circunion(x) 341s + if(length(y) != 1 || max(abs(y[[1]] - a)) > .Machine$double.eps) 341s + stop(paste("Incorrect result from circunion in case", id), 341s + call.=FALSE) 341s + invisible(NULL) 341s + } 341s + 341s + assertsingle(list(c(pi/3, pi), c(pi/2, 3*pi/2)), 341s + c(pi/3, 3*pi/2), 341s + 1) 341s + assertsingle(list(c(0, pi/2), c(pi/4, pi)), 341s + c(0,pi), 341s + 2) 341s + assertsingle(list(c(-pi/4, pi/2), c(pi/4, pi)), 341s + c((2-1/4)*pi, pi), 341s + 3) 341s + } 341s + }) 341s > 341s > 341s > #' 341s > #' tests/closecore.R 341s > #' 341s > #' check 'closepairs/crosspairs' code 341s > #' invoked in core package 341s > #' 341s > #' $Revision: 1.4 $ $Date: 2021/04/17 04:16:43 $ 341s > #' 341s > #' ------- All this code must be run on every hardware ------- 341s > #' 341s > 341s > local({ 341s + #' weightedclosepairs is in wtdclosepair.R 341s + wi <- weightedclosepairs(redwood, 0.05, "isotropic") 341s + if(FULLTEST) { 341s + wt <- weightedclosepairs(redwood, 0.05, "translate") 341s + wp <- weightedclosepairs(redwood, 0.05, "periodic") 341s + } 341s + #' markmarkscatter uses closepairs.pp3 341s + X <- runifpoint3(100) 341s + marks(X) <- runif(100) 341s + markmarkscatter(X, 0.2) 341s + if(FULLTEST) { 341s + markmarkscatter(X[FALSE], 0.2) 341s + } 341s + }) 341s > 341s > #' 341s > #' contact.R 341s > #' 341s > #' Check machinery for first contact distributions 341s > #' 341s > #' $Revision: 1.8 $ $Date: 2021/04/17 02:25:55 $ 341s > 341s > local({ 341s + if(ALWAYS) { 341s + #' reduce complexity 341s + Y <- as.mask(heather$coarse, dimyx=c(50, 25)) 341s + 341s + X <- runifpoint(100, win = complement.owin(Y)) 341s + if(FULLTEST) G <- Gfox(X, Y) 341s + J <- Jfox(X, Y) 341s + 341s + Y <- as.polygonal(Y) 341s + X <- runifpoint(100, win = complement.owin(Y)) 341s + if(FULLTEST) G <- Gfox(X, Y) 341s + J <- Jfox(X, Y) 341s + 341s + op <- spatstat.options(exactdt.checks.data=TRUE) 341s + U <- exactdt(X) 341s + spatstat.options(op) 341s + } 341s + }) 342s > 342s > reset.spatstat.options() 342s > 342s BEGIN TEST testsD.R 342s 342s R version 4.4.3 (2025-02-28) -- "Trophy Case" 342s Copyright (C) 2025 The R Foundation for Statistical Computing 342s Platform: aarch64-unknown-linux-gnu 342s 342s R is free software and comes with ABSOLUTELY NO WARRANTY. 342s You are welcome to redistribute it under certain conditions. 342s Type 'license()' or 'licence()' for distribution details. 342s 342s R is a collaborative project with many contributors. 342s Type 'contributors()' for more information and 342s 'citation()' on how to cite R or R packages in publications. 342s 342s Type 'demo()' for some demos, 'help()' for on-line help, or 342s 'help.start()' for an HTML browser interface to help. 342s Type 'q()' to quit R. 342s 342s > #' 342s > #' Header for all (concatenated) test files 342s > #' 342s > #' Require spatstat.explore 342s > #' Obtain environment variable controlling tests. 342s > #' 342s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 342s > 342s > require(spatstat.explore) 342s Loading required package: spatstat.explore 342s Loading required package: spatstat.data 344s Loading required package: spatstat.univar 344s spatstat.univar 3.1-1 344s Loading required package: spatstat.geom 344s spatstat.geom 3.3-5 344s Loading required package: spatstat.random 344s spatstat.random 3.3-2 344s Loading required package: nlme 344s spatstat.explore 3.3-4 344s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 344s > ALWAYS <- TRUE 344s > cat(paste("--------- Executing", 344s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 344s + "test code -----------\n")) 344s --------- Executing **RESTRICTED** subset of test code ----------- 344s > #' 344s > #' tests/density.R 344s > #' 344s > #' Test behaviour of density() methods, 344s > #' relrisk(), Smooth() 344s > #' and inhomogeneous summary functions 344s > #' and idw, adaptive.density, intensity 344s > #' and SpatialMedian, SpatialQuantile 344s > #' 344s > #' $Revision: 1.67 $ $Date: 2024/01/29 07:07:16 $ 344s > #' 344s > 344s > if(!FULLTEST) 344s + spatstat.options(npixel=32, ndummy.min=16) 344s > 344s > 344s > local({ 344s + 344s + # test all cases of density.ppp and densityfun.ppp 344s + 344s + tryit <- function(..., do.fun=TRUE, badones=FALSE) { 344s + Z <- density(cells, ..., at="pixels") 344s + Z <- density(cells, ..., at="points") 344s + if(do.fun) { 344s + f <- densityfun(cells, ...) 344s + U <- f(0.1, 0.3) 344s + if(badones) { 344s + U2 <- f(1.1, 0.3) 344s + U3 <- f(1.1, 0.3, drop=FALSE) 344s + } 344s + } 344s + return(invisible(NULL)) 344s + } 344s + 344s + if(ALWAYS) { 344s + tryit(0.05) 344s + tryit(0.05, diggle=TRUE) 344s + tryit(0.05, se=TRUE) 344s + tryit(0.05, weights=expression(x)) 344s + tryit(0.07, kernel="epa") 344s + tryit(sigma=Inf) 344s + tryit(0.05, badones=TRUE) 344s + } 344s + if(FULLTEST) { 344s + tryit(0.07, kernel="quartic") 344s + tryit(0.07, kernel="disc") 344s + tryit(0.07, kernel="epa", weights=expression(x)) 344s + tryit(sigma=Inf, weights=expression(x)) 344s + } 344s + 344s + V <- diag(c(0.05^2, 0.07^2)) 344s + 344s + if(ALWAYS) { 344s + tryit(varcov=V) 344s + } 344s + if(FULLTEST) { 344s + tryit(varcov=V, diggle=TRUE) 344s + tryit(varcov=V, weights=expression(x)) 344s + tryit(varcov=V, weights=expression(x), diggle=TRUE) 344s + Z <- distmap(runifpoint(5, Window(cells))) 344s + tryit(0.05, weights=Z) 344s + tryit(0.05, weights=Z, diggle=TRUE) 344s + } 344s + 344s + trymost <- function(...) tryit(..., do.fun=FALSE) 344s + wdf <- data.frame(a=1:42,b=42:1) 344s + if(ALWAYS) { 344s + trymost(0.05, weights=wdf) 344s + trymost(sigma=Inf, weights=wdf) 344s + } 344s + if(FULLTEST) { 344s + trymost(0.05, weights=wdf, diggle=TRUE) 344s + trymost(varcov=V, weights=wdf) 344s + trymost(varcov=V, weights=expression(cbind(x,y))) 344s + } 344s + 344s + ## check conservation of mass 344s + checkconserve <- function(X, xname, sigma, toler=0.01) { 344s + veritas <- npoints(X) 344s + vino <- integral(density(X, sigma, diggle=TRUE)) 344s + relerr <- abs(vino - veritas)/veritas 344s + if(relerr > toler) 344s + stop(paste("density.ppp(diggle=TRUE) fails to conserve mass:", 344s + vino, "!=", veritas, 344s + "for", sQuote(xname)), 344s + call.=FALSE) 344s + return(relerr) 344s + } 344s + if(FULLTEST) { 344s + checkconserve(cells, "cells", 0.15) 344s + } 344s + if(ALWAYS) { 344s + checkconserve(split(chorley)[["lung"]], "lung", 2) 344s + } 344s + 344s + ## run C algorithm 'denspt' 344s + opa <- spatstat.options(densityC=TRUE, densityTransform=FALSE) 344s + if(ALWAYS) { 344s + tryit(varcov=V) 344s + } 344s + if(FULLTEST) { 344s + tryit(varcov=V, weights=expression(x)) 344s + trymost(varcov=V, weights=wdf) 344s + } 344s + spatstat.options(opa) 344s + 344s + crossit <- function(..., sigma=NULL) { 344s + U <- runifpoint(20, Window(cells)) 344s + a <- densitycrossEngine(cells, U, ..., sigma=sigma) 344s + a <- densitycrossEngine(cells, U, ..., sigma=sigma, diggle=TRUE) 344s + invisible(NULL) 344s + } 344s + if(ALWAYS) { 344s + crossit(varcov=V, weights=cells$x) 344s + crossit(sigma=Inf) 344s + } 344s + if(FULLTEST) { 344s + crossit(varcov=V, weights=wdf) 344s + crossit(sigma=0.1, weights=wdf) 344s + crossit(sigma=0.1, kernel="epa", weights=wdf) 344s + } 344s + 344s + ## apply different discretisation rules 344s + if(ALWAYS) { 344s + Z <- density(cells, 0.05, fractional=TRUE) 344s + } 344s + if(FULLTEST) { 344s + Z <- density(cells, 0.05, preserve=TRUE) 344s + Z <- density(cells, 0.05, fractional=TRUE, preserve=TRUE) 344s + } 344s + 344s + ## compare results with different algorithms 344s + crosscheque <- function(expr) { 344s + e <- as.expression(substitute(expr)) 344s + ename <- sQuote(deparse(substitute(expr))) 344s + ## interpreted R 344s + opa <- spatstat.options(densityC=FALSE, densityTransform=FALSE) 344s + val.interpreted <- eval(e) 344s + ## established C algorithm 'denspt' 344s + spatstat.options(densityC=TRUE, densityTransform=FALSE) 344s + val.C <- eval(e) 344s + ## new C algorithm 'Gdenspt' using transformed coordinates 344s + spatstat.options(densityC=TRUE, densityTransform=TRUE) 344s + val.Transform <- eval(e) 344s + spatstat.options(opa) 344s + if(max(abs(val.interpreted - val.C)) > 0.001) 344s + stop(paste("Numerical discrepancy between R and C algorithms in", 344s + ename)) 344s + if(max(abs(val.C - val.Transform)) > 0.001) 344s + stop(paste("Numerical discrepancy between C algorithms", 344s + "using transformed and untransformed coordinates in", 344s + ename)) 344s + invisible(NULL) 344s + } 344s + 344s + ## execute & compare results of density(at="points") with different algorithms 344s + wdfr <- cbind(1:npoints(redwood), 2) 344s + if(ALWAYS) { 344s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE)) 344s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 344s + weights=wdfr[,1])) 344s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 344s + weights=wdfr)) 344s + } 344s + 344s + ## correctness of non-Gaussian kernel calculation 344s + leavein <- function(ker, maxd=0.025) { 344s + ZI <- density(redwood, 0.12, kernel=ker, edge=FALSE, 344s + dimyx=256)[redwood] 344s + ZP <- density(redwood, 0.12, kernel=ker, edge=FALSE, 344s + at="points", leaveoneout=FALSE) 344s + discrep <- max(abs(ZP - ZI))/npoints(redwood) 344s + if(discrep > maxd) 344s + stop(paste("Discrepancy", 344s + signif(discrep, 3), 344s + "in calculation for", ker, "kernel")) 344s + return(invisible(NULL)) 344s + } 344s + if(ALWAYS) { 344s + leavein("epanechnikov", 0.015) 344s + } 344s + if(FULLTEST) { 344s + leavein("quartic", 0.010) 344s + leavein("disc", 0.100) 344s + } 344s + 344s + ## bandwidth selection code blocks 344s + sigvec <- 0.01 * 2:15 344s + sigran <- range(sigvec) 344s + if(ALWAYS) { 344s + bw.ppl(redwood, sigma=sigvec) 344s + bw.CvL(redwood, sigma=sigvec) 344s + } 344s + if(FULLTEST) { 344s + bw.ppl(redwood, srange=sigran, ns=5) 344s + bw.CvL(redwood, srange=sigran, ns=5) 344s + } 344s + ## adaptive bandwidth 344s + if(ALWAYS) { 344s + a <- bw.abram(redwood) 344s + } 344s + if(FULLTEST) { 344s + a <- bw.abram(redwood, pilot=density(redwood, 0.2)) 344s + a <- bw.abram(redwood, smoother="densityVoronoi", at="pixels") 344s + } 344s + 344s + ## Kinhom 344s + if(ALWAYS) { 344s + lam <- density(redwood) 344s + K <- Kinhom(redwood, lam) 344s + 344s + lamX <- density(redwood, at="points") 344s + KX <- Kinhom(redwood, lamX) 344s + } 344s + 344s + ## test all code cases of new 'relrisk.ppp' algorithm 344s + pants <- function(..., X=ants, sigma=100, se=TRUE) { 344s + a <- relrisk(X, sigma=sigma, se=se, ...) 344s + return(TRUE) 344s + } 344s + if(ALWAYS) { 344s + pants() 344s + pants(diggle=TRUE) 344s + pants(edge=FALSE) 344s + pants(at="points") 344s + pants(casecontrol=FALSE) 344s + pants(relative=TRUE) 344s + pants(sigma=Inf) 344s + pants(sigma=NULL, varcov=diag(c(100,100)^2)) 344s + f <- 1/area(Window(ants)) 344s + pants(fudge=f) 344s + } 344s + if(FULLTEST) { 344s + pants(diggle=TRUE, at="points") 344s + pants(edge=FALSE, at="points", fudge=f) 344s + pants(casecontrol=FALSE, relative=TRUE) 344s + pants(casecontrol=FALSE,at="points") 344s + pants(relative=TRUE,at="points", fudge=f) 344s + pants(casecontrol=FALSE, relative=TRUE,at="points") 344s + pants(relative=TRUE, control="Cataglyphis", case="Messor", fudge=f) 344s + pants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 344s + pants(casecontrol=FALSE, case="Messor", se=FALSE) 344s + pants(case=2, at="pixels", relative=TRUE) 344s + pants(case=2, at="points", relative=TRUE) 344s + pants(case=2, at="pixels", relative=FALSE) 344s + pants(case=2, at="points", relative=FALSE) 344s + } 344s + if(ALWAYS) { 344s + ## underflow example from stackoverflow! 344s + funky <- scanpp("funky.tab", owin(c(4, 38), c(0.3, 17))) 344s + P <- relrisk(funky, 0.5) 344s + R <- relrisk(funky, 0.5, relative=TRUE) 344s + } 344s + ## more than 2 types 344s + if(ALWAYS) { 344s + pants(X=sporophores) 344s + pants(X=sporophores, sigma=20, at="points") 344s + pants(X=sporophores, sigma=20, at="points", fudge=f) 344s + bw.relrisk(sporophores, method="leastsquares") 344s + } 344s + if(FULLTEST) { 344s + pants(X=sporophores, sigma=20, relative=TRUE, at="points", fudge=f) 344s + pants(X=sporophores, sigma=20, at="pixels", se=FALSE) 344s + pants(X=sporophores, sigma=20, relative=TRUE, at="pixels", se=FALSE) 344s + bw.relrisk(sporophores, method="weightedleastsquares") 344s + } 344s + 344s + ## execute Smooth.ppp and Smoothfun.ppp in all cases 344s + stroke <- function(..., Y = longleaf, FUN=TRUE) { 344s + Z <- Smooth(Y, ..., at="pixels") 344s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 344s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 344s + if(FUN) { 344s + f <- Smoothfun(Y, ...) 344s + f(120, 80) 344s + f(Y[1:2]) 344s + f(Y[FALSE]) 344s + U <- as.im(f) 344s + } 344s + return(invisible(NULL)) 344s + } 344s + if(ALWAYS) { 344s + stroke() 344s + stroke(5, diggle=TRUE) 344s + stroke(5, geometric=TRUE) 344s + stroke(1e-6) # generates warning about small bandwidth 344s + stroke(5, weights=expression(x)) 344s + stroke(5, kernel="epa") 344s + stroke(sigma=Inf) 344s + stroke(varcov1=diag(c(1,1))) # 'anisotropic' code 344s + } 344s + if(FULLTEST) { 344s + Z <- as.im(function(x,y){abs(x)+1}, Window(longleaf)) 344s + stroke(5, weights=Z) 344s + stroke(5, weights=runif(npoints(longleaf))) 344s + stroke(varcov=diag(c(25, 36))) 344s + stroke(varcov=diag(c(25, 36)), weights=runif(npoints(longleaf))) 344s + stroke(5, Y=longleaf %mark% 1) 344s + stroke(5, Y=cut(longleaf,breaks=3)) 344s + stroke(5, weights=Z, geometric=TRUE) 344s + g <- function(x,y) { dnorm(x, sd=10) * dnorm(y, sd=10) } 344s + stroke(kernel=g, cutoff=30, FUN=FALSE) 344s + stroke(kernel=g, cutoff=30, scalekernel=TRUE, sigma=1, FUN=FALSE) 344s + } 344s + if(FULLTEST) { 344s + ## standard errors - single column of marks 344s + stroke(sigma=5, se=TRUE) 344s + stroke(sigma=5, se=TRUE, loctype="f") 344s + w <- runif(npoints(longleaf)) 344s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="i") 344s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="m") 344s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="i") 344s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="m") 344s + } 344s + 344s + niets <- markmean(longleaf, 9) 344s + 344s + strike <- function(..., Y=finpines) { 344s + Z <- Smooth(Y, ..., at="pixels") 344s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 344s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 344s + f <- Smoothfun(Y, ...) 344s + f(4, 1) 344s + f(Y[1:2]) 344s + f(Y[FALSE]) 344s + U <- as.im(f) 344s + return(invisible(NULL)) 344s + } 344s + if(ALWAYS) { 344s + strike() 344s + strike(sigma=1.5, kernel="epa") 344s + strike(varcov=diag(c(1.2, 2.1))) 344s + strike(sigma=1e-6) 344s + strike(sigma=Inf) 344s + } 344s + if(FULLTEST) { 344s + strike(sigma=1e-6, kernel="epa") 344s + strike(1.5, weights=runif(npoints(finpines))) 344s + strike(1.5, weights=expression(y)) 344s + strike(1.5, geometric=TRUE) 344s + strike(1.5, Y=finpines[FALSE]) 344s + flatfin <- finpines %mark% data.frame(a=rep(1, npoints(finpines)), b=2) 344s + strike(1.5, Y=flatfin) 344s + strike(1.5, Y=flatfin, geometric=TRUE) 344s + } 344s + if(FULLTEST) { 344s + ## standard errors - multivariate marks 344s + strike(sigma=1.5, se=TRUE) 344s + strike(sigma=1.5, se=TRUE, loctype="f") 344s + w <- runif(npoints(finpines)) 344s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="i") 344s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="m") 344s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="i") 344s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="m") 344s + } 344s + opx <- spatstat.options(densityTransform=FALSE) 344s + if(ALWAYS) { 344s + stroke(5, Y=longleaf[order(longleaf$x)], sorted=TRUE) 344s + } 344s + if(FULLTEST) { 344s + strike(1.5, Y=finpines[order(finpines$x)], sorted=TRUE) 344s + } 344s + spatstat.options(opx) 344s + 344s + ## detect special cases 344s + if(ALWAYS) { 344s + Smooth(longleaf[FALSE]) 344s + Smooth(longleaf, minnndist(longleaf)) 344s + Xconst <- cells %mark% 1 344s + Smooth(Xconst, 0.1) 344s + Smooth(Xconst, 0.1, at="points") 344s + Smooth(cells %mark% runif(42), sigma=Inf) 344s + Smooth(cells %mark% runif(42), sigma=Inf, at="points") 344s + Smooth(cells %mark% runif(42), sigma=Inf, at="points", leaveoneout=FALSE) 344s + Smooth(cut(longleaf, breaks=4)) 344s + } 344s + 344s + ## code not otherwise reached 344s + if(ALWAYS) { 344s + smoothpointsEngine(cells, values=rep(1, npoints(cells)), sigma=0.2) 344s + } 344s + if(FULLTEST) { 344s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=Inf) 344s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=1e-16) 344s + } 344s + 344s + ## validity of Smooth.ppp(at='points') 344s + Y <- longleaf %mark% runif(npoints(longleaf), min=41, max=43) 344s + Z <- Smooth(Y, 5, at="points", leaveoneout=TRUE) 344s + rZ <- range(Z) 344s + if(rZ[1] < 40 || rZ[2] > 44) 344s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=TRUE)") 344s + 344s + Z <- Smooth(Y, 5, at="points", leaveoneout=FALSE) 344s + rZ <- range(Z) 344s + if(rZ[1] < 40 || rZ[2] > 44) 344s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=FALSE)") 344s + 344s + ## compare Smooth.ppp results with different algorithms 344s + if(ALWAYS) { 344s + crosscheque(Smooth(longleaf, at="points", sigma=6)) 344s + wt <- runif(npoints(longleaf)) 344s + crosscheque(Smooth(longleaf, at="points", sigma=6, weights=wt)) 344s + } 344s + if(FULLTEST) { 344s + vc <- diag(c(25,36)) 344s + crosscheque(Smooth(longleaf, at="points", varcov=vc)) 344s + crosscheque(Smooth(longleaf, at="points", varcov=vc, weights=wt)) 344s + } 344s + ## drop-dimension coding errors 344s + if(FULLTEST) { 344s + X <- longleaf 344s + marks(X) <- cbind(marks(X), 1) 344s + Z <- Smooth(X, 5) 344s + 344s + ZZ <- bw.smoothppp(finpines, hmin=0.01, hmax=0.012, nh=2) # reshaping problem 344s + } 344s + 344s + ## geometric-mean smoothing 344s + if(ALWAYS) { 344s + U <- Smooth(longleaf, 5, geometric=TRUE) 344s + } 344s + if(FULLTEST) { 344s + UU <- Smooth(X, 5, geometric=TRUE) 344s + V <- Smooth(longleaf, 5, geometric=TRUE, at="points") 344s + VV <- Smooth(X, 5, geometric=TRUE, at="points") 344s + } 344s + 344s + if(FULLTEST) { 344s + ## isotropic and anisotropic cases of bw.smoothppp 344s + bi <- bw.smoothppp(longleaf) 344s + ba <- bw.smoothppp(longleaf, varcov1=diag(c(1,1))) 344s + ## should be equal 344s + if(abs(bi-ba) > 0.001) 344s + stop(paste("Inconsistency in bw.smoothppp: isotropic =", bi, 344s + "!=", ba, "= anisotropic")) 344s + } 344s + }) 348s > 348s > reset.spatstat.options() 348s > 348s > local({ 348s + if(ALWAYS) { 348s + #' Kmeasure, second.moment.engine 348s + #' Expansion of window 348s + Zno <- Kmeasure(redwood, sigma=0.2, expand=FALSE) 348s + Zyes <- Kmeasure(redwood, sigma=0.2, expand=TRUE) 348s + #' All code blocks 348s + sigmadouble <- rep(0.1, 2) 348s + diagmat <- diag(sigmadouble^2) 348s + generalmat <- matrix(c(1, 0.5, 0.5, 1)/100, 2, 2) 348s + Z <- Kmeasure(redwood, sigma=sigmadouble) 348s + Z <- Kmeasure(redwood, varcov=diagmat) 348s + Z <- Kmeasure(redwood, varcov=generalmat) 348s + A <- second.moment.calc(redwood, 0.1, what="all", debug=TRUE) 348s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 348s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 348s + D <- second.moment.calc(redwood, varcov=generalmat, what="all") 348s + PR <- pixellate(redwood) 348s + DRno <- second.moment.calc(PR, 0.2, debug=TRUE, expand=FALSE, 348s + npts=npoints(redwood), obswin=Window(redwood)) 348s + DRyes <- second.moment.calc(PR, 0.2, debug=TRUE, expand=TRUE, 348s + npts=npoints(redwood), obswin=Window(redwood)) 348s + DR2 <- second.moment.calc(solist(PR, PR), 0.2, debug=TRUE, expand=TRUE, 348s There were 22 warnings (use warnings() to see them) 348s + npts=npoints(redwood), obswin=Window(redwood)) 348s + Gmat <- generalmat * 100 348s + isoGauss <- function(x,y) {dnorm(x) * dnorm(y)} 348s + ee <- evaluate2Dkernel(isoGauss, runif(10), runif(10), 348s + varcov=Gmat, scalekernel=TRUE) 348s + isoGaussIm <- as.im(isoGauss, square(c(-3,3))) 348s + gg <- evaluate2Dkernel(isoGaussIm, runif(10), runif(10), 348s + varcov=Gmat, scalekernel=TRUE) 348s + ## experimental code 348s + op <- spatstat.options(developer=TRUE) 348s + DR <- density(redwood, 0.1) 348s + spatstat.options(op) 348s + } 348s + }) 349s smooth: maximum imaginary part= 4.59e-18 349s smooth: mass error= 0 349s 2nd moment measure: maximum imaginary part= 1.06e-16 349s 2nd moment measure: mass error= 0 349s smooth: maximum imaginary part= 2.27e-18 349s smooth: mass error= 0 349s 2nd moment measure: maximum imaginary part= 7.68e-17 349s 2nd moment measure: mass error= 0 349s smooth: maximum imaginary part= 6.13e-18 349s smooth: mass error= -4.97e-14 349s 2nd moment measure: maximum imaginary part= 3.87e-16 349s 2nd moment measure: mass error= 4.55e-13 349s smooth component 1 : maximum imaginary part= 6.13e-18 349s smooth component 1 : mass error= -4.97e-14 349s smooth component 2 : maximum imaginary part= 6.13e-18 349s smooth component 2 : mass error= -4.97e-14 349s 2nd moment measure: maximum imaginary part= 3.87e-16 349s 2nd moment measure: mass error= 4.55e-13 349s 2nd moment measure: maximum imaginary part= 3.87e-16 349s 2nd moment measure: mass error= 4.55e-13 349s > 349s > local({ 349s + if(FULLTEST) { 349s + #' bandwidth selection 349s + op <- spatstat.options(n.bandwidth=8) 349s + bw.diggle(cells) 349s + bw.diggle(cells, method="interpreted") # undocumented test 349s + ## bw.relrisk(urkiola, hmax=20) is tested in man/bw.relrisk.Rd 349s + bw.relrisk(urkiola, hmax=20, method="leastsquares") 349s + bw.relrisk(urkiola, hmax=20, method="weightedleastsquares") 349s + ZX <- density(swedishpines, at="points") 349s + bw.pcf(swedishpines, lambda=ZX) 349s + bw.pcf(swedishpines, lambda=ZX, 349s + bias.correct=FALSE, simple=FALSE, cv.method="leastSQ") 349s + spatstat.options(op) 349s + } 349s + }) 349s > 349s > local({ 349s + if(FULLTEST) { 349s + ## idw 349s + Z <- idw(longleaf, power=4) 349s + Z <- idw(longleaf, power=4, se=TRUE) 349s + ZX <- idw(longleaf, power=4, at="points") 349s + ZX <- idw(longleaf, power=4, at="points", se=TRUE) 349s + } 349s + if(ALWAYS) { 349s + ## former bug in densityVoronoi.ppp 349s + X <- redwood[1:2] 349s + A <- densityVoronoi(X, f=0.51, counting=FALSE, fixed=FALSE, nrep=50, verbose=FALSE) 349s + ## dodgy code blocks in densityVoronoi.R 349s + A <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE) 349s + B <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE, fixed=TRUE) 349s + D <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE) 349s + E <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE, fixed=TRUE) 349s + } 349s + if(FULLTEST) { 349s + #' adaptive kernel estimation 349s + d10 <- nndist(nztrees, k=10) 349s + d10fun <- distfun(nztrees, k=10) 349s + d10im <- as.im(d10fun) 349s + uN <- 2 * runif(npoints(nztrees)) 349s + AA <- densityAdaptiveKernel(nztrees, bw=d10) 349s + BB <- densityAdaptiveKernel(nztrees, bw=d10, weights=uN) 349s + DD <- densityAdaptiveKernel(nztrees, bw=d10fun, weights=uN) 349s + EE <- densityAdaptiveKernel(nztrees, bw=d10im, weights=uN) 349s + } 349s + }) 350s Computing 2 intensity estimates...1, 350s 2. 350s Done. 350s Computing 2 intensity estimates...1, 350s 2. 350s Done. 350s Computing 2 intensity estimates...1, 350s 2. 350s Done. 350s Computing 2 intensity estimates...1, 350s 2. 350s Done. 350s > 350s > local({ 350s + if(FULLTEST) { 350s + ## cases of 'intensity' etc 350s + a <- intensity(amacrine, weights=expression(x)) 350s + SA <- split(amacrine) 350s + a <- intensity(SA, weights=expression(x)) 350s + a <- intensity(SA, weights=amacrine$x) 350s + 350s + ## check infrastructure for 'densityfun' 350s + f <- densityfun(cells, 0.05) 350s + Z <- as.im(f) 350s + Z <- as.im(f, W=square(0.5)) 350s + } 350s + }) 350s > 350s > local({ 350s + if(FULLTEST) { 350s + ## other cases of SpatialQuantile.ppp 350s + X <- longleaf 350s + marks(X) <- round(marks(X), -1) 350s + Z <- SpatialMedian(X, 30, type=4) 350s + ZX <- SpatialMedian(X, 30, type=4, at="points") 350s + ZXP <- SpatialMedian(X, 30, at="points", leaveoneout=FALSE) 350s + } 350s + }) 350s > 350s > 350s > 350s > reset.spatstat.options() 350s > 350s > 350s BEGIN TEST testsEtoF.R 350s 350s R version 4.4.3 (2025-02-28) -- "Trophy Case" 350s Copyright (C) 2025 The R Foundation for Statistical Computing 350s Platform: aarch64-unknown-linux-gnu 350s 350s R is free software and comes with ABSOLUTELY NO WARRANTY. 350s You are welcome to redistribute it under certain conditions. 350s Type 'license()' or 'licence()' for distribution details. 350s 350s R is a collaborative project with many contributors. 350s Type 'contributors()' for more information and 350s 'citation()' on how to cite R or R packages in publications. 350s 350s Type 'demo()' for some demos, 'help()' for on-line help, or 350s 'help.start()' for an HTML browser interface to help. 350s Type 'q()' to quit R. 350s 350s > #' 350s > #' Header for all (concatenated) test files 350s > #' 350s > #' Require spatstat.explore 350s > #' Obtain environment variable controlling tests. 350s > #' 350s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 350s > 350s > require(spatstat.explore) 350s Loading required package: spatstat.explore 350s Loading required package: spatstat.data 352s Loading required package: spatstat.univar 352s spatstat.univar 3.1-1 352s Loading required package: spatstat.geom 352s spatstat.geom 3.3-5 352s Loading required package: spatstat.random 352s spatstat.random 3.3-2 352s Loading required package: nlme 352s spatstat.explore 3.3-4 352s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 352s > ALWAYS <- TRUE 352s > cat(paste("--------- Executing", 352s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 352s + "test code -----------\n")) 352s --------- Executing **RESTRICTED** subset of test code ----------- 352s > # 352s > # tests/envelopes.R 352s > # 352s > # Test validity of envelope data 352s > # 352s > # $Revision: 1.29 $ $Date: 2024/01/10 13:45:29 $ 352s > # 352s > 352s > local({ 352s + 352s + 352s + 352s + ## check envelope calls from 'alltypes' 352s + if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE) 352s + if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE) 352s + ## check 'transform' idioms 352s + if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x)) 352s + if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x)) 352s + 352s + 352s + # check conditional simulation 352s + if(FULLTEST) { 352s + e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE) 352s + e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE) 352s + e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE) 352s + e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks 352s + e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE) 352s + } 352s + 352s + 352s + ## check pooling of envelopes in global case 352s + E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE) 352s + E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE) 352s + p12 <- pool(E1, E2) 352s + p12 <- pool(E1, E2, savefuns=TRUE) 352s + if(FULLTEST) { 352s + F1 <- envelope(cells, Kest, nsim=5, 352s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 352s + F2 <- envelope(cells, Kest, nsim=12, 352s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 352s + p12 <- pool(F1, F2) 352s + p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE) 352s + E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE, 352s + ginterval=c(0.05, 0.15)) 352s + E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE, 352s + ginterval=c(0.05, 0.15)) 352s + p12r <- pool(E1r, E2r) 352s + } 352s + 352s + if(FULLTEST) { 352s + #' as.data.frame.envelope 352s + Nsim <- 5 352s + E <- envelope(cells, nsim=Nsim, savefuns=TRUE) 352s + A <- as.data.frame(E) 352s + B <- as.data.frame(E, simfuns=TRUE) 352s + stopifnot(ncol(B) - ncol(A) == Nsim) 352s + } 352s + 352s + if(FULLTEST) { 352s + #' cases not covered elsewhere 352s + A <- envelope(cells, nsim=5, alternative="less", 352s + do.pwrong=TRUE, use.theory=FALSE, 352s + savepatterns=TRUE, savefuns=TRUE) 352s + print(A) 352s + B <- envelope(A, nsim=5, savefuns=TRUE) 352s + D <- envelope(cells, "Lest", nsim=5) 352s + 352s + UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE) 352s + 352s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE) 352s + AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE) 352s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 352s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 352s + 352s + #' spotted by Art Stock - bugs in ratfv class support 352s + BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="border") 352s + CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border") 352s + DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="trans") 352s + EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans") 352s + 352s + #' envelopes based on sample variance 352s + E <- envelope(cells, nsim=8, VARIANCE=TRUE) 352s + G <- envelope(cells, nsim=8, VARIANCE=TRUE, 352s + use.theory=FALSE, do.pwrong=TRUE) 352s + print(G) 352s + #' summary method 352s + summary(E) 352s + summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42)))) 352s + #' weights argument 352s + H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 352s + H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 352s + J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 352s + J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 352s + #' pooling with weights 352s + H <- pool(H1, H2) 352s + J <- pool(J1, J2) 352s + #' pooling envelopes with non-identical attributes 352s + H0 <- envelope(cells, nsim=4, savefuns=TRUE) 352s + HH <- pool(H0, H1) 352s + #' malformed argument 'simulate' 352s + A <- replicate(3, list(list(runifpoint(ex=cells)))) # list(list(ppp), list(ppp), list(ppp)) 352s + E <- envelope(cells, simulate=A, nsim=3) 352s + #' undocumented/secret 352s + K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE) 352s + #' so secret I've even forgotten how to do it 352s + M <- envelope(cells, nsim=4, internal=list(eject="patterns")) 352s + } 352s + 352s + 352s + if(ALWAYS) { 352s + #' Test robustness of envelope() sorting procedure when NA's are present 352s + #' Fails with spatstat.utils 1.12-0 352s + set.seed(42) 352s + EP <- envelope(longleaf, pcf, nsim=10, nrank=2) 352s + 352s + #' Test case when the maximum permitted number of failures is exceeded 352s + X <- amacrine[1:153] # contains exactly one point with mark='off' 352s + #' High probability of generating a pattern with no marks = 'off' 352s + E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn") 352s + A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2) 352s + } 352s + 352s + if(ALWAYS) { 352s + #' Internals: envelope.matrix 352s + Y <- matrix(rnorm(200), 10, 20) 352s + rr <- 1:10 352s + oo <- rnorm(10) 352s + zz <- numeric(10) 352s + E <- envelope(Y, rvals=rr, observed=oo, nsim=10) 352s + E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10) 352s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 352s + type="global", use.theory=TRUE) 352s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 352s + type="global", use.theory=TRUE, nsim=10) 352s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 352s + type="global", use.theory=FALSE, nsim=10) 352s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 352s + nsim=10, nsim2=10) 352s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 352s + jsim=1:10, jsim.mean=11:20) 352s + if(FULLTEST) print(E) 352s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 352s + nsim=10, jsim.mean=11:20) 352s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 352s + jsim=1:10, nsim2=10) 352s + } 352s + 352s + if(ALWAYS) { 352s + #' quirk with handmade summary functions ('conserve' attribute) 352s + Kdif <- function(X, r=NULL) { # note no ellipsis 352s + Y <- split(X) 352s + K1 <- Kest(Y[[1]], r=r) 352s + K2 <- Kest(Y[[2]], r=r) 352s + D <- eval.fv(K1-K2) 352s + return(D) 352s + } 352s + envelope(amacrine, Kdif, nsim=3) 352s + } 352s + 352s + 352s + ## close 'local' 352s + }) 353s Generating 4 simulations of CSR ... 353s 1, 2, 3, 353s 4. 353s 353s Done. 353s Generating 5 simulations of CSR ... 353s 1, 2, 3, 4, 353s 5. 353s 353s Done. 353s Generating 12 simulations of CSR ... 353s 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 353s 12. 353s 353s Done. 353s Generating 10 simulations of CSR ... 353s 1, 2, 3, 4, 5, 6, 7, 8, 9, 353s 10. 353s 353s Done. 353s Generating 39 simulations of CSR ... 353s [retrying] 353s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 353s No points have mark i = off 353s 1, 2, 3, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 353s No points have mark i = off 353s 4, [retrying] 353s 5, 6, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 353s No points have mark i = off 353s 353s Done. 354s Generating 3 simulations of CSR ... 354s 1, 2, 354s 3. 354s 354s Done. 354s Pointwise critical envelopes for K1(r)-K2(r) 354s and observed value for ‘amacrine’ 354s Edge correction: “iso” 354s Obtained from 3 simulations of CSR 354s Alternative: two.sided 354s Significance level of pointwise Monte Carlo test: 2/4 = 0.5 354s ................................................................................ 354s Math.label 354s r r 354s obs hat((K1-K2))[obs](r) 354s theo (K1-K2)[theo](r) 354s lo hat((K1-K2))[lo](r) 354s hi hat((K1-K2))[hi](r) 354s Description 354s r distance argument r 354s obs observed value of K1(r)-K2(r) for data pattern 354s theo theoretical value of K1(r)-K2(r) for CSR 354s lo lower pointwise envelope of K1(r)-K2(r) from simulations 354s hi upper pointwise envelope of K1(r)-K2(r) from simulations 354s ................................................................................ 354s Default plot formula: .~r 354s where “.” stands for ‘obs’, ‘theo’, ‘hi’, ‘lo’ 354s Columns ‘lo’ and ‘hi’ will be plotted as shading (by default) 354s Recommended range of argument r: [0, 0.25] 354s Available range of argument r: [0, 0.25] 354s Unit of length: 662 microns 354s Warning messages: 354s 1: Exceeded maximum permissible number of (maxnerr = 2) when evaluating summary function for simulated point patterns 354s 2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) : 354s 3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns 354s number of data points exceeds 0 - computing border correction estimate only 354s > # 354s > # tests/fastK.R 354s > # 354s > # check fast and slow code for Kest 354s > # and options not tested elsewhere 354s > # 354s > # $Revision: 1.5 $ $Date: 2020/04/28 12:58:26 $ 354s > # 354s > if(ALWAYS) { 354s + local({ 354s + ## fast code 354s + Kb <- Kest(cells, nlarge=0) 354s + Ku <- Kest(cells, correction="none") 354s + Kbu <- Kest(cells, correction=c("none", "border")) 354s + ## slow code, full set of corrections, sqrt transformation, ratios 354s + Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE) 354s + ## Lotwick-Silverman var approx (rectangular window) 354s + Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE) 354s + ## Code for large dataset 354s + nbig <- .Machine$integer.max 354s + if(!is.null(nbig)) { 354s + nn <- ceiling(sqrt(nbig)) 354s + if(nn < 1e6) Kbig <- Kest(runifpoint(nn), 354s + correction=c("border", "bord.modif", "none"), 354s + ratio=TRUE) 354s + } 354s + 354s + ## Kinhom 354s + lam <- density(cells, at="points", leaveoneout=TRUE) 354s + ## fast code 354s + Kib <- Kinhom(cells, lam, nlarge=0) 354s + Kiu <- Kest(cells, lam, correction="none") 354s + Kibu <- Kest(cells, lam, correction=c("none", "border")) 354s + ## slow code 354s + Lidd <- Linhom(unmark(demopat), sigma=bw.scott) 354s + }) 354s + 354s + } 356s number of data points exceeds 0 - computing border correction estimate only 356s Warning message: 356s Periodic correction is not defined for non-rectangular windows 356s > ## 356s > ## tests/fvproblems.R 356s > ## 356s > ## problems with fv, ratfv and fasp code 356s > ## 356s > ## $Revision: 1.15 $ $Date: 2020/04/28 12:58:26 $ 356s > 356s > #' This appears in the workshop notes 356s > #' Problem detected by Martin Bratschi 356s > 356s > if(FULLTEST) { 356s + local({ 356s + Jdif <- function(X, ..., i) { 356s + Jidot <- Jdot(X, ..., i=i) 356s + J <- Jest(X, ...) 356s + dif <- eval.fv(Jidot - J) 356s + return(dif) 356s + } 356s + Z <- Jdif(amacrine, i="on") 356s + }) 356s + } 356s > #' 356s > #' Test mathlegend code 356s > #' 356s > local({ 356s + K <- Kest(cells) 356s + if(FULLTEST) { 356s + plot(K) 356s + plot(K, . ~ r) 356s + plot(K, . - theo ~ r) 356s + } 356s + if(ALWAYS) { 356s + plot(K, sqrt(./pi) ~ r) 356s + } 356s + if(FULLTEST) { 356s + plot(K, cbind(iso, theo) ~ r) 356s + plot(K, cbind(iso, theo) - theo ~ r) 356s + plot(K, sqrt(cbind(iso, theo)/pi) ~ r) 356s + plot(K, cbind(iso/2, -theo) ~ r) 356s + plot(K, cbind(iso/2, trans/2) - theo ~ r) 356s + } 356s + if(FULLTEST) { 356s + ## test expansion of .x and .y 356s + plot(K, . ~ .x) 356s + plot(K, . - theo ~ .x) 356s + plot(K, .y - theo ~ .x) 356s + } 356s + if(ALWAYS) { 356s + plot(K, sqrt(.y) - sqrt(theo) ~ .x) 356s + } 356s + 356s + # problems with parsing weird strings in levels(marks(X)) 356s + # noted by Ulf Mehlig 356s + if(ALWAYS) { 356s + levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis") 356s + plot(Kcross(amacrine)) 356s + plot(alltypes(amacrine, "K")) 356s + } 356s + if(FULLTEST) { 356s + plot(alltypes(amacrine, "J")) 356s + plot(alltypes(amacrine, pcfcross)) 356s + } 356s + }) 356s > 356s > #' 356s > #' Test quirks related to 'alim' attribute 356s > 356s > if(FULLTEST) { 356s + local({ 356s + K <- Kest(cells) 356s + attr(K, "alim") <- NULL 356s + plot(K) 356s + attr(K, "alim") <- c(0, 0.1) 356s + plot(tail(K)) 356s + }) 356s + } 356s > 356s > #' 356s > #' Check that default 'r' vector passes the test for fine spacing 356s > 356s > if(ALWAYS) { 356s + local({ 356s + a <- Fest(cells) 356s + A <- Fest(cells, r=a$r) 356s + b <- Hest(heather$coarse) 356s + B <- Hest(heather$coarse, r=b$r) 356s + # from Cenk Icos 356s + X <- runifpoint(100, owin(c(0,3), c(0,10))) 356s + FX <- Fest(X) 356s + FXr <- Fest(X, r=FX$r) 356s + JX <- Jest(X) 356s + }) 356s + } 357s > 357s > ##' various functionality in fv.R 357s > 357s > if(ALWAYS) { 357s + local({ 357s + M <- cbind(1:20, matrix(runif(100), 20, 5)) 357s + A <- as.fv(M) 357s + fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)") 357s + A <- rename.fv(A, "M", quote(M(r))) 357s + A <- tweak.fv.entry(A, "V1", new.tag="r") 357s + A[,3] <- NULL 357s + A$hogwash <- runif(nrow(A)) 357s + fvnames(A, ".") <- NULL 357s + #' bind.fv with qualitatively different functions 357s + GK <- harmonise(G=Gest(cells), K=Kest(cells)) 357s + G <- GK$G 357s + K <- GK$K 357s + ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10)) 357s + U <- bind.fv(G, K[ss, ], clip=TRUE) 357s + #' 357s + H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2) 357s + H <- rebadge.as.dotfun(K, "H", "inhom", 3) 357s + #' text layout 357s + op <- options(width=27) 357s + print(K) 357s + options(width=18) 357s + print(K) 357s + options(op) 357s + #' collapse.fv 357s + Kb <- Kest(cells, correction="border") 357s + Ki <- Kest(cells, correction="isotropic") 357s + collapse.fv(Kb, Ki, same="theo") 357s + collapse.fv(anylist(B=Kb, I=Ki), same="theo") 357s + collapse.fv(anylist(B=Kb), I=Ki, same="theo") 357s + Xlist <- replicate(3, runifpoint(30), simplify=FALSE) 357s + Klist <- anylapply(Xlist, Kest) 357s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 357s + names(Klist) <- LETTERS[24:26] 357s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 357s + }) 357s + } 357s Function value object 357s (class ‘fv’) 357s for the function r -> K(r) 357s ........................... 357s Math.label 357s r r 357s theo K[pois](r) 357s border hat(K)[bord](r) 357s trans hat(K)[trans](r) 357s iso hat(K)[iso](r) 357s Description 357s r distance argument r 357s theo theoretical [..] 357s border [..] 357s trans [..] 357s iso [..] 357s ........................... 357s Default plot formula: .~r 357s where “.” stands for 357s ‘iso’, ‘trans’, 357s ‘border’, ‘theo’ 357s Recommended range of 357s argument r: [0, 0.25] 357s Available range of 357s argument r: [0, 0.25] 357s Function value 357s object (class 357s ‘fv’) 357s for the function 357s r -> K(r) 357s .................. 357s Math.label 357s r r 357s theo K[pois](r) 357s border hat(K)[bord](r) 357s trans hat(K)[trans](r) 357s iso hat(K)[iso](r) 357s Description 357s r [..] 357s theo [..] 357s border [..] 357s trans [..] 357s iso [..] 357s .................. 357s Default plot 357s formula: .~r 357s where “.” 357s stands for 357s ‘iso’, 357s ‘trans’, 357s ‘border’, 357s ‘theo’ 357s Recommended range 357s of argument r: 357s [0, 0.25] 357s Available range 357s of argument r: 357s [0, 0.25] 357s Function value object (class ‘fv’) 357s for the function r -> K(r) 357s ................................................................ 357s Math.label Description 357s r r distance argument r 357s theo K[pois](r) theoretical Poisson K(r) 357s Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r) 357s Xiso X~hat(K)[iso](r) X isotropic-corrected estimate of K(r) 357s Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r) 357s Yiso Y~hat(K)[iso](r) Y isotropic-corrected estimate of K(r) 357s Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r) 357s Ziso Z~hat(K)[iso](r) Z isotropic-corrected estimate of K(r) 357s ................................................................ 357s Default plot formula: .~.x 357s where “.” stands for ‘theo’, ‘Xborder’, ‘Xiso’, ‘Yborder’, 357s ‘Yiso’, ‘Zborder’, ‘Ziso’ 357s Recommended range of argument r: [0, 0.25] 357s Available range of argument r: [0, 0.25] 357s Warning message: 357s In bind.fv(G, K[ss, ], clip = TRUE) : 357s The column name ‘theo’ was duplicated. Unique names were generated 357s > 357s > if(FULLTEST) { 357s + local({ 357s + ## rat 357s + K <- Kest(cells, ratio=TRUE) 357s + G <- Gest(cells, ratio=TRUE) 357s + print(K) 357s + compatible(K, K) 357s + compatible(K, G) 357s + H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE) 357s + }) 357s + } 357s > 357s > if(FULLTEST) { 357s + local({ 357s + ## bug in Jmulti.R colliding with breakpts.R 357s + B <- owin(c(0,3), c(0,10)) 357s + Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B)) 357s + JDX <- Jdot(Y) 357s + JCX <- Jcross(Y) 357s + Jdif <- function(X, ..., i) { 357s + Jidot <- Jdot(X, ..., i=i) 357s + J <- Jest(X, ...) 357s + dif <- eval.fv(Jidot - J) 357s + return(dif) 357s + } 357s + E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y))) 357s + }) 357s + } 357s > 357s > if(FULLTEST) { 357s + local({ 357s + #' fasp axes, title, dimnames 357s + a <- alltypes(amacrine) 357s + a$title <- NULL 357s + plot(a, samex=TRUE, samey=TRUE) 357s + dimnames(a) <- lapply(dimnames(a), toupper) 357s + 357s + b <- as.fv(a) 357s + }) 357s + } 357s > 357s > if(FULLTEST) { 357s + local({ 357s + ## plot.anylist (fv) 357s + b <- anylist(A=Kcross(amacrine), B=Kest(amacrine)) 357s + plot(b, equal.scales=TRUE, main=expression(sqrt(pi))) 357s + plot(b, arrange=FALSE) 357s + }) 357s + } 357s > 357s BEGIN TEST testsGtoJ.R 357s 357s R version 4.4.3 (2025-02-28) -- "Trophy Case" 357s Copyright (C) 2025 The R Foundation for Statistical Computing 357s Platform: aarch64-unknown-linux-gnu 357s 357s R is free software and comes with ABSOLUTELY NO WARRANTY. 357s You are welcome to redistribute it under certain conditions. 357s Type 'license()' or 'licence()' for distribution details. 357s 357s R is a collaborative project with many contributors. 357s Type 'contributors()' for more information and 357s 'citation()' on how to cite R or R packages in publications. 357s 357s Type 'demo()' for some demos, 'help()' for on-line help, or 357s 'help.start()' for an HTML browser interface to help. 357s Type 'q()' to quit R. 357s 357s > #' 357s > #' Header for all (concatenated) test files 357s > #' 357s > #' Require spatstat.explore 357s > #' Obtain environment variable controlling tests. 357s > #' 357s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 357s > 357s > require(spatstat.explore) 357s Loading required package: spatstat.explore 357s Loading required package: spatstat.data 359s Loading required package: spatstat.univar 359s spatstat.univar 3.1-1 359s Loading required package: spatstat.geom 359s spatstat.geom 3.3-5 359s Loading required package: spatstat.random 359s spatstat.random 3.3-2 359s Loading required package: nlme 359s spatstat.explore 3.3-4 359s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 359s > ALWAYS <- TRUE 359s > cat(paste("--------- Executing", 359s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 359s + "test code -----------\n")) 359s --------- Executing **RESTRICTED** subset of test code ----------- 359s > ## 359s > ## tests/gcc323.R 359s > ## 359s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 359s > ## 359s > if(ALWAYS) { # depends on hardware 359s + local({ 359s + # critical R values that provoke GCC bug #323 359s + a <- marktable(lansing, R=0.25) 359s + a <- marktable(lansing, R=0.21) 359s + a <- marktable(lansing, R=0.20) 359s + a <- marktable(lansing, R=0.10) 359s + }) 359s + } 360s > #' tests/hypotests.R 360s > #' Hypothesis tests 360s > #' 360s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 360s > 360s > if(FULLTEST) { 360s + local({ 360s + 360s + hopskel.test(redwood, method="MonteCarlo", nsim=5) 360s + 360s + #' quadrat test - spatial methods 360s + a <- quadrat.test(redwood, 3) 360s + domain(a) 360s + shift(a, c(1,1)) 360s + 360s + #' quadrat test - correctness of mapping from table to quadrats 360s + Q2 <- quadratcount(humberside, 2, 3) 360s + T2 <- suppressWarnings(quadrat.test(Q2)) 360s + R2 <- cbind(as.numeric(t(Q2)), round(10 * residuals(T2))) 360s + R2correct <- cbind(c(2, 20, 13, 11, 34, 123), 360s + c(-46, -12, -62, -41, 50, 134)) 360s + if(!all(R2 == R2correct)) 360s + stop("Incorrect count-residual map for quadrat.test(2,3)") 360s + 360s + Q5 <- quadratcount(humberside, 5, 3) 360s + T5 <- suppressWarnings(quadrat.test(Q5)) 360s + R5 <- cbind(as.numeric(t(Q5)), round(10 * residuals(T5))) 360s + R5correct <- cbind( 360s + c( 0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3), 360s + c(-19, -33, -42, 16, -37, -49, -28, -35, -5, -21, 295, 40, -32)) 360s + if(!all(R5 == R5correct)) 360s + stop("Incorrect count-residual map for quadrat.test(5,3)") 360s + 360s + #' cases of studpermu.test 360s + #' X is a hyperframe 360s + b <- studpermu.test(pyramidal, nperm=9) 360s + b <- studpermu.test(pyramidal, nperm=9, use.Tbar=TRUE) 360s + #' X is a list of lists of ppp 360s + ZZ <- split(pyramidal$Neurons, pyramidal$group) 360s + bb <- studpermu.test(ZZ, nperm=9) 360s + 360s + #' Issue #115 360s + X <- runifpoint(50, nsim = 3) 360s + Y <- runifpoint(3000, nsim = 3) 360s + h <- hyperframe(ppp = c(X, Y), group = rep(1:2, 3)) 360s + studpermu.test(h, ppp ~ group) 360s + 360s + #' scan test 360s + Z <- scanmeasure(cells, 0.1, method="fft") 360s + rr <- c(0.05, 1) 360s + scan.test(amacrine, rr, nsim=5, 360s + method="binomial", alternative="less") 360s + }) 360s + } 360s > # 360s > # tests/imageops.R 360s > # 360s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 360s > # 360s > 360s > 360s > if(FULLTEST) { 360s + local({ 360s + #' case of "[.im" and "[<-.im" where index is an ssf 360s + d <- distmap(cells, dimyx=32) 360s + Empty <- cells[FALSE] 360s + EmptyFun <- ssf(Empty, numeric(0)) 360s + ff <- d[EmptyFun] 360s + d[EmptyFun] <- 42 360s + 360s + #' Smooth.im -> blur.im with sigma=NULL 360s + Z <- as.im(function(x,y) { x - y }, letterR, dimyx=32) 360s + ZS <- Smooth(Z) 360s + 360s + #' deprecated -> im.apply(DA, which.max) 360s + Z <- which.max.im(bei.extra) 360s + 360s + #' rotmean 360s + U <- rotmean(Z, origin="midpoint", result="im", padzero=FALSE) 360s + 360s + #' cases of distcdf 360s + distcdf(cells[1:5]) 360s + distcdf(W=cells[1:5], dW=1:5) 360s + distcdf(W=Window(cells), V=cells[1:5]) 360s + distcdf(W=Window(cells), V=cells[1:5], dV=1:5) 360s + }) 360s + } 360s > 360s > 360s BEGIN TEST testsK.R 360s 360s R version 4.4.3 (2025-02-28) -- "Trophy Case" 360s Copyright (C) 2025 The R Foundation for Statistical Computing 360s Platform: aarch64-unknown-linux-gnu 360s 360s R is free software and comes with ABSOLUTELY NO WARRANTY. 360s You are welcome to redistribute it under certain conditions. 360s Type 'license()' or 'licence()' for distribution details. 360s 360s R is a collaborative project with many contributors. 360s Type 'contributors()' for more information and 360s 'citation()' on how to cite R or R packages in publications. 360s 360s Type 'demo()' for some demos, 'help()' for on-line help, or 360s 'help.start()' for an HTML browser interface to help. 360s Type 'q()' to quit R. 360s 360s > #' 360s > #' Header for all (concatenated) test files 360s > #' 360s > #' Require spatstat.explore 360s > #' Obtain environment variable controlling tests. 360s > #' 360s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 360s > 360s > require(spatstat.explore) 360s Loading required package: spatstat.explore 360s Loading required package: spatstat.data 362s Loading required package: spatstat.univar 362s spatstat.univar 3.1-1 362s Loading required package: spatstat.geom 362s spatstat.geom 3.3-5 362s Loading required package: spatstat.random 362s spatstat.random 3.3-2 362s Loading required package: nlme 362s spatstat.explore 3.3-4 362s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 362s > ALWAYS <- TRUE 362s > cat(paste("--------- Executing", 362s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 362s + "test code -----------\n")) 362s --------- Executing **RESTRICTED** subset of test code ----------- 362s > #' 362s > #' tests/kernelstuff.R 362s > #' 362s > #' $Revision: 1.2 $ $Date: 2023/11/05 01:49:45 $ 362s > 362s > local({ 362s + if(FULLTEST) { 362s + #' test all cases in kernels.R 362s + kernames <- c("gaussian", "rectangular", "triangular", 362s + "epanechnikov", "biweight", "cosine", "optcosine") 362s + X <- rnorm(20) 362s + U <- runif(20) 362s + for(ker in kernames) { 362s + dX <- dkernel(X, ker) 362s + fX <- pkernel(X, ker) 362s + qU <- qkernel(U, ker) 362s + m0 <- kernel.moment(0, 0, ker) 362s + m1 <- kernel.moment(1, 0, ker) 362s + m2 <- kernel.moment(2, 0, ker) 362s + m3 <- kernel.moment(3, 0, ker) 362s + } 362s + } 362s + }) 362s > 362s > #' 362s > #' tests/Kfuns.R 362s > #' 362s > #' Various K and L functions and pcf 362s > #' 362s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 362s > #' 362s > #' Assumes 'EveryStart.R' was run 362s > 362s > if(FULLTEST) { 362s + Cells <- cells 362s + Amacrine <- amacrine 362s + Redwood <- redwood 362s + } else { 362s + ## reduce numbers of data + dummy points 362s + spatstat.options(npixel=32, ndummy.min=16) 362s + Cells <- cells[c(FALSE, TRUE)] 362s + Amacrine <- amacrine[c(FALSE, TRUE)] 362s + Redwood <- redwood[c(FALSE, TRUE)] 362s + } 362s > 362s > 362s > myfun <- function(x,y){(x+1) * y } # must be outside 362s > 362s > local({ 362s + if(FULLTEST) { 362s + #' supporting code 362s + rmax.rule("Kscaled", owin(), 42) 362s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 362s + "polygonal", TRUE) 362s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 362s + "mask", TRUE) 362s + implemented.for.K(c("border", "isotropic"), "mask", TRUE) 362s + implemented.for.K(c("border", "isotropic"), "mask", FALSE) 362s + #' shortcuts 362s + D <- density(Cells) 362s + K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 362s + K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 362s + allcor <- c("none", "border", "bord.modif","isotropic", "translate") 362s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor) 362s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 362s + weights=D) 362s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 362s + use.integers=FALSE) 362s + #' Kest special code blocks 362s + K <- Kest(Cells, var.approx=TRUE, ratio=FALSE) 362s + Z <- distmap(Cells) + 1 362s + Kb <- Kest(Cells, correction=c("border","bord.modif"), 362s + weights=Z, ratio=TRUE) 362s + Kn <- Kest(Cells, correction="none", 362s + weights=Z, ratio=TRUE) 362s + Knb <- Kest(Cells, correction=c("border","bord.modif","none"), 362s + weights=Z, ratio=TRUE) 362s + } 362s + if(ALWAYS) { 362s + bigint <- 50000 # This is only "big" on a 32-bit system where 362s + # sqrt(.Machine$integer.max) = 46340.9 362s + X <- runifpoint(bigint) 362s + Z <- as.im(1/bigint, owin()) 362s + Kb <- Kest(X, correction=c("border","bord.modif"), 362s + rmax=0.02, weights=Z, ratio=TRUE) 362s + } 362s + if(FULLTEST) { 362s + Kn <- Kest(X, correction="none", 362s + rmax=0.02, weights=Z, ratio=TRUE) 362s + Knb <- Kest(X, correction=c("border","bord.modif","none"), 362s + rmax=0.02, weights=Z, ratio=TRUE) 362s + #' pcf.ppp special code blocks 362s + pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE) 362s + pc <- pcf(Cells, domain=square(0.5)) 362s + pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE) 362s + pw <- pcf(Redwood, correction="none") 362s + pwr <- pcf(Redwood, correction="none", ratio=TRUE) 362s + pv <- pcf(Redwood, kernel="rectangular") 362s + p1 <- pcf(Redwood[1]) 362s + #' pcf.fv 362s + K <- Kest(Redwood) 362s + g <- pcf(K, method="a") 362s + g <- pcf(K, method="c") 362s + g <- pcf(K, method="d") 362s + #' Kinhom code blocks 362s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 362s + lambda <- 100 * X$x 362s + Kin <- Kinhom(X, lambda, correction=c("none", "border")) 362s + lambda2 <- outer(lambda, lambda, "*") 362s + Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE, 362s + correction=c("translate", "isotropic")) 362s + } 362s + if(ALWAYS) { 362s + #' edge corrections 362s + rr <- rep(0.1, npoints(Cells)) 362s + eC <- edge.Ripley(Cells, rr) 362s + eI <- edge.Ripley(Cells, rr, method="interpreted") 362s + if(max(abs(eC-eI)) > 0.1) 362s + stop("Ripley edge correction results do not match") 362s + } 362s + if(FULLTEST) { 362s + a <- rmax.Ripley(square(1)) 362s + a <- rmax.Rigid(square(1)) 362s + a <- rmax.Ripley(as.polygonal(square(1))) 362s + a <- rmax.Rigid(as.polygonal(square(1))) 362s + a <- rmax.Ripley(letterR) 362s + a <- rmax.Rigid(letterR) 362s + } 362s + if(ALWAYS) { 362s + #' run slow code for edge correction and compare results 362s + op <- spatstat.options(npixel=128) 362s + X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)] 362s + Window(X) <- as.polygonal(Window(X)) 362s + Eapprox <- edge.Trans(X) 362s + Eexact <- edge.Trans(X, exact=TRUE) 362s + maxrelerr <- max(abs(1 - range(Eapprox/Eexact))) 362s + if(maxrelerr > 0.1) 362s + stop(paste("Exact and approximate algorithms for edge.Trans disagree by", 362s + paste0(round(100*maxrelerr), "%")), 362s + call.=FALSE) 362s + spatstat.options(op) 362s + } 362s + }) 362s > 362s > local({ 362s + if(FULLTEST) { 362s + #' ---- multitype ------ 362s + K <- Kcross(Amacrine, correction=c("none", "bord.modif")) 362s + K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"), 362s + ratio=TRUE) 362s + #' inhomogeneous multitype 362s + K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine)) 362s + K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points")) 362s + K5 <- Kcross.inhom(Amacrine, correction="bord.modif") 362s + #' markconnect, markcorr 362s + M <- markconnect(Amacrine, "on", "off", normalise=TRUE) 362s + M <- markcorr(longleaf, normalise=TRUE, 362s + correction=c("isotropic", "translate", "border", "none")) 362s + M <- markcorr(longleaf, normalise=TRUE, fargs=list()) 362s + #' Kmark (=markcorrint) 362s + X <- runifpoint(100) %mark% runif(100) 362s + km <- Kmark(X, f=atan2) 362s + km <- Kmark(X, f1=sin) 362s + km <- Kmark(X, f="myfun") 362s + aa <- Kmark(X, normalise=FALSE, returnL=FALSE) 362s + aa <- Kmark(X, normalise=FALSE, returnL=TRUE) 362s + aa <- Kmark(X, normalise=TRUE, returnL=FALSE) 362s + aa <- Kmark(X, normalise=TRUE, returnL=TRUE) 362s + } 362s + }) 362s > 362s > local({ 362s + if(FULLTEST) { 362s + #' various modified K functions 362s + #' 362s + #' directional K functions 362s + #' 362s + a <- Ksector(swedishpines, 362s + -pi/2, pi/2, units="radians", 362s + correction=c("none", "border", "bord.modif", 362s + "Ripley", "translate"), 362s + ratio=TRUE) 362s + plot(a) 362s + #' 362s + #' local K functions 362s + #' 362s + Z <- as.im(intensity(swedishpines), W=Window(swedishpines)) 362s + ZX <- Z[swedishpines] 362s + a <- localLinhom(swedishpines, lambda=Z) 362s + a <- localLinhom(swedishpines, lambda=ZX) 362s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 362s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 362s + a <- localLcross(Amacrine) 362s + a <- localLcross(Amacrine, from="off", to="off") 362s + a <- localKdot(Amacrine) 362s + a <- localLdot(Amacrine) 362s + a <- localKcross.inhom(Amacrine) 362s + a <- localLcross.inhom(Amacrine) 362s + Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine)) 362s + Lum <- evaluateCovariateAtPoints(Zed, Amacrine) 362s + moff <- (marks(Amacrine) == "off") 362s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 362s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 362s + a <- localLcross.inhom(Amacrine, from="off", to="on", 362s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 362s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 362s + correction="none") 362s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 362s + correction="translate") 362s + #' 362s + #' cases of resolve.lambdacross 362s + #' 362s + h <- resolve.lambdacross(Amacrine, moff, !moff) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, 362s + lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, 362s + lambdaI=Lum[moff], lambdaJ=Lum[!moff]) 362s + d <- densityfun(unmark(Amacrine), sigma=0.1) 362s + dm <- lapply(split(Amacrine), densityfun, sigma=0.1) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=d) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, 362s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 362s + h <- resolve.lambdacross(Amacrine, moff, !moff, 362s + lambdaX=function(x,y,m){ d(x,y) }) 362s + #' 362s + #' multitype inhomogeneous pcf 362s + #' 362s + g <- pcfcross.inhom(Amacrine, 362s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 362s + 362s + #' 362s + #' lohboot code blocks 362s + #' 362s + Ared <- lohboot(Redwood, fun="Kest", block=TRUE, 362s + Vcorrection=TRUE, global=FALSE, correction="none") 362s + Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE) 362s + Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE, 362s + correction="translate") 362s + Dred <- lohboot(Redwood, Lest) 362s + Kred <- lohboot(Redwood, Kinhom) 362s + Lred <- lohboot(Redwood, Linhom) 362s + gred <- lohboot(Redwood, pcfinhom, sigma=0.1) 362s + #' 362s + X <- runifpoint(100, letterR) 362s + AX <- lohboot(X, block=TRUE, nx=7, ny=10) 362s + #' multitype 362s + b <- lohboot(Amacrine, Kcross) 362s + b <- lohboot(Amacrine, Lcross) 362s + b <- lohboot(Amacrine, Kdot) 362s + b <- lohboot(Amacrine, Ldot) 362s + b <- lohboot(Amacrine, Kcross.inhom) 362s + b <- lohboot(Amacrine, Lcross.inhom) 362s + 362s + ## Kscaled 362s + A <- Lscaled(japanesepines, renormalise=TRUE, correction="all") 362s + } 362s + }) 362s > 362s > local({ 362s + if(ALWAYS) { 362s + #' From Ege, in response to a stackoverflow question. 362s + discrepancy in isotropic edge correction at interior point of rectangle is 2.22e-16, within tolerance of 1e-06 362s discrepancy in isotropic edge correction near corner of rectangle is 8.882e-16, within tolerance of 1e-06 362s discrepancy in isotropic edge correction at interior point of polygon (debug on) is 6.439e-15, within tolerance of 1e-06 362s discrepancy in isotropic edge correction at interior point of polygon (debug off) is 6.439e-15, within tolerance of 1e-06 362s #' The following example has two points separated by r = 1 with 1/4 of the 362s + #' circumference outside the 10x10 window (i.e. area 100). 362s + #' Thus the value of K^(r) should jump from 0 to 362s + #' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333. 362s + x <- c(4.5,5.5) 362s + y <- c(10,10)-sqrt(2)/2 362s + W <- square(10) 362s + X <- ppp(x, y, W) 362s + compere <- function(a, b, where, tol=1e-6) { 362s + descrip <- paste("discrepancy in isotropic edge correction", where) 362s + err <- as.numeric(a) - as.numeric(b) 362s + maxerr <- max(abs(err)) 362s + blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","), 362s + if(maxerr > tol) "exceeding" else "within", 362s + "tolerance of", tol) 362s + message(blurb) 362s + if(maxerr > tol) { 362s + message(paste("Discrepancies:", paste(err, collapse=", "))) 362s + stop(paste("excessive", descrip), call.=FALSE) 362s + } 362s + invisible(TRUE) 362s + } 362s + ## Testing: 362s + eX <- edge.Ripley(X, c(1,1)) 362s + compere(eX, c(4/3,4/3), "at interior point of rectangle") 362s + ## Corner case: 362s + Y <- X 362s + Y$x <- X$x-4.5+sqrt(2)/2 362s + eY <- edge.Ripley(Y, c(1,1)) 362s + compere(eY, c(2,4/3), "near corner of rectangle") 362s + ## Invoke polygonal code 362s + Z <- rotate(Y, pi/4) 362s + eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE)) 362s + compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)") 362s + ## test validity without debugger,in case of quirks of compiler optimisation 362s + eZ <- edge.Ripley(Z, c(1,1)) 362s + compere(eZ, c(2,4/3), "at interior point of polygon (debug off)") 362s + } 362s + }) 362s /// Debug level 3 /// 362s ------- centre[0] = (-6.071068, 7.071068) ------ 362s boundary distance 0.707107 362s radius[0] = 1.000000 362s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 362s Left: det = -35.857864 362s Right: det = -171.715729 362s Top: det = -34143.145751 362s Finished cutting; ncut = 0 362s contrib = -0.000000 362s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 362s Left: det = -171.715729 362s Right: det = -35.857864 362s Top: det = -34143.145751 362s Finished cutting; ncut = 0 362s contrib = 0.000000 362s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 362s Left: det = -35.857864 362s Right: det = 0.000000 362s det = 0 362s Top: det = 200.000000 362s det > 0 362s hits + segment: t = 1.000000, theta = 3.141593 362s hits - segment: t = 0.858579, theta = 1.570796 362s Finished cutting; ncut = 2 362s theta[0] = 1.570796 362s theta[1] = 3.141593 362s Interval 0, width 1.570796:inside 362s Interval 1, width 1.570796:outside 362s Interval 2, width 3.141593:inside 362s contrib = 4.712389 362s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 362s Left: det = 0.000000 362s det = 0 362s Right: det = -35.857864 362s Top: det = 200.000000 362s det > 0 362s hits + segment: t = 0.141421, theta = -1.570796 362s hits - segment: t = 0.000000, theta = 3.141593 362s Finished cutting; ncut = 2 362s theta[0] = 3.141593 362s theta[1] = 4.712389 362s Interval 0, width 3.141593:outside 362s Interval 1, width 1.570796:inside 362s Interval 2, width 1.570796:outside 362s contrib = -1.570796 362s 362s Total = 3.141593 = 0.500000 * (2 * pi) 362s ------- centre[1] = (-5.363961, 7.778175) ------ 362s boundary distance 0.707107 362s radius[0] = 1.000000 362s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 362s Left: det = -27.772078 362s Right: det = -153.629942 362s Top: det = -34143.145751 362s Finished cutting; ncut = 0 362s contrib = -0.000000 362s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 362s Left: det = -153.629942 362s Right: det = -27.772078 362s Top: det = -27108.831175 362s Finished cutting; ncut = 0 362s contrib = 0.000000 362s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 362s Left: det = -27.772078 362s Right: det = -1.914214 362s Top: det = 200.000000 362s det > 0 362s hits + segment: t = 0.900000, theta = 3.141593 362s hits - segment: t = 0.758579, theta = 1.570796 362s Finished cutting; ncut = 2 362s theta[0] = 1.570796 362s theta[1] = 3.141593 362s Interval 0, width 1.570796:inside 362s Interval 1, width 1.570796:outside 362s Interval 2, width 3.141593:inside 362s contrib = 4.712389 362s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 362s Left: det = -1.914214 362s Right: det = -27.772078 362s Top: det = -765.685425 362s Finished cutting; ncut = 0 362s contrib = -0.000000 362s 362s Total = 4.712389 = 0.750000 * (2 * pi) 362s > 362s > 362s > 362s > reset.spatstat.options() 362s > 362s BEGIN TEST testsL.R 362s 362s R version 4.4.3 (2025-02-28) -- "Trophy Case" 362s Copyright (C) 2025 The R Foundation for Statistical Computing 362s Platform: aarch64-unknown-linux-gnu 362s 362s R is free software and comes with ABSOLUTELY NO WARRANTY. 362s You are welcome to redistribute it under certain conditions. 362s Type 'license()' or 'licence()' for distribution details. 362s 362s R is a collaborative project with many contributors. 362s Type 'contributors()' for more information and 362s 'citation()' on how to cite R or R packages in publications. 362s 362s Type 'demo()' for some demos, 'help()' for on-line help, or 362s 'help.start()' for an HTML browser interface to help. 362s Type 'q()' to quit R. 362s 363s > #' 363s > #' Header for all (concatenated) test files 363s > #' 363s > #' Require spatstat.explore 363s > #' Obtain environment variable controlling tests. 363s > #' 363s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 363s > 363s > require(spatstat.explore) 363s Loading required package: spatstat.explore 363s Loading required package: spatstat.data 364s Loading required package: spatstat.univar 364s spatstat.univar 3.1-1 364s Loading required package: spatstat.geom 364s spatstat.geom 3.3-5 364s Loading required package: spatstat.random 364s spatstat.random 3.3-2 364s Loading required package: nlme 364s spatstat.explore 3.3-4 364s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 364s > ALWAYS <- TRUE 364s > cat(paste("--------- Executing", 364s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 364s + "test code -----------\n")) 364s --------- Executing **RESTRICTED** subset of test code ----------- 364s > ## 364s > ## tests/localpcf.R 364s > ## 364s > ## temporary test file for localpcfmatrix 364s > ## $Revision: 1.2 $ $Date: 2015/12/29 08:54:49 $ 364s > 364s > local({ 364s + a <- localpcfmatrix(redwood) 364s + if(FULLTEST) { 364s + a 364s + plot(a) 364s + a[, 3:5] 364s + } 364s + }) 364s > 364s BEGIN TEST testsM.R 364s 364s R version 4.4.3 (2025-02-28) -- "Trophy Case" 364s Copyright (C) 2025 The R Foundation for Statistical Computing 364s Platform: aarch64-unknown-linux-gnu 364s 364s R is free software and comes with ABSOLUTELY NO WARRANTY. 364s You are welcome to redistribute it under certain conditions. 364s Type 'license()' or 'licence()' for distribution details. 364s 364s R is a collaborative project with many contributors. 364s Type 'contributors()' for more information and 364s 'citation()' on how to cite R or R packages in publications. 364s 364s Type 'demo()' for some demos, 'help()' for on-line help, or 364s 'help.start()' for an HTML browser interface to help. 364s Type 'q()' to quit R. 364s 365s > #' 365s > #' Header for all (concatenated) test files 365s > #' 365s > #' Require spatstat.explore 365s > #' Obtain environment variable controlling tests. 365s > #' 365s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 365s > 365s > require(spatstat.explore) 365s Loading required package: spatstat.explore 365s Loading required package: spatstat.data 366s Loading required package: spatstat.univar 366s spatstat.univar 3.1-1 366s Loading required package: spatstat.geom 366s spatstat.geom 3.3-5 366s Loading required package: spatstat.random 366s spatstat.random 3.3-2 366s Loading required package: nlme 366s spatstat.explore 3.3-4 366s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 366s > ALWAYS <- TRUE 366s > cat(paste("--------- Executing", 366s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 366s + "test code -----------\n")) 366s --------- Executing **RESTRICTED** subset of test code ----------- 366s > ## 366s > ## tests/markcor.R 366s > ## 366s > ## Tests of mark correlation code (etc) 366s > ## 366s > ## $Revision: 1.7 $ $Date: 2020/11/25 01:23:32 $ 366s > 366s > local({ 366s + if(ALWAYS) { 366s + ## check.testfun checks equality of functions 366s + ## and is liable to break if the behaviour of all.equal is changed 366s + fe <- function(m1, m2) {m1 == m2} 366s + fm <- function(m1, m2) {m1 * m2} 366s + fs <- function(m1, m2) {sqrt(m1)} 366s + if(check.testfun(fe, X=amacrine)$ftype != "equ") 366s + warning("check.testfun fails to recognise mark equality function") 366s + if(check.testfun(fm, X=longleaf)$ftype != "mul") 366s + warning("check.testfun fails to recognise mark product function") 366s + check.testfun(fs, X=longleaf) 366s + check.testfun("mul") 366s + check.testfun("equ") 366s + } 366s + 366s + if(FULLTEST) { 366s + ## test all is well in Kmark -> Kinhom 366s + MA <- Kmark(amacrine,function(m1,m2){m1==m2}) 366s + set.seed(42) 366s + AR <- rlabel(amacrine) 366s + MR <- Kmark(AR,function(m1,m2){m1==m2}) 366s + if(isTRUE(all.equal(MA,MR))) 366s + stop("Kmark unexpectedly ignores marks") 366s + 366s + ## cover code blocks in markcorr() 366s + X <- runifpoint(100) %mark% runif(100) 366s + Y <- X %mark% data.frame(u=runif(100), v=runif(100)) 366s + ww <- runif(100) 366s + fone <- function(x) { x/2 } 366s + ffff <- function(x,y) { fone(x) * fone(y) } 366s + aa <- markcorr(Y) 366s + bb <- markcorr(Y, ffff, weights=ww, normalise=TRUE) 366s + bb <- markcorr(Y, ffff, weights=ww, normalise=FALSE) 366s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=TRUE) 366s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=FALSE) 366s + 366s + ## markcrosscorr 366s + a <- markcrosscorr(betacells, normalise=FALSE) 366s + if(require(sm)) { 366s + b <- markcrosscorr(betacells, method="sm") 366s + } 367s + 367s + ## Vmark with normalisation 367s + v <- Vmark(spruces, normalise=TRUE) 367s + v <- Vmark(finpines, normalise=TRUE) 367s + } 367s + }) 367s > #' tests/mctests.R 367s > #' Monte Carlo tests 367s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 367s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 367s > 367s > local({ 367s + if(FULLTEST) { 367s + envelopeTest(cells, Lest, exponent=1, nsim=9, savepatterns=TRUE) 367s + (a3 <- envelopeTest(cells, Lest, exponent=3, nsim=9, savepatterns=TRUE)) 367s + 367s + envelopeTest(a3, Lest, exponent=3, nsim=9, alternative="less") 367s + 367s + envelopeTest(redwood, Lest, exponent=1, nsim=19, 367s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 367s + envelopeTest(redwood, pcf, exponent=Inf, nsim=19, 367s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 367s + } 367s + }) 367s > 367s > 367s > 367s BEGIN TEST testsNtoO.R 367s Warning messages: 367s 1: In eval(quote({ : 367s check.testfun fails to recognise mark equality function 367s 2: In eval(quote({ : 367s check.testfun fails to recognise mark product function 367s 367s R version 4.4.3 (2025-02-28) -- "Trophy Case" 367s Copyright (C) 2025 The R Foundation for Statistical Computing 367s Platform: aarch64-unknown-linux-gnu 367s 367s R is free software and comes with ABSOLUTELY NO WARRANTY. 367s You are welcome to redistribute it under certain conditions. 367s Type 'license()' or 'licence()' for distribution details. 367s 367s R is a collaborative project with many contributors. 367s Type 'contributors()' for more information and 367s 'citation()' on how to cite R or R packages in publications. 367s 367s Type 'demo()' for some demos, 'help()' for on-line help, or 367s 'help.start()' for an HTML browser interface to help. 367s Type 'q()' to quit R. 367s 367s > #' 367s > #' Header for all (concatenated) test files 367s > #' 367s > #' Require spatstat.explore 367s > #' Obtain environment variable controlling tests. 367s > #' 367s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 367s > 367s > require(spatstat.explore) 367s Loading required package: spatstat.explore 367s Loading required package: spatstat.data 368s Loading required package: spatstat.univar 368s spatstat.univar 3.1-1 368s Loading required package: spatstat.geom 368s spatstat.geom 3.3-5 368s Loading required package: spatstat.random 368s spatstat.random 3.3-2 368s Loading required package: nlme 368s spatstat.explore 3.3-4 368s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 368s > ALWAYS <- TRUE 368s > cat(paste("--------- Executing", 368s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 368s + "test code -----------\n")) 368s --------- Executing **RESTRICTED** subset of test code ----------- 368s > # 368s > # tests/nnstat.R 368s > # 368s > # Check code that uses nndist/nnwhich 368s > # 368s > # nnorient() 368s > # stienen() 368s > # 368s > # $Revision: 1.1 $ $Date: 2020/12/04 03:45:44 $ 368s > # 368s > 368s > 368s > local({ 368s + if(FULLTEST) { 368s + #' test nnorient 368s + nnorient(cells, domain=erosion(Window(cells), 0.1)) 368s + #' degenerate case 368s + X <- cells[nndist(cells) > bdist.points(cells)] 368s + f <- nnorient(X) 368s + #' nnclean 368s + A <- nnclean(shapley, k=17, edge.correct=TRUE) 368s + B <- nnclean(runifpoint3(300), 3) 368s + #' stienen set 368s + #' bug when disc radius is zero 368s + Y <- unmark(humberside)[40:100] # contains duplicated points 368s + stienen(Y) 368s + Z <- stienenSet(Y) 368s + #' other cases 368s + U <- stienen(cells[1]) 368s + V <- stienenSet(cells, edge=FALSE) 368s + } 368s + }) 368s > 368s > 368s > 368s > 368s BEGIN TEST testsP1.R 368s 368s R version 4.4.3 (2025-02-28) -- "Trophy Case" 368s Copyright (C) 2025 The R Foundation for Statistical Computing 368s Platform: aarch64-unknown-linux-gnu 368s 368s R is free software and comes with ABSOLUTELY NO WARRANTY. 368s You are welcome to redistribute it under certain conditions. 368s Type 'license()' or 'licence()' for distribution details. 368s 368s R is a collaborative project with many contributors. 368s Type 'contributors()' for more information and 368s 'citation()' on how to cite R or R packages in publications. 368s 368s Type 'demo()' for some demos, 'help()' for on-line help, or 368s 'help.start()' for an HTML browser interface to help. 368s Type 'q()' to quit R. 368s 369s > #' 369s > #' Header for all (concatenated) test files 369s > #' 369s > #' Require spatstat.explore 369s > #' Obtain environment variable controlling tests. 369s > #' 369s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 369s > 369s > require(spatstat.explore) 369s Loading required package: spatstat.explore 369s Loading required package: spatstat.data 370s Loading required package: spatstat.univar 370s spatstat.univar 3.1-1 370s Loading required package: spatstat.geom 370s spatstat.geom 3.3-5 370s Loading required package: spatstat.random 370s spatstat.random 3.3-2 370s Loading required package: nlme 370s spatstat.explore 3.3-4 370s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 370s > ALWAYS <- TRUE 370s > cat(paste("--------- Executing", 370s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 370s + "test code -----------\n")) 370s --------- Executing **RESTRICTED** subset of test code ----------- 370s > ## 370s > ## tests/pixelgripes.R 370s > ## Problems related to pixellation of windows 370s > ## 370s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 370s > 370s > if(FULLTEST) { 370s + local({ 370s + 370s + 370s + }) 370s + } 370s > 370s BEGIN TEST testsP2.R 370s 370s R version 4.4.3 (2025-02-28) -- "Trophy Case" 370s Copyright (C) 2025 The R Foundation for Statistical Computing 370s Platform: aarch64-unknown-linux-gnu 370s 370s R is free software and comes with ABSOLUTELY NO WARRANTY. 370s You are welcome to redistribute it under certain conditions. 370s Type 'license()' or 'licence()' for distribution details. 370s 370s R is a collaborative project with many contributors. 370s Type 'contributors()' for more information and 370s 'citation()' on how to cite R or R packages in publications. 370s 370s Type 'demo()' for some demos, 'help()' for on-line help, or 370s 'help.start()' for an HTML browser interface to help. 370s Type 'q()' to quit R. 370s 371s > #' 371s > #' Header for all (concatenated) test files 371s > #' 371s > #' Require spatstat.explore 371s > #' Obtain environment variable controlling tests. 371s > #' 371s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 371s > 371s > require(spatstat.explore) 371s Loading required package: spatstat.explore 371s Loading required package: spatstat.data 372s Loading required package: spatstat.univar 372s spatstat.univar 3.1-1 372s Loading required package: spatstat.geom 372s spatstat.geom 3.3-5 372s Loading required package: spatstat.random 372s spatstat.random 3.3-2 372s Loading required package: nlme 372s spatstat.explore 3.3-4 372s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 372s > ALWAYS <- TRUE 372s > cat(paste("--------- Executing", 372s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 372s + "test code -----------\n")) 372s --------- Executing **RESTRICTED** subset of test code ----------- 372s > 372s BEGIN TEST testsQ.R 372s 372s R version 4.4.3 (2025-02-28) -- "Trophy Case" 372s Copyright (C) 2025 The R Foundation for Statistical Computing 372s Platform: aarch64-unknown-linux-gnu 372s 372s R is free software and comes with ABSOLUTELY NO WARRANTY. 372s You are welcome to redistribute it under certain conditions. 372s Type 'license()' or 'licence()' for distribution details. 372s 372s R is a collaborative project with many contributors. 372s Type 'contributors()' for more information and 372s 'citation()' on how to cite R or R packages in publications. 372s 372s Type 'demo()' for some demos, 'help()' for on-line help, or 372s 'help.start()' for an HTML browser interface to help. 372s Type 'q()' to quit R. 372s 372s > #' 372s > #' Header for all (concatenated) test files 372s > #' 372s > #' Require spatstat.explore 372s > #' Obtain environment variable controlling tests. 372s > #' 372s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 372s > 372s > require(spatstat.explore) 372s Loading required package: spatstat.explore 372s Loading required package: spatstat.data 374s Loading required package: spatstat.univar 374s spatstat.univar 3.1-1 374s Loading required package: spatstat.geom 374s spatstat.geom 3.3-5 374s Loading required package: spatstat.random 374s spatstat.random 3.3-2 374s Loading required package: nlme 374s spatstat.explore 3.3-4 374s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 374s > ALWAYS <- TRUE 374s > cat(paste("--------- Executing", 374s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 374s + "test code -----------\n")) 374s --------- Executing **RESTRICTED** subset of test code ----------- 374s > 374s BEGIN TEST testsR1.R 374s 374s R version 4.4.3 (2025-02-28) -- "Trophy Case" 374s Copyright (C) 2025 The R Foundation for Statistical Computing 374s Platform: aarch64-unknown-linux-gnu 374s 374s R is free software and comes with ABSOLUTELY NO WARRANTY. 374s You are welcome to redistribute it under certain conditions. 374s Type 'license()' or 'licence()' for distribution details. 374s 374s R is a collaborative project with many contributors. 374s Type 'contributors()' for more information and 374s 'citation()' on how to cite R or R packages in publications. 374s 374s Type 'demo()' for some demos, 'help()' for on-line help, or 374s 'help.start()' for an HTML browser interface to help. 374s Type 'q()' to quit R. 374s 374s > #' 374s > #' Header for all (concatenated) test files 374s > #' 374s > #' Require spatstat.explore 374s > #' Obtain environment variable controlling tests. 374s > #' 374s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 374s > 374s > require(spatstat.explore) 374s Loading required package: spatstat.explore 374s Loading required package: spatstat.data 376s Loading required package: spatstat.univar 376s spatstat.univar 3.1-1 376s Loading required package: spatstat.geom 376s spatstat.geom 3.3-5 376s Loading required package: spatstat.random 376s spatstat.random 3.3-2 376s Loading required package: nlme 376s spatstat.explore 3.3-4 376s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 376s > ALWAYS <- TRUE 376s > cat(paste("--------- Executing", 376s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 376s + "test code -----------\n")) 376s --------- Executing **RESTRICTED** subset of test code ----------- 376s > ## 376s > ## tests/rhohat.R 376s > ## 376s > ## Test all combinations of options for rhohatCalc 376s > ## 376s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 376s > 376s > local({ 376s + if(FULLTEST) { 376s + X <- rpoispp(function(x,y){exp(3+3*x)}) 376s + Z <- as.im(function(x,y) { x }, Window(X)) 376s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 376s + 376s + ## rhohat.ppp 376s + ## done in example(rhohat): 376s + ## rhoA <- rhohat(X, "x") 376s + ## rhoB <- rhohat(X, "x", method="reweight") 376s + ## rhoC <- rhohat(X, "x", method="transform") 376s + ## alternative smoother (if package locfit available) 376s + rhoA <- rhohat(X, "x", smoother="local") 376s + rhoB <- rhohat(X, "x", smoother="local", method="reweight") 376s + rhoC <- rhohat(X, "x", smoother="local", method="transform") 376s + 376s + #' code blocks 376s + rhoD <- rhohat(X, "y", positiveCI=TRUE) 376s + rhoE <- rhohat(X, Z, positiveCI=TRUE) 376s + #' weights 376s + rhoF <- rhohat(X, Z, weights=f(X)) 376s + rhoG <- rhohat(X, Z, weights=f) 376s + rhoH <- rhohat(X, Z, weights=as.im(f)) 376s + 376s + lam <- as.im(function(x,y) {exp(3+2*x)}, W=Window(Z)) 376s + 376s + ## Baseline 376s + rhoAb <- rhohat(X, "x", baseline=lam) 376s + rhoBb <- rhohat(X, "x", method="reweight", baseline=lam) 376s + rhoCb <- rhohat(X, "x", method="transform", baseline=lam) 376s + 376s + ## Horvitz-Thompson 376s + rhoAH <- rhohat(X, "x", horvitz=TRUE) 376s + rhoBH <- rhohat(X, "x", method="reweight", horvitz=TRUE) 376s + rhoCH <- rhohat(X, "x", method="transform", horvitz=TRUE) 376s + 376s + ## class support 376s + plot(rhoA) 376s + plot(rhoA, rho ~ x, shade=NULL) 376s + plot(rhoA, log(rho) ~ x, shade=NULL) 376s + plot(rhoA, log(.) ~ x) 376s + 376s + ## rho2hat 376s + r2xy <- rho2hat(X, "x", "y") 376s + r2xyw <- rho2hat(X, "x", "y", method="reweight") 376s + print(r2xyw) 376s + plot(r2xy, do.points=TRUE) 376s + xcoord <- function(x,y) x 376s + ycoord <- function(x,y) y 376s + xim <- as.im(xcoord, W=Window(X)) 376s + r2fi <- rho2hat(X, ycoord, xim) 376s + r2if <- rho2hat(X, xim, ycoord) 376s + } 376s + }) 376s > 376s BEGIN TEST testsR2.R 376s 376s R version 4.4.3 (2025-02-28) -- "Trophy Case" 376s Copyright (C) 2025 The R Foundation for Statistical Computing 376s Platform: aarch64-unknown-linux-gnu 376s 376s R is free software and comes with ABSOLUTELY NO WARRANTY. 376s You are welcome to redistribute it under certain conditions. 376s Type 'license()' or 'licence()' for distribution details. 376s 376s R is a collaborative project with many contributors. 376s Type 'contributors()' for more information and 376s 'citation()' on how to cite R or R packages in publications. 376s 376s Type 'demo()' for some demos, 'help()' for on-line help, or 376s 'help.start()' for an HTML browser interface to help. 376s Type 'q()' to quit R. 376s 376s > #' 376s > #' Header for all (concatenated) test files 376s > #' 376s > #' Require spatstat.explore 376s > #' Obtain environment variable controlling tests. 376s > #' 376s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 376s > 376s > require(spatstat.explore) 376s Loading required package: spatstat.explore 376s Loading required package: spatstat.data 377s Loading required package: spatstat.univar 377s spatstat.univar 3.1-1 377s Loading required package: spatstat.geom 377s spatstat.geom 3.3-5 377s Loading required package: spatstat.random 378s spatstat.random 3.3-2 378s Loading required package: nlme 378s spatstat.explore 3.3-4 378s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 378s > ALWAYS <- TRUE 378s > cat(paste("--------- Executing", 378s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 378s + "test code -----------\n")) 378s --------- Executing **RESTRICTED** subset of test code ----------- 378s > 378s BEGIN TEST testsS.R 378s 378s R version 4.4.3 (2025-02-28) -- "Trophy Case" 378s Copyright (C) 2025 The R Foundation for Statistical Computing 378s Platform: aarch64-unknown-linux-gnu 378s 378s R is free software and comes with ABSOLUTELY NO WARRANTY. 378s You are welcome to redistribute it under certain conditions. 378s Type 'license()' or 'licence()' for distribution details. 378s 378s R is a collaborative project with many contributors. 378s Type 'contributors()' for more information and 378s 'citation()' on how to cite R or R packages in publications. 378s 378s Type 'demo()' for some demos, 'help()' for on-line help, or 378s 'help.start()' for an HTML browser interface to help. 378s Type 'q()' to quit R. 378s 378s > #' 378s > #' Header for all (concatenated) test files 378s > #' 378s > #' Require spatstat.explore 378s > #' Obtain environment variable controlling tests. 378s > #' 378s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 378s > 378s > require(spatstat.explore) 378s Loading required package: spatstat.explore 378s Loading required package: spatstat.data 379s Loading required package: spatstat.univar 379s spatstat.univar 3.1-1 379s Loading required package: spatstat.geom 379s spatstat.geom 3.3-5 379s Loading required package: spatstat.random 379s spatstat.random 3.3-2 379s Loading required package: nlme 379s spatstat.explore 3.3-4 379s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 379s > ALWAYS <- TRUE 379s > cat(paste("--------- Executing", 379s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 379s + "test code -----------\n")) 379s --------- Executing **RESTRICTED** subset of test code ----------- 379s > #' tests/sdr.R 379s > #' 379s > #' $Revision: 1.2 $ $Date: 2020/05/01 09:59:59 $ 379s > 380s > if(FULLTEST) { 380s + local({ 380s + AN <- sdr(bei, bei.extra, method="NNIR") 380s + AV <- sdr(bei, bei.extra, method="SAVE") 380s + AI <- sdr(bei, bei.extra, method="SIR") 380s + AT <- sdr(bei, bei.extra, method="TSE") 380s + subspaceDistance(AN$B, AV$B) 380s + dimhat(AN$M) 380s + }) 380s + } 380s > ## 380s > ## tests/segments.R 380s > ## Tests of psp class and related code 380s > ## [SEE ALSO: tests/xysegment.R] 380s > ## 380s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 380s > 380s > 380s > local({ 380s + if(ALWAYS) { # C code 380s + #' tests of density.psp 380s + Y <- edges(letterR) 380s + Window(Y) <- grow.rectangle(Frame(Y), 0.4) 380s + YC <- density(Y, 0.2, method="C", edge=FALSE, dimyx=64) 380s + YI <- density(Y, 0.2, method="interpreted", edge=FALSE, dimyx=64) 380s + YF <- density(Y, 0.2, method="FFT", edge=FALSE, dimyx=64) 380s + xCI <- max(abs(YC/YI - 1)) 380s + xFI <- max(abs(YF/YI - 1)) 380s + cat(paste("xCI =", xCI, "\txFI =", signif(xFI, 5)), fill=TRUE) 380s + if(xCI > 0.01) stop(paste("density.psp C algorithm relative error =", xCI)) 380s + if(xFI > 0.1) stop(paste("density.psp FFT algorithm relative error =", xFI)) 380s + 380s + B <- square(0.3) 380s + density(Y, 0.2, at=B) 380s + density(Y, 0.2, at=B, edge=TRUE, method="C") 380s + Z <- runifrect(3, B) 380s + density(Y, 0.2, at=Z) 380s + density(Y, 0.2, at=Z, edge=TRUE, method="C") 380s + } 380s + 380s + if(FULLTEST) { 380s + #' segment clipping in window (bug found by Rolf) 380s + set.seed(42) 380s + X <- runifpoint(50, letterR) 380s + SP <- dirichletEdges(X) #' clip to polygonal window 380s + Window(X) <- as.mask(Window(X)) 380s + SM <- dirichletEdges(X) #' clip to mask window 380s + } 380s + 380s + if(FULLTEST) { 380s + #' test rshift.psp and append.psp with marks (Ute Hahn) 380s + m <- data.frame(A=1:10, B=letters[1:10]) 380s + g <- gl(3, 3, length=10) 380s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 380s + Y <- rshift(X, radius = 0.1) 380s + Y <- rshift(X, radius = 0.1, group=g) 380s + #' mark management 380s + b <- data.frame(A=1:10) 380s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=b) 380s + stopifnot(is.data.frame(marks(X))) 380s + Y <- rshift(X, radius = 0.1) 380s + Y <- rshift(X, radius = 0.1, group=g) 380s + } 380s + 380s + }) 380s xCI = 2.55351295663786e-15 xFI = 0.073128 381s > 381s > 381s > 381s > # 381s > ## tests/sigtraceprogress.R 381s > # 381s > ## Tests of *.sigtrace and *.progress 381s > # 381s > ## $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 381s Warning message: 381s the images ‘dens’ and ‘edg’ were not compatible 381s > 381s > if(FULLTEST) { 381s + local({ 381s + plot(dclf.sigtrace(redwood, nsim=19, alternative="greater", rmin=0.02, 381s + verbose=FALSE)) 381s + plot(dclf.progress(redwood, nsim=19, alternative="greater", rmin=0.02, 381s + verbose=FALSE)) 381s + plot(dg.sigtrace(redwood, nsim=5, alternative="greater", rmin=0.02, 381s + verbose=FALSE)) 382s + plot(dg.progress(redwood, nsim=5, alternative="greater", rmin=0.02, 382s + verbose=FALSE)) 382s + ## test 'leave-two-out' algorithm 382s + a <- dclf.sigtrace(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 382s + verbose=FALSE) 382s + aa <- dclf.progress(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 382s + verbose=FALSE) 382s + b <- dg.sigtrace(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2) 382s + bb <- dg.progress(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2, 382s + verbose=FALSE) 382s + ## other code blocks 382s + e <- mad.progress(redwood, nsim=5) 382s + e <- mad.progress(redwood, nsim=19, alpha=0.05) 382s + f <- dclf.progress(redwood, nsim=5, scale=function(x) x^2) 382s + f <- dclf.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 382s + g <- dg.progress(redwood, nsim=5, scale=function(x) x^2) 382s + g <- dg.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 382s + }) 382s + } 382s > #' 382s > #' tests/ssf.R 382s > #' 382s > #' Tests of 'ssf' class 382s > #' 382s > #' $Revision: 1.5 $ $Date: 2020/12/04 08:02:25 $ 382s > #' 382s > 382s > if(FULLTEST) { 382s + local({ 382s + Y <- cells[1:5] 382s + X <- rsyst(Window(Y), 5) 382s + Z <- runifpoint(3, Window(Y)) 382s + f1 <- ssf(X, nncross(X,Y,what="dist")) 382s + f2 <- ssf(X, nncross(X,Y,what="dist", k=1:2)) 382s + image(f1) 382s + g1 <- as.function(f1) 382s + g1(Z) 382s + g2 <- as.function(f2) 382s + g2(Z) 382s + plot(f1, style="contour") 382s + plot(f1, style="imagecontour") 382s + contour(f1) 382s + apply.ssf(f2, 1, sum) 382s + range(f1) 382s + min(f1) 382s + max(f1) 382s + integral(f1, weights=tile.areas(dirichlet(X))) 382s + }) 382s + } 382s > #' 382s > #' tests/sumfun.R 382s > #' 382s > #' Tests of code for summary functions 382s > #' 382s > #' $Revision: 1.9 $ $Date: 2022/05/22 08:45:23 $ 382s > 382s > if(ALWAYS) { # involves C code 382s + local({ 382s + W <- owin(c(0,1), c(-1/2, 0)) 382s + Gr <- Gest(redwood, correction="all",domain=W) 382s + Fr <- Fest(redwood, correction="all",domain=W) 382s + Jr <- Jest(redwood, correction="all",domain=W) 382s + 382s + F0 <- Fest(redwood[FALSE], correction="all") 382s + Fh <- Fest(humberside, domain=erosion(Window(humberside), 100)) 382s + 382s + FIr <- Finhom(redwood, savelambda=TRUE, ratio=TRUE) 382s + JIr <- Jinhom(redwood, savelambda=TRUE, ratio=TRUE) 382s + 382s + Ga <- Gcross(amacrine, correction="all") 382s + Ia <- Iest(amacrine, correction="all") 382s + lam <- intensity(amacrine) 382s + lmin <- 0.9 * min(lam) 382s + nJ <- sum(marks(amacrine) == "off") 382s + FM <- FmultiInhom(amacrine, marks(amacrine) == "off", 382s + lambdaJ=rep(lam["off"], nJ), 382s + lambdamin = lmin) 382s + GM <- GmultiInhom(amacrine, marks(amacrine) == "on", 382s + marks(amacrine) == "off", 382s + lambda=lam[marks(amacrine)], 382s + lambdamin=lmin, 382s + ReferenceMeasureMarkSetI=42) 382s + 382s + a <- compileCDF(D=nndist(redwood), 382s + B=bdist.points(redwood), 382s + r=seq(0, 1, length=256)) 382s + 382s + #' Tstat (triplet) function, all code blocks 382s + a <- Tstat(redwood, ratio=TRUE, 382s + correction=c("none", "border", "bord.modif", "translate")) 382s + 382s + ## distance argument spacing and breakpoints 382s + e <- check.finespacing(c(0,1,2), eps=0.1, action="silent") 382s + b <- as.breakpts(pi, 20) 382s + b <- as.breakpts(42, max=pi, npos=20) 382s + b <- even.breaks.owin(letterR) 382s + }) 382s + } 384s Searching 59340 potential triangles; estimated time 0.000426 sec 384s > 384s BEGIN TEST testsT.R 384s 384s R version 4.4.3 (2025-02-28) -- "Trophy Case" 384s Copyright (C) 2025 The R Foundation for Statistical Computing 384s Platform: aarch64-unknown-linux-gnu 384s 384s R is free software and comes with ABSOLUTELY NO WARRANTY. 384s You are welcome to redistribute it under certain conditions. 384s Type 'license()' or 'licence()' for distribution details. 384s 384s R is a collaborative project with many contributors. 384s Type 'contributors()' for more information and 384s 'citation()' on how to cite R or R packages in publications. 384s 384s Type 'demo()' for some demos, 'help()' for on-line help, or 384s 'help.start()' for an HTML browser interface to help. 384s Type 'q()' to quit R. 384s 384s > #' 384s > #' Header for all (concatenated) test files 384s > #' 384s > #' Require spatstat.explore 384s > #' Obtain environment variable controlling tests. 384s > #' 384s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 384s > 384s > require(spatstat.explore) 384s Loading required package: spatstat.explore 384s Loading required package: spatstat.data 386s Loading required package: spatstat.univar 386s spatstat.univar 3.1-1 386s Loading required package: spatstat.geom 386s spatstat.geom 3.3-5 386s Loading required package: spatstat.random 386s spatstat.random 3.3-2 386s Loading required package: nlme 386s spatstat.explore 3.3-4 386s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 386s > ALWAYS <- TRUE 386s > cat(paste("--------- Executing", 386s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 386s + "test code -----------\n")) 386s --------- Executing **RESTRICTED** subset of test code ----------- 386s > #' 386s > #' tests/threedee.R 386s > #' 386s > #' Tests of 3D code 386s > #' 386s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 386s > #' 386s > 386s > local({ 386s + X <- runifpoint3(30) 386s + Y <- runifpoint3(20) 386s + if(FULLTEST) { 386s + A <- runifpoint3(10, nsim=2) 386s + Z <- ppsubset(X, 2:4) 386s + } 386s + ## 386s + if(ALWAYS) { # includes C code 386s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 386s + d <- crossdist(X, Y, squared=TRUE) 386s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 386s + #' 386s + h <- has.close(X, 0.2) 386s + h <- has.close(X, 0.2, periodic=TRUE) 386s + h <- has.close(X, 0.2, Y=Y) 386s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 386s + #' code blocks not otherwise reached 386s + rmax <- 0.6 * max(nndist(X)) 386s + g <- G3est(X, rmax=rmax, correction="rs") 386s + g <- G3est(X, rmax=rmax, correction="km") 386s + g <- G3est(X, rmax=rmax, correction="Hanisch") 386s + g <- G3est(X, rmax=rmax, sphere="ideal") 386s + g <- G3est(X, rmax=rmax, sphere="digital") 386s + v <- sphere.volume() 386s + v <- digital.volume() 386s + #' older code 386s + co <- coords(X) 386s + xx <- co$x 386s + yy <- co$y 386s + zz <- co$z 386s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 386s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 386s + ff1 <- f3engine(xx, yy, zz, correction="no") 386s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 386s + } 386s + ## 386s + if(ALWAYS) { 386s + #'class support 386s + X <- runifpoint3(10) 386s + print(X) 386s + print(X %mark% runif(10)) 386s + print(X %mark% factor(letters[c(1:5,5:1)])) 386s + print(X %mark% data.frame(a=1:10, b=runif(10))) 386s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 386s + print(X %mark% da) 386s + print(X %mark% data.frame(a=1:10, b=da)) 386s + } 386s + }) 386s Three-dimensional point pattern: 10 points 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s Marked three-dimensional point pattern: 10 points 386s marks are numeric, of storage type ‘double’ 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s Marked three-dimensional point pattern: 10 points 386s Multitype, with levels = a, b, c, d, e 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s Marked three-dimensional point pattern: 10 points 386s Mark variables: a, b 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s Marked three-dimensional point pattern: 10 points 386s marks are dates, of class ‘Date’ 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s Marked three-dimensional point pattern: 10 points 386s Mark variables: a, b 386s Box: [0, 1] x [0, 1] x [0, 1] units 386s > 386s BEGIN TEST testsUtoZ.R 386s Warning messages: 386s 1: In G3est: unrecognised argument ‘sphere’ was ignored 386s 2: In G3est: unrecognised argument ‘sphere’ was ignored 386s 386s R version 4.4.3 (2025-02-28) -- "Trophy Case" 386s Copyright (C) 2025 The R Foundation for Statistical Computing 386s Platform: aarch64-unknown-linux-gnu 386s 386s R is free software and comes with ABSOLUTELY NO WARRANTY. 386s You are welcome to redistribute it under certain conditions. 386s Type 'license()' or 'licence()' for distribution details. 386s 386s R is a collaborative project with many contributors. 386s Type 'contributors()' for more information and 386s 'citation()' on how to cite R or R packages in publications. 386s 386s Type 'demo()' for some demos, 'help()' for on-line help, or 386s 'help.start()' for an HTML browser interface to help. 386s Type 'q()' to quit R. 386s 386s > #' 386s > #' Header for all (concatenated) test files 386s > #' 386s > #' Require spatstat.explore 386s > #' Obtain environment variable controlling tests. 386s > #' 386s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 386s > 386s > require(spatstat.explore) 386s Loading required package: spatstat.explore 386s Loading required package: spatstat.data 388s Loading required package: spatstat.univar 388s spatstat.univar 3.1-1 388s Loading required package: spatstat.geom 388s spatstat.geom 3.3-5 388s Loading required package: spatstat.random 388s spatstat.random 3.3-2 388s Loading required package: nlme 388s spatstat.explore 3.3-4 388s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 388s > ALWAYS <- TRUE 388s > cat(paste("--------- Executing", 388s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 388s + "test code -----------\n")) 388s --------- Executing **RESTRICTED** subset of test code ----------- 388s > 388s autopkgtest [16:03:55]: test run-unit-test: -----------------------] 389s autopkgtest [16:03:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 389s run-unit-test PASS 389s autopkgtest [16:03:56]: test pkg-r-autopkgtest: preparing testbed 604s autopkgtest [16:07:31]: testbed dpkg architecture: arm64 604s autopkgtest [16:07:31]: testbed apt version: 2.9.33 604s autopkgtest [16:07:31]: @@@@@@@@@@@@@@@@@@@@ test bed setup 604s autopkgtest [16:07:31]: testbed release detected to be: plucky 605s autopkgtest [16:07:32]: updating testbed package index (apt update) 606s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 606s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 606s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 606s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 606s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 607s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 607s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 607s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 607s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 607s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 607s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 608s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 608s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 608s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 608s Fetched 1078 kB in 2s (549 kB/s) 609s Reading package lists... 610s Reading package lists... 610s Building dependency tree... 610s Reading state information... 611s Calculating upgrade... 611s Calculating upgrade... 612s The following packages will be upgraded: 612s pinentry-curses python3-jinja2 strace 612s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 612s Need to get 647 kB of archives. 612s After this operation, 11.3 kB of additional disk space will be used. 612s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 613s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 613s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 614s Fetched 647 kB in 2s (425 kB/s) 614s (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.) 614s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 614s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 614s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 614s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 614s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 615s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 615s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 615s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 615s Setting up strace (6.13+ds-1ubuntu1) ... 615s Processing triggers for man-db (2.13.0-1) ... 616s Reading package lists... 616s Building dependency tree... 616s Reading state information... 617s Solving dependencies... 617s The following packages will be REMOVED: 617s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 617s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 617s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 617s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 618s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 618s After this operation, 267 MB disk space will be freed. 618s (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.) 618s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 618s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 618s Removing libpython3.12t64:arm64 (3.12.9-1) ... 618s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 618s Removing libnsl2:arm64 (1.3.0-3build3) ... 618s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 618s Removing libunwind8:arm64 (1.6.2-3.1) ... 618s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 619s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 621s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 621s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 621s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 621s /etc/kernel/postrm.d/initramfs-tools: 621s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 621s /etc/kernel/postrm.d/zz-flash-kernel: 621s flash-kernel: Kernel 6.11.0-8-generic has been removed. 621s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 622s /etc/kernel/postrm.d/zz-update-grub: 622s Sourcing file `/etc/default/grub' 622s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 622s Generating grub configuration file ... 622s Found linux image: /boot/vmlinuz-6.14.0-10-generic 622s Found initrd image: /boot/initrd.img-6.14.0-10-generic 623s Warning: os-prober will not be executed to detect other bootable partitions. 623s Systems on them will not be added to the GRUB boot configuration. 623s Check GRUB_DISABLE_OS_PROBER documentation entry. 623s Adding boot menu entry for UEFI Firmware Settings ... 623s done 623s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 623s Processing triggers for libc-bin (2.41-1ubuntu1) ... 623s (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.) 623s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 623s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 623s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 624s autopkgtest [16:07:51]: upgrading testbed (apt dist-upgrade and autopurge) 624s Reading package lists... 624s Building dependency tree... 624s Reading state information... 625s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 625s Starting 2 pkgProblemResolver with broken count: 0 625s Done 626s Entering ResolveByKeep 626s 627s Calculating upgrade... 627s The following packages will be upgraded: 627s libc-bin libc-dev-bin libc6 libc6-dev locales 627s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 627s Need to get 9530 kB of archives. 627s After this operation, 0 B of additional disk space will be used. 627s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 629s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 630s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 633s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 633s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 639s Preconfiguring packages ... 639s Fetched 9530 kB in 11s (834 kB/s) 639s (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.) 639s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 639s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 640s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 640s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 640s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 640s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 640s Setting up libc6:arm64 (2.41-1ubuntu2) ... 640s (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.) 640s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 640s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 640s Setting up libc-bin (2.41-1ubuntu2) ... 641s (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.) 641s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 641s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 641s Setting up locales (2.41-1ubuntu2) ... 642s Generating locales (this might take a while)... 644s en_US.UTF-8... done 644s Generation complete. 644s Setting up libc-dev-bin (2.41-1ubuntu2) ... 644s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 644s Processing triggers for man-db (2.13.0-1) ... 645s Processing triggers for systemd (257.3-1ubuntu3) ... 646s Reading package lists... 646s Building dependency tree... 646s Reading state information... 647s Starting pkgProblemResolver with broken count: 0 647s Starting 2 pkgProblemResolver with broken count: 0 647s Done 647s Solving dependencies... 648s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 648s autopkgtest [16:08:15]: rebooting testbed after setup commands that affected boot 682s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 693s Reading package lists... 693s Building dependency tree... 693s Reading state information... 693s Starting pkgProblemResolver with broken count: 0 693s Starting 2 pkgProblemResolver with broken count: 0 693s Done 694s The following NEW packages will be installed: 694s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 694s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 694s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 694s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 694s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 694s libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 694s libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev 694s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 694s libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev 694s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev 694s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev 694s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 694s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 694s libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6 694s libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev 694s libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 694s libxrender1 libxss1 libxt6t64 pkg-r-autopkgtest pkgconf pkgconf-bin 694s r-base-core r-base-dev r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 694s r-cran-lattice r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-polyclip 694s r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 694s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 694s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 694s r-cran-spatstat.univar r-cran-spatstat.utils r-cran-survival r-cran-tensor 694s unzip x11-common xdg-utils zip zlib1g-dev 694s 0 upgraded, 124 newly installed, 0 to remove and 0 not upgraded. 694s Need to get 176 MB of archives. 694s After this operation, 473 MB of additional disk space will be used. 694s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 696s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 696s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 714s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 714s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 714s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 714s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 714s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 714s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 714s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 722s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 725s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 732s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 736s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 740s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 747s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 801s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 802s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 802s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 802s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 808s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 835s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 835s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 835s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 835s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 835s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 835s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 836s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 837s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 838s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 838s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 838s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 839s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 840s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 859s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 859s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 859s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 859s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 859s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 860s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 860s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 860s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 861s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 861s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 861s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 861s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 862s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 862s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 862s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 862s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 862s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 862s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 864s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 865s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 865s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 865s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 886s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 887s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 887s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 887s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 887s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 887s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 891s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 899s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 899s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 899s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 900s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 900s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 900s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 900s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 900s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 900s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 900s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 901s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 901s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 901s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 902s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 902s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 903s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 904s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 904s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 904s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 904s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 905s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 905s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 906s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 906s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 906s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 906s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 907s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 907s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 908s Get:92 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 908s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 908s Get:94 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 940s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 940s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 940s Get:97 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 940s Get:98 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 940s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 940s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 940s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 940s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 941s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 941s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-gsl arm64 2.1-8-1build1 [485 kB] 942s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 944s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 950s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 953s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 958s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 958s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 969s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 970s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 971s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 971s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.utils arm64 3.1-2-1 [381 kB] 972s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.data all 3.1-4-1 [4047 kB] 978s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.univar arm64 3.1-1-1build1 [308 kB] 979s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.geom arm64 3.3-5-1 [3929 kB] 984s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.random arm64 3.3-2-1 [1159 kB] 986s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 986s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 986s Get:121 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 991s Get:122 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 995s Get:123 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 997s Get:124 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 1003s Preconfiguring packages ... 1003s Fetched 176 MB in 5min 8s (573 kB/s) 1003s Selecting previously unselected package libisl23:arm64. 1003s (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.) 1003s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ... 1003s Unpacking libisl23:arm64 (0.27-1) ... 1003s Selecting previously unselected package libmpc3:arm64. 1003s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ... 1003s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 1003s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 1003s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1003s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1004s Selecting previously unselected package cpp-14. 1004s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 1004s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 1004s Selecting previously unselected package cpp-aarch64-linux-gnu. 1004s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1004s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1004s Selecting previously unselected package cpp. 1004s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 1004s Unpacking cpp (4:14.2.0-1ubuntu1) ... 1004s Selecting previously unselected package libcc1-0:arm64. 1004s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 1004s Selecting previously unselected package libgomp1:arm64. 1004s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 1004s Selecting previously unselected package libitm1:arm64. 1004s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 1004s Selecting previously unselected package libasan8:arm64. 1004s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 1004s Selecting previously unselected package liblsan0:arm64. 1004s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 1004s Selecting previously unselected package libtsan2:arm64. 1004s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 1004s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 1005s Selecting previously unselected package libubsan1:arm64. 1005s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 1005s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 1005s Selecting previously unselected package libhwasan0:arm64. 1005s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 1005s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 1005s Selecting previously unselected package libgcc-14-dev:arm64. 1005s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1005s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 1005s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 1005s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1005s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1006s Selecting previously unselected package gcc-14. 1006s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 1006s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 1006s Selecting previously unselected package gcc-aarch64-linux-gnu. 1006s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1006s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1006s Selecting previously unselected package gcc. 1006s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 1006s Unpacking gcc (4:14.2.0-1ubuntu1) ... 1006s Selecting previously unselected package libstdc++-14-dev:arm64. 1006s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1006s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 1006s Selecting previously unselected package g++-14-aarch64-linux-gnu. 1006s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1006s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1006s Selecting previously unselected package g++-14. 1006s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ... 1006s Unpacking g++-14 (14.2.0-17ubuntu3) ... 1006s Selecting previously unselected package g++-aarch64-linux-gnu. 1006s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1006s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1006s Selecting previously unselected package g++. 1007s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 1007s Unpacking g++ (4:14.2.0-1ubuntu1) ... 1007s Selecting previously unselected package build-essential. 1007s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ... 1007s Unpacking build-essential (12.10ubuntu1) ... 1007s Selecting previously unselected package dctrl-tools. 1007s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ... 1007s Unpacking dctrl-tools (2.24-3build3) ... 1007s Selecting previously unselected package fonts-dejavu-mono. 1007s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... 1007s Unpacking fonts-dejavu-mono (2.37-8) ... 1007s Selecting previously unselected package fonts-dejavu-core. 1007s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ... 1007s Unpacking fonts-dejavu-core (2.37-8) ... 1007s Selecting previously unselected package fontconfig-config. 1007s Preparing to unpack .../028-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 1007s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 1007s Selecting previously unselected package libfontconfig1:arm64. 1007s Preparing to unpack .../029-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 1007s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 1008s Selecting previously unselected package fontconfig. 1008s Preparing to unpack .../030-fontconfig_2.15.0-2ubuntu1_arm64.deb ... 1008s Unpacking fontconfig (2.15.0-2ubuntu1) ... 1008s Selecting previously unselected package libgfortran5:arm64. 1008s Preparing to unpack .../031-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 1008s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 1008s Selecting previously unselected package libgfortran-14-dev:arm64. 1008s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1008s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 1008s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 1008s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1008s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1008s Selecting previously unselected package gfortran-14. 1008s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 1008s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 1008s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1008s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1008s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1008s Selecting previously unselected package gfortran. 1008s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 1008s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 1008s Selecting previously 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package libjpeg8:arm64. 1010s Preparing to unpack .../058-libjpeg8_8c-2ubuntu11_arm64.deb ... 1010s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1010s Selecting previously unselected package libjpeg8-dev:arm64. 1010s Preparing to unpack .../059-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 1010s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1010s Selecting previously unselected package libjpeg-dev:arm64. 1010s Preparing to unpack .../060-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 1010s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 1010s Selecting previously unselected package liblapack3:arm64. 1010s Preparing to unpack .../061-liblapack3_3.12.1-2_arm64.deb ... 1010s Unpacking liblapack3:arm64 (3.12.1-2) ... 1010s Selecting previously unselected package liblapack-dev:arm64. 1010s Preparing to unpack .../062-liblapack-dev_3.12.1-2_arm64.deb ... 1010s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 1010s Selecting previously unselected package liblerc4:arm64. 1010s Preparing to unpack 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... 1012s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 1012s Selecting previously unselected package zip. 1012s Preparing to unpack .../090-zip_3.0-14ubuntu2_arm64.deb ... 1012s Unpacking zip (3.0-14ubuntu2) ... 1012s Selecting previously unselected package unzip. 1012s Preparing to unpack .../091-unzip_6.0-28ubuntu6_arm64.deb ... 1012s Unpacking unzip (6.0-28ubuntu6) ... 1012s Selecting previously unselected package xdg-utils. 1012s Preparing to unpack .../092-xdg-utils_1.2.1-2ubuntu1_all.deb ... 1012s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 1012s Selecting previously unselected package r-base-core. 1012s Preparing to unpack .../093-r-base-core_4.4.3-1_arm64.deb ... 1012s Unpacking r-base-core (4.4.3-1) ... 1013s Selecting previously unselected package liblzma-dev:arm64. 1013s Preparing to unpack .../094-liblzma-dev_5.6.4-1_arm64.deb ... 1013s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 1013s Selecting previously unselected package pkgconf-bin. 1013s Preparing to unpack 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previously unselected package r-cran-deldir. 1013s Preparing to unpack .../101-r-cran-deldir_2.0-4-1build1_arm64.deb ... 1013s Unpacking r-cran-deldir (2.0-4-1build1) ... 1013s Selecting previously unselected package r-cran-goftest. 1013s Preparing to unpack .../102-r-cran-goftest_1.2-3-1_arm64.deb ... 1013s Unpacking r-cran-goftest (1.2-3-1) ... 1013s Selecting previously unselected package r-cran-gsl. 1013s Preparing to unpack .../103-r-cran-gsl_2.1-8-1build1_arm64.deb ... 1013s Unpacking r-cran-gsl (2.1-8-1build1) ... 1013s Selecting previously unselected package r-cran-lattice. 1013s Preparing to unpack .../104-r-cran-lattice_0.22-6-1_arm64.deb ... 1013s Unpacking r-cran-lattice (0.22-6-1) ... 1013s Selecting previously unselected package r-cran-matrix. 1013s Preparing to unpack .../105-r-cran-matrix_1.7-3-1_arm64.deb ... 1013s Unpacking r-cran-matrix (1.7-3-1) ... 1013s Selecting previously unselected package r-cran-nlme. 1013s Preparing to unpack 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(4.4.3-1) ... 1018s Setting up r-cran-rpart (4.1.24-1) ... 1018s Setting up r-cran-spatstat.random (3.3-2-1) ... 1018s Setting up r-cran-spatstat.explore (3.3-4-1) ... 1018s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 1018s Setting up r-cran-spatstat.model (3.3-4-1) ... 1018s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 1018s Setting up r-cran-spatstat (3.3-1-1) ... 1018s Processing triggers for install-info (7.1.1-1) ... 1018s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1019s Processing triggers for man-db (2.13.0-1) ... 1023s autopkgtest [16:14:30]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1023s autopkgtest [16:14:30]: test pkg-r-autopkgtest: [----------------------- 1023s Test: Try to load the R library spatstat.explore 1024s 1024s R version 4.4.3 (2025-02-28) -- "Trophy Case" 1024s Copyright (C) 2025 The R Foundation for Statistical Computing 1024s Platform: aarch64-unknown-linux-gnu 1024s 1024s R is free software and comes with ABSOLUTELY NO WARRANTY. 1024s You are welcome to redistribute it under certain conditions. 1024s Type 'license()' or 'licence()' for distribution details. 1024s 1024s R is a collaborative project with many contributors. 1024s Type 'contributors()' for more information and 1024s 'citation()' on how to cite R or R packages in publications. 1024s 1024s Type 'demo()' for some demos, 'help()' for on-line help, or 1024s 'help.start()' for an HTML browser interface to help. 1024s Type 'q()' to quit R. 1024s 1024s > library('spatstat.explore') 1024s Loading required package: spatstat.data 1025s Loading required package: spatstat.univar 1025s spatstat.univar 3.1-1 1025s Loading required package: spatstat.geom 1025s spatstat.geom 3.3-5 1025s Loading required package: spatstat.random 1025s spatstat.random 3.3-2 1025s Loading required package: nlme 1025s > 1025s > 1025s spatstat.explore 3.3-4 1025s Other tests are currently unsupported! 1025s They will be progressively added. 1025s autopkgtest [16:14:32]: test pkg-r-autopkgtest: -----------------------] 1026s autopkgtest [16:14:33]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1026s pkg-r-autopkgtest PASS 1026s autopkgtest [16:14:33]: @@@@@@@@@@@@@@@@@@@@ summary 1026s run-unit-test PASS 1026s pkg-r-autopkgtest PASS 1044s nova [W] Using flock in prodstack6-arm64 1044s Creating nova instance adt-plucky-arm64-r-cran-spatstat.explore-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-b29006cb-5109-49c1-b699-81555d687b84 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1044s nova [W] Timed out waiting for 30fdc573-8cd0-4f90-8893-1696907ce590 to get deleted. 1044s nova [W] Using flock in prodstack6-arm64 1044s Creating nova instance adt-plucky-arm64-r-cran-spatstat.explore-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-b29006cb-5109-49c1-b699-81555d687b84 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1044s nova [W] Timed out waiting for ae142f1d-c4e8-4c88-9fc5-dad02450d566 to get deleted.