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.0ntiabdn/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.geom --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-arm64-34.secgroup --name adt-plucky-arm64-r-cran-spatstat.geom-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-a63e14f4-a5ce-4fa0-8e11-71e5178b5118 --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/ 159s autopkgtest [16:00:06]: testbed dpkg architecture: arm64 159s autopkgtest [16:00:06]: testbed apt version: 2.9.33 160s autopkgtest [16:00:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 160s autopkgtest [16:00:07]: testbed release detected to be: None 161s autopkgtest [16:00:08]: updating testbed package index (apt update) 161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 161s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 161s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 162s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 162s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 162s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 162s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 162s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 162s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 162s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 162s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 163s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 163s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 163s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 163s Fetched 1078 kB in 2s (576 kB/s) 164s Reading package lists... 165s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Calculating upgrade... 166s Calculating upgrade... 166s The following packages will be upgraded: 166s pinentry-curses python3-jinja2 strace 166s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 647 kB of archives. 166s After this operation, 11.3 kB of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 167s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 167s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 168s Fetched 647 kB in 1s (530 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 ... 117701 files and directories currently installed.) 168s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 168s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 168s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 168s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 168s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 169s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 169s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 169s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 169s Setting up strace (6.13+ds-1ubuntu1) ... 169s Processing triggers for man-db (2.13.0-1) ... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Solving dependencies... 172s The following packages will be REMOVED: 172s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 172s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 172s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 172s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 173s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 173s After this operation, 267 MB disk space will be freed. 173s (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.) 173s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 173s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 173s Removing libpython3.12t64:arm64 (3.12.9-1) ... 173s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 173s Removing libnsl2:arm64 (1.3.0-3build3) ... 173s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 173s Removing libunwind8:arm64 (1.6.2-3.1) ... 173s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 174s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 175s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 175s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 175s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 175s /etc/kernel/postrm.d/initramfs-tools: 175s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 175s /etc/kernel/postrm.d/zz-flash-kernel: 175s flash-kernel: Kernel 6.11.0-8-generic has been removed. 175s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 176s /etc/kernel/postrm.d/zz-update-grub: 176s Sourcing file `/etc/default/grub' 176s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 176s Generating grub configuration file ... 176s Found linux image: /boot/vmlinuz-6.14.0-10-generic 176s Found initrd image: /boot/initrd.img-6.14.0-10-generic 176s Warning: os-prober will not be executed to detect other bootable partitions. 176s Systems on them will not be added to the GRUB boot configuration. 176s Check GRUB_DISABLE_OS_PROBER documentation entry. 176s Adding boot menu entry for UEFI Firmware Settings ... 176s done 176s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 177s Processing triggers for libc-bin (2.41-1ubuntu1) ... 177s (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.) 177s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 177s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 177s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 177s autopkgtest [16:00:24]: upgrading testbed (apt dist-upgrade and autopurge) 177s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 179s Starting 2 pkgProblemResolver with broken count: 0 179s Done 180s Entering ResolveByKeep 180s 180s Calculating upgrade... 181s The following packages will be upgraded: 181s libc-bin libc-dev-bin libc6 libc6-dev locales 181s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 9530 kB of archives. 181s After this operation, 0 B of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 184s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 184s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 189s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 190s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 198s Preconfiguring packages ... 198s Fetched 9530 kB in 16s (585 kB/s) 198s (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.) 198s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 198s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 198s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 198s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 198s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 199s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 199s Setting up libc6:arm64 (2.41-1ubuntu2) ... 199s (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.) 199s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 199s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 199s Setting up libc-bin (2.41-1ubuntu2) ... 200s (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.) 200s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 200s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 200s Setting up locales (2.41-1ubuntu2) ... 201s Generating locales (this might take a while)... 204s en_US.UTF-8... done 204s Generation complete. 204s Setting up libc-dev-bin (2.41-1ubuntu2) ... 204s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 204s Processing triggers for man-db (2.13.0-1) ... 205s Processing triggers for systemd (257.3-1ubuntu3) ... 207s Reading package lists... 207s Building dependency tree... 207s Reading state information... 208s Starting pkgProblemResolver with broken count: 0 208s Starting 2 pkgProblemResolver with broken count: 0 208s Done 208s Solving dependencies... 209s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 209s autopkgtest [16:00:56]: rebooting testbed after setup commands that affected boot 244s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 251s autopkgtest [16:01:38]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 254s autopkgtest [16:01:41]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.geom 257s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.geom 3.3-5-1 (dsc) [2418 B] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.geom 3.3-5-1 (tar) [776 kB] 257s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-spatstat.geom 3.3-5-1 (diff) [3044 B] 257s gpgv: Signature made Fri Jan 31 07:28:48 2025 UTC 257s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 257s gpgv: issuer "plessy@debian.org" 257s gpgv: Can't check signature: No public key 257s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.geom_3.3-5-1.dsc: no acceptable signature found 257s autopkgtest [16:01:44]: testing package r-cran-spatstat.geom version 3.3-5-1 258s autopkgtest [16:01:45]: build not needed 260s autopkgtest [16:01:47]: test run-unit-test: preparing testbed 261s Reading package lists... 261s Building dependency tree... 261s Reading state information... 262s Starting pkgProblemResolver with broken count: 0 262s Starting 2 pkgProblemResolver with broken count: 0 262s Done 264s The following NEW packages will be installed: 264s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 264s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 264s libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 264s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 264s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 264s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 264s libxft2 libxrender1 libxss1 libxt6t64 r-base-core r-cran-abind r-cran-deldir 264s r-cran-goftest r-cran-lattice r-cran-matrix r-cran-mgcv r-cran-nlme 264s r-cran-polyclip r-cran-rpart r-cran-spatial r-cran-spatstat 264s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 264s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 264s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 264s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 264s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 264s Need to get 81.2 MB of archives. 264s After this operation, 133 MB of additional disk space will be used. 264s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 265s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 266s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 266s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 266s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 266s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 267s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 267s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 267s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 267s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 267s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 267s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 267s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 268s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 268s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 268s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 268s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 269s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 269s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 269s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 269s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 269s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 271s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 272s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 272s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 272s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 272s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 272s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 272s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 272s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 272s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 272s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 272s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 273s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 273s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 273s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 274s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 274s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 274s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 275s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 275s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 275s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 275s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 275s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 308s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 308s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 308s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 308s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 310s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 314s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 317s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 320s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 320s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 330s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 331s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 331s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.utils arm64 3.1-2-1 [381 kB] 331s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.data all 3.1-4-1 [4047 kB] 336s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.univar arm64 3.1-1-1build1 [308 kB] 336s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.geom arm64 3.3-5-1 [3929 kB] 341s Get:60 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.random arm64 3.3-2-1 [1159 kB] 342s Get:61 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 342s Get:62 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 342s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 346s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 350s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 352s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 358s Preconfiguring packages ... 359s Fetched 81.2 MB in 1min 34s (866 kB/s) 359s Selecting previously unselected package fonts-dejavu-mono. 359s (Reading database ... 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cache... done. 369s Setting up libxft2:arm64 (2.3.6-1build1) ... 369s Setting up libtk8.6:arm64 (8.6.16-1) ... 369s Setting up libpango-1.0-0:arm64 (1.56.2-1) ... 369s Setting up libcairo2:arm64 (1.18.2-2) ... 369s Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... 369s Setting up libpangoft2-1.0-0:arm64 (1.56.2-1) ... 369s Setting up libpangocairo-1.0-0:arm64 (1.56.2-1) ... 369s Setting up r-base-core (4.4.3-1) ... 369s Creating config file /etc/R/Renviron with new version 369s Setting up r-cran-lattice (0.22-6-1) ... 369s Setting up r-cran-nlme (3.1.167-1) ... 369s Setting up r-cran-spatstat.utils (3.1-2-1) ... 369s Setting up r-cran-tensor (1.5-4) ... 369s Setting up r-cran-spatstat.univar (3.1-1-1build1) ... 369s Setting up r-cran-spatial (7.3-18-1) ... 369s Setting up r-cran-abind (1.4-8-1) ... 369s Setting up r-cran-polyclip (1.10-7-1) ... 369s Setting up r-cran-deldir (2.0-4-1build1) ... 369s Setting up r-cran-goftest (1.2-3-1) ... 369s Setting up r-cran-matrix (1.7-3-1) ... 369s Setting up r-cran-spatstat.sparse (3.1-0-1) ... 369s Setting up r-cran-mgcv (1.9-1-1) ... 369s Setting up r-cran-survival (3.8-3-1) ... 369s Setting up r-cran-spatstat.data (3.1-4-1) ... 369s Setting up r-cran-spatstat.geom (3.3-5-1) ... 369s Setting up r-cran-rpart (4.1.24-1) ... 369s Setting up r-cran-spatstat.random (3.3-2-1) ... 369s Setting up r-cran-spatstat.explore (3.3-4-1) ... 369s Setting up r-cran-spatstat.model (3.3-4-1) ... 369s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 369s Setting up r-cran-spatstat (3.3-1-1) ... 369s Processing triggers for install-info (7.1.1-1) ... 369s Processing triggers for libc-bin (2.41-1ubuntu2) ... 369s Processing triggers for man-db (2.13.0-1) ... 373s autopkgtest [16:03:40]: test run-unit-test: [----------------------- 373s BEGIN TEST testsAtoC.R 373s 373s R version 4.4.3 (2025-02-28) -- "Trophy Case" 373s Copyright (C) 2025 The R Foundation for Statistical Computing 373s Platform: aarch64-unknown-linux-gnu 373s 373s R is free software and comes with ABSOLUTELY NO WARRANTY. 373s You are welcome to redistribute it under certain conditions. 373s Type 'license()' or 'licence()' for distribution details. 373s 373s R is a collaborative project with many contributors. 373s Type 'contributors()' for more information and 373s 'citation()' on how to cite R or R packages in publications. 373s 373s Type 'demo()' for some demos, 'help()' for on-line help, or 373s 'help.start()' for an HTML browser interface to help. 373s Type 'q()' to quit R. 373s 373s > #' 373s > #' Header for all (concatenated) test files 373s > #' 373s > #' Require spatstat.geom 373s > #' Obtain environment variable controlling tests. 373s > #' 373s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 373s > 373s > require(spatstat.geom) 373s Loading required package: spatstat.geom 373s Loading required package: spatstat.data 375s Loading required package: spatstat.univar 375s spatstat.univar 3.1-1 375s spatstat.geom 3.3-5 375s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 375s > ALWAYS <- TRUE 375s > cat(paste("--------- Executing", 375s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 375s + "test code -----------\n")) 375s --------- Executing **RESTRICTED** subset of test code ----------- 375s > ## badwindowcheck.R 375s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 375s > ## 375s > 375s > local({ 375s + if(ALWAYS) { 375s + ## Simple example of self-crossing polygon 375s + x <- read.table("selfcross.txt", header=TRUE) 375s + ## Auto-repair 375s + w <- owin(poly=x) 375s + 375s + ## Real data involving various quirks 375s + b <- read.table("badwindow.txt", header=TRUE) 375s + b <- split(b, factor(b$i)) 375s + b <- lapply(b, function(z) { as.list(z[,-3]) }) 375s + ## make owin without checking 375s + W <- owin(poly=b, check=FALSE, fix=FALSE) 375s + ## Apply stringent checks 375s + owinpolycheck(W,verbose=FALSE) 375s + ## Auto-repair 375s + W2 <- owin(poly=b) 375s + } 375s + }) 375s > 375s > 375s > 375s > 375s > ## tests/closeshave.R 375s > ## check 'closepairs/crosspairs' code 375s > ## validity and memory allocation 375s > ## $Revision: 1.29 $ $Date: 2022/06/06 10:09:56 $ 375s > 375s > ## ------- All this code must be run on every hardware ------- 375s > local({ 375s + r <- 0.12 375s + 375s + close.all <- closepairs(redwood, r) 375s + close.ij <- closepairs(redwood, r, what="indices") 375s + close.ijd <- closepairs(redwood, r, what="ijd") 375s + close.every <- closepairs(redwood, r, what="all", distinct=FALSE) 375s + 375s + ## test agreement 375s + stopifnot(identical(close.ij, close.all[c("i","j")])) 375s + stopifnot(identical(close.ijd, close.all[c("i","j","d")])) 375s + 375s + ## validate basic format of result 375s + checkformat <- function(object, callstring) { 375s + if(length(unique(lengths(object))) > 1) 375s + stop(paste("Result of", callstring, 375s + "contains vectors with different lengths")) 375s + return(invisible(TRUE)) 375s + } 375s + checkformat(close.all, "closepairs(redwood, r)") 375s + checkformat(close.ij, "closepairs(redwood, r, what='indices')") 375s + checkformat(close.ijd, "closepairs(redwood, r, what='ijd')") 375s + checkformat(close.every, 375s + "closepairs(redwood, r, what='all', distinct=FALSE)") 375s + 375s + #' test memory overflow code 375s + close.cigar <- closepairs(redwood, r, what="ijd", nsize=2) 375s + close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE) 375s + 375s + #' test special cases 375s + onepoint <- redwood[1] 375s + checkformat(closepairs(onepoint, r), 375s + "closepairs(onepoint, r)") 375s + checkformat(closepairs(onepoint, r, what="indices"), 375s + "closepairs(onepoint, r, what='indices')") 375s + checkformat(closepairs(onepoint, r, what="ijd"), 375s + "closepairs(onepoint, r, what='ijd')") 375s + checkformat(closepairs(onepoint, r, what="all", distinct=FALSE), 375s + "closepairs(onepoint, r, what='all', distinct=FALSE)") 375s + 375s + #' .............. crosspairs .................................. 375s + Y <- split(amacrine) 375s + on <- Y$on 375s + off <- Y$off 375s + 375s + cross.all <- crosspairs(on, off, r) 375s + cross.ij <- crosspairs(on, off, r, what="indices") 375s + cross.ijd <- crosspairs(on, off, r, what="ijd") 375s + cross.every <- crosspairs(on, off, r, what="all", distinct=FALSE) 375s + cross.period <- crosspairs(on, off, r, periodic=TRUE) 375s + cross.exclude <- crosspairs(cells, cells[1:32], 0.1, iX=1:42, iY=1:32) 375s + 375s + ## validate basic format 375s + checkformat(cross.all, "crosspairs(on, off, r)") 375s + checkformat(cross.ij, "crosspairs(on, off, r, what='indices')") 375s + checkformat(cross.ijd, "crosspairs(on, off, r, what='ijd')") 375s + checkformat(cross.every, "crosspairs(on, off, r, what='all', distinct=FALSE)") 375s + checkformat(cross.period, "crosspairs(on, off, r, periodic=TRUE)") 375s + checkformat(cross.exclude, "crosspairs(cells, cells[], r, iX, iY)") 375s + 375s + ## test agreement 375s + stopifnot(identical(cross.ij, cross.all[c("i","j")])) 375s + stopifnot(identical(cross.ijd, cross.all[c("i","j","d")])) 375s + 375s + # closethresh vs closepairs: EXACT agreement 375s + thresh <- 0.08 375s + clt <- closethresh(redwood, r, thresh) 375s + cl <- with(closepairs(redwood, r), 375s + list(i=i, j=j, th = (d <= thresh))) 375s + if(!identical(cl, clt)) 375s + stop("closepairs and closethresh disagree") 375s + 375s + reordered <- function(a) { 375s + o <- with(a, order(i,j)) 375s + as.list(as.data.frame(a)[o,,drop=FALSE]) 375s + } 375s + samesame <- function(a, b) { 375s + identical(reordered(a), reordered(b)) 375s + } 375s + 375s + ## ............................................... 375s + #' compare with older, slower code 375s + op <- spatstat.options(closepairs.newcode=FALSE, 375s + closepairs.altcode=FALSE, 375s + crosspairs.newcode=FALSE) 375s + ## ............................................... 375s + old.close.ij <- closepairs(redwood, r, what="indices") 375s + old.cross.ij <- crosspairs(on, off, r, what="indices") 375s + stopifnot(samesame(close.ij, old.close.ij)) 375s + stopifnot(samesame(cross.ij, old.cross.ij)) 375s + # execute only: 375s + old.close.every <- closepairs(redwood, r, what="all", distinct=FALSE) 375s + old.close.once <- closepairs(redwood, r, what="all", twice=FALSE) 375s + #' test memory overflow code 375s + old.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2) 375s + old.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE) 375s + 375s + ## ............................................... 375s + spatstat.options(op) 375s + ## ............................................... 375s + 375s + ## ............................................... 375s + #' alternative code - execution only 375s + op <- spatstat.options(closepairs.newcode=FALSE, 375s + closepairs.altcode=TRUE) 375s + alt.close.ij <- closepairs(redwood, r, what="indices") 375s + alt.close.ijd <- closepairs(redwood, r, what="ijd") 375s + alt.close.all <- closepairs(redwood, r, what="all") 375s + #' test memory overflow code 375s + alt.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2) 375s + alt.close.cigar <- closepairs(redwood, r, what="ijd", nsize=2, periodic=TRUE) 375s + spatstat.options(op) 375s + ## ............................................... 375s + 375s + # Rasmus' example 375s + R <- 0.04 375s + U <- as.ppp(gridcenters(owin(), 50, 50), W=owin()) 375s + cp <- crosspairs(U, U, R) 375s + G <- matrix(0, npoints(U), npoints(U)) 375s + G[cbind(cp$i, cp$j)] <- 1 375s + if(!isSymmetric(G)) 375s + stop("crosspairs is not symmetric in Rasmus example") 375s + 375s + #' periodic distance 375s + pclose <- function(X, R, method=c("raw", "C")) { 375s + method <- match.arg(method) 375s + switch(method, 375s + raw = { 375s + D <- pairdist(X, periodic=TRUE) 375s + diag(D) <- Inf 375s + result <- which(D <= R, arr.ind=TRUE) 375s + }, 375s + C = { 375s + result <- closepairs(X, R, periodic=TRUE, what="indices") 375s + }) 375s + result <- as.data.frame(result) 375s + colnames(result) <- c("i","j") 375s + return(result) 375s + } 375s + #' pick a threshold value which avoids GCC bug 323 375s + RR <- 0.193 375s + A <- pclose(redwood, RR, "raw") 375s + B <- pclose(redwood, RR, "C") 375s + if(!samesame(A,B)) 375s + stop("closepairs.ppp(periodic=TRUE) gives wrong answer") 375s + 375s + #' other functions that don't have a help file 375s + niets <- crosspairquad(quadscheme(cells), 0.1) 375s + 375s + #' other code blocks 375s + u <- closepairs(cells, 0.09, periodic=TRUE, what="all") 375s + v <- closepairs(cells, 0.07, twice=FALSE, neat=TRUE) 375s + #' tight cluster - guess count does not work 375s + Xc <- runifrect(100, square(0.01)) 375s + Window(Xc) <- square(1) 375s + z <- closepairs(Xc, 0.02, what="indices", distinct=FALSE) 375s + z <- closepairs(Xc, 0.02, what="ijd", distinct=FALSE) 375s + z <- closepairs(Xc, 0.02, what="all", distinct=FALSE) 375s + #' same task, older code 375s + aop <- spatstat.options(closepairs.newcode=FALSE) 375s + z <- closepairs(Xc, 0.02, what="indices", distinct=FALSE) 375s + z <- closepairs(Xc, 0.02, what="ijd", distinct=FALSE) 375s + z <- closepairs(Xc, 0.02, what="all", distinct=FALSE) 375s + spatstat.options(aop) 375s + 375s + #' experimental 375s + r <- 0.08 375s + a <- closepairs(redwood, r) 375s + b <- tweak.closepairs(a, r, 26, 0.1, 0.1) 375s + }) 375s Using nsize = 2 375s Using nsize = 2 375s Using nsize = 2 375s Using nsize = 2 375s Using nsize = 2 375s Using nsize = 2 376s > 376s > local({ 376s + #' Three-dimensional 376s + ## X <- runifpoint3(100) 376s + X <- pp3(runif(100), runif(100), runif(100), box3(c(0,1))) 376s + cl <- closepairs(X, 0.2, what="indices") 376s + cl <- closepairs(X, 0.2, what="ijd") 376s + cl <- closepairs(X, 0.2, distinct=FALSE) 376s + cl <- closepairs(X, 0.2, distinct=FALSE, what="indices") 376s + cl <- closepairs(X, 0.2, distinct=FALSE, what="ijd") 376s + cl <- closepairs(X, 0.2, twice=FALSE, neat=TRUE) 376s + #' Test memory overflow code 376s + cl <- closepairs(X, 0.2, what="ijd", nsize=2) 376s + #' trap obsolete usage 376s + cl <- closepairs(X, 0.2, ordered=FALSE) 376s + #' crosspairs 376s + ## Y <- runifpoint3(100) 376s + Y <- pp3(runif(100), runif(100), runif(100), box3(c(0,1))) 376s + cr <- crosspairs(X, Y, 0.2, what="indices") 376s + cr <- crosspairs(X, Y, 0.2, what="ijd") 376s + #' Test memory overflow code 376s + cr <- crosspairs(X, Y, 0.2, what="ijd", nsize=2) 376s + #' experimental 376s + rr <- 0.2 376s + cl <- closepairs(X, rr) 376s + ii <- cl$i[[1]] 376s + xl <- tweak.closepairs(cl, rr, ii, 0.05, -0.05, 0.05) 376s + }) 376s Using nsize = 2 376s Using nsize = 2 376s > 376s > reset.spatstat.options() 376s > #' 376s > #' tests/cluck.R 376s > #' 376s > #' Tests of "click*" functions 376s > #' using queueing feature of spatstatLocator 376s > #' 376s > #' $Revision: 1.8 $ $Date: 2022/10/23 00:45:36 $ 376s > 376s > local({ 376s + #' clickppp 376s + if(ALWAYS) { 376s + spatstat.utils::queueSpatstatLocator(runif(5), runif(5)) 376s + XA <- clickppp(hook=square(0.5)) 376s + } 376s + if(FULLTEST) { 376s + spatstat.utils::queueSpatstatLocator(runif(6), runif(6)) 376s + XB <- clickppp(n=3, types=c("a", "b")) 376s + } 376s + if(ALWAYS) { 376s + #' clickbox 376s + spatstat.utils::queueSpatstatLocator(runif(2), runif(2)) 376s + BB <- clickbox() 376s + #' clickdist 376s + spatstat.utils::queueSpatstatLocator(runif(2), runif(2)) 376s + dd <- clickdist() 376s + #' clickpoly 376s + hex <- vertices(disc(radius=0.4, centre=c(0.5, 0.5), npoly=6)) 376s + spatstat.utils::queueSpatstatLocator(hex) 376s + PA <- clickpoly() 376s + } 376s + if(FULLTEST) { 376s + holy <- vertices(disc(radius=0.2, centre=c(0.5, 0.5), npoly=6)) 376s + holy <- lapply(holy, rev) 376s + spatstat.utils::queueSpatstatLocator(concatxy(hex, holy)) 376s + PB <- clickpoly(np=2, nv=6) 376s + } 376s + if(ALWAYS) { 376s + #' identify.psp 376s + E <- edges(letterR)[c(FALSE, TRUE)] 376s + Z <- ppp(c(2.86, 3.65, 3.15), c(1.69, 1.98, 2.56), window=Frame(letterR)) 376s + spatstat.utils::queueSpatstatLocator(Z) 376s + identify(E) 376s + } 376s + }) 376s Warning message: 376s In closepairs.pp3(X, 0.2, ordered = FALSE) : 376s Obsolete argument 'ordered' has been replaced by 'twice' 376s Ready to click.. 376s Click two corners of a box 376s to add points: click left mouse button in window 376s to exit: press ESC or click middle mouse button 376s [The last point should NOT repeat the first point] 376s [1] 10 3 15 376s > ## tests/colour.R 376s > ## 376s > ## Colour value manipulation and colour maps 376s > ## 376s > ## $Revision: 1.10 $ $Date: 2022/10/23 00:37:44 $ 376s > ## 376s > 376s > local({ 376s + if(FULLTEST) { 376s + f <- function(n) grey(seq(0,1,length=n)) 376s + z <- to.grey(f) 376s + 376s + h <- colourmap(rainbow(9), range=c(0.01, 0.1)) 376s + plot(h, labelmap=100) 376s + } 376s + 376s + if(ALWAYS) { 376s + a <- colourmap(rainbow(12), range=as.Date(c("2018-01-01", "2018-12-31"))) 376s + print(a) 376s + print(summary(a)) 376s + a(as.Date("2018-06-15")) 376s + 376s + g <- colourmap(rainbow(4), 376s + breaks=as.Date(c("2018-01-01", "2018-04-01", 376s + "2018-07-01", "2018-10-01", "2018-12-31"))) 376s + print(g) 376s + print(summary(g)) 376s + g(as.Date("2018-06-15")) 376s + } 376s + 376s + if(FULLTEST) { 376s + b <- colourmap(rainbow(12), inputs=month.name) 376s + print(b) 376s + print(summary(b)) 376s + to.grey(b) 376s + to.grey(b, transparent=TRUE) 376s + plot(b, vertical=FALSE) 376s + plot(b, vertical=TRUE) 376s + plot(b, vertical=FALSE, gap=0) 376s + plot(b, vertical=TRUE, gap=0) 376s + plot(b, vertical=FALSE, xlim=c(0, 2)) 376s + plot(b, vertical=TRUE, xlim=c(0,2)) 376s + plot(b, vertical=FALSE, ylim=c(0, 2)) 376s + plot(b, vertical=TRUE, ylim=c(0,2)) 376s + 376s + argh <- list(a="iets", e="niets", col=b, f=42) 376s + arr <- col.args.to.grey(argh) 376s + rrgh <- col.args.to.grey(argh, transparent=TRUE) 376s + } 376s + 376s + if(ALWAYS) { 376s + #' constant colour map 376s + colourmap("grey", range=c(0.01, 0.1)) 376s + colourmap("grey", range=as.Date(c("2018-01-01", "2018-12-31"))) 376s + colourmap("grey", 376s + breaks=as.Date(c("2018-01-01", "2018-04-01", 376s + "2018-07-01", "2018-10-01", "2018-12-31"))) 376s + colourmap("grey", inputs=month.name) 376s + } 376s + 376s + if(FULLTEST) { 376s + #' empty colour map 376s + niets <- lut() 376s + print(niets) 376s + summary(niets) 376s + niets <- colourmap() 376s + print(niets) 376s + summary(niets) 376s + plot(niets) 376s + } 376s + 376s + if(FULLTEST) { 376s + #' interpolation - of transparent colours 376s + co <- colourmap(inputs=c(0, 0.5, 1), 376s + rgb(red=c(1,0,0), green=c(0,1,0), blue=c(0,0,1), 376s + alpha=c(0.3, 0.6, 0.9))) 376s + tco <- interp.colourmap(co) 376s + } 376s + }) 376s Colour map for the range [2018-01-01, 2018-12-31] 376s interval colour 376s 1 [2018-01-01, 2018-01-31) #FF0000 376s 2 [2018-01-31, 2018-03-03) #FF8000 376s 3 [2018-03-03, 2018-04-02) #FFFF00 376s 4 [2018-04-02, 2018-05-02) #80FF00 376s 5 [2018-05-02, 2018-06-02) #00FF00 376s 6 [2018-06-02, 2018-07-02) #00FF80 376s 7 [2018-07-02, 2018-08-01) #00FFFF 376s 8 [2018-08-01, 2018-09-01) #0080FF 376s 9 [2018-09-01, 2018-10-01) #0000FF 376s 10 [2018-10-01, 2018-10-31) #8000FF 376s 11 [2018-10-31, 2018-12-01) #FF00FF 376s 12 [2018-12-01, 2018-12-31] #FF0080 376s Colour map for the range [2018-01-01, 2018-12-31] 376s interval colour 376s 1 [2018-01-01, 2018-01-31) #FF0000 376s 2 [2018-01-31, 2018-03-03) #FF8000 376s 3 [2018-03-03, 2018-04-02) #FFFF00 376s 4 [2018-04-02, 2018-05-02) #80FF00 376s 5 [2018-05-02, 2018-06-02) #00FF00 376s 6 [2018-06-02, 2018-07-02) #00FF80 376s 7 [2018-07-02, 2018-08-01) #00FFFF 376s 8 [2018-08-01, 2018-09-01) #0080FF 376s 9 [2018-09-01, 2018-10-01) #0000FF 376s 10 [2018-10-01, 2018-10-31) #8000FF 376s 11 [2018-10-31, 2018-12-01) #FF00FF 376s 12 [2018-12-01, 2018-12-31] #FF0080 376s Colour map for the range [2018-01-01, 2018-12-31] 376s interval colour 376s 1 [2018-01-01, 2018-04-01) #FF0000 376s 2 [2018-04-01, 2018-07-01) #80FF00 376s 3 [2018-07-01, 2018-10-01) #00FFFF 376s 4 [2018-10-01, 2018-12-31] #8000FF 376s Colour map for the range [2018-01-01, 2018-12-31] 376s interval colour 376s 1 [2018-01-01, 2018-04-01) #FF0000 376s 2 [2018-04-01, 2018-07-01) #80FF00 376s 3 [2018-07-01, 2018-10-01) #00FFFF 376s 4 [2018-10-01, 2018-12-31] #8000FF 376s > 376s > # tests/correctC.R 376s > # check for agreement between C and interpreted code 376s > # for interpoint distances etc. 376s > # $Revision: 1.10 $ $Date: 2023/12/08 07:10:34 $ 376s > 376s > if(ALWAYS) { # depends on hardware 376s + local({ 376s + eps <- .Machine$double.eps * 4 376s + 376s + checkagree <- function(A, B, blurb) { 376s + maxerr <- max(abs(A-B)) 376s + cat("Discrepancy", maxerr, "for", blurb, fill=TRUE) 376s + if(maxerr > eps) 376s + stop(paste("Algorithms for", blurb, "disagree")) 376s + return(TRUE) 376s + } 376s + 376s + ## pairdist.ppp 376s + set.seed(190901) 376s + ## X <- rpoispp(42) 376s + X <- runifrect(max(2, rpois(1, 42))) 376s + dC <- pairdist(X, method="C") 376s + dR <- pairdist(X, method="interpreted") 376s + checkagree(dC, dR, "pairdist()") 376s + 376s + dCp <- pairdist(X, periodic=TRUE, method="C") 376s + dRp <- pairdist(X, periodic=TRUE, method="interpreted") 376s + checkagree(dCp, dRp, "pairdist(periodic=TRUE)") 376s + 376s + dCp2 <- pairdist(X, periodic=TRUE, squared=TRUE, method="C") 376s + dRp2 <- pairdist(X, periodic=TRUE, squared=TRUE, method="interpreted") 376s + checkagree(dCp2, dRp2, "pairdist(periodic=TRUE, squared=TRUE)") 376s + 376s + ## crossdist.ppp 376s + ## Y <- rpoispp(42) 376s + Y <- runifrect(max(2, rpois(1, 42))) 376s + dC <- crossdist(X, Y, method="C") 376s + dR <- crossdist(X, Y, method="interpreted") 376s + checkagree(dC, dR, "crossdist()") 376s + 376s + dC <- crossdist(X, Y, periodic=TRUE, method="C") 376s + dR <- crossdist(X, Y, periodic=TRUE, method="interpreted") 376s + checkagree(dC, dR, "crossdist(periodic=TRUE)") 376s + 376s + dC2 <- crossdist(X, Y, periodic=TRUE, squared=TRUE, method="C") 376s + dR2 <- crossdist(X, Y, periodic=TRUE, squared=TRUE, method="interpreted") 376s + checkagree(dC2, dR2, "crossdist(periodic=TRUE, squared=TRUE)") 376s + 376s + # nndist.ppp 376s + nnC <- nndist(X, method="C") 376s + nnI <- nndist(X, method="interpreted") 376s + checkagree(nnC, nnI, "nndist()") 376s + 376s + nn3C <- nndist(X, k=3, method="C") 376s + nn3I <- nndist(X, k=3, method="interpreted") 376s + checkagree(nn3C, nn3I, "nndist(k=3)") 376s + 376s + # nnwhich.ppp 376s + nwC <- nnwhich(X, method="C") 376s + nwI <- nnwhich(X, method="interpreted") 376s + checkagree(nwC, nwI, "nnwhich()") 376s + 377s + nw3C <- nnwhich(X, k=3, method="C") 377s + nw3I <- nnwhich(X, k=3, method="interpreted") 377s + checkagree(nw3C, nw3I, "nnwhich(k=3)") 377s + 377s + }) 377s + 377s + } 377s Discrepancy 1.110223e-16 for pairdist() 377s Discrepancy 0 for pairdist(periodic=TRUE) 377s Discrepancy 0 for pairdist(periodic=TRUE, squared=TRUE) 377s Discrepancy 1.110223e-16 for crossdist() 377s Discrepancy 0 for crossdist(periodic=TRUE) 377s Discrepancy 0 for crossdist(periodic=TRUE, squared=TRUE) 377s Discrepancy 1.387779e-17 for nndist() 377s Discrepancy 2.775558e-17 for nndist(k=3) 377s Discrepancy 0 for nnwhich() 377s Discrepancy 0 for nnwhich(k=3) 377s [1] TRUE 377s > 377s > 377s END TEST testsAtoC.R with result 0 377s BEGIN TEST testsD.R 377s 377s R version 4.4.3 (2025-02-28) -- "Trophy Case" 377s Copyright (C) 2025 The R Foundation for Statistical Computing 377s Platform: aarch64-unknown-linux-gnu 377s 377s R is free software and comes with ABSOLUTELY NO WARRANTY. 377s You are welcome to redistribute it under certain conditions. 377s Type 'license()' or 'licence()' for distribution details. 377s 377s R is a collaborative project with many contributors. 377s Type 'contributors()' for more information and 377s 'citation()' on how to cite R or R packages in publications. 377s 377s Type 'demo()' for some demos, 'help()' for on-line help, or 377s 'help.start()' for an HTML browser interface to help. 377s Type 'q()' to quit R. 377s 377s > #' 377s > #' Header for all (concatenated) test files 377s > #' 377s > #' Require spatstat.geom 377s > #' Obtain environment variable controlling tests. 377s > #' 377s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 377s > 377s > require(spatstat.geom) 377s Loading required package: spatstat.geom 377s Loading required package: spatstat.data 378s Loading required package: spatstat.univar 378s spatstat.univar 3.1-1 378s spatstat.geom 3.3-5 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 > #' tests/dominic.R 378s > #' 378s > #' Additional tests for Dominic Schuhmacher's code 378s > #' 378s > #' $Revision: 1.5 $ $Date: 2020/12/03 03:23:25 $ 378s > 378s > if(ALWAYS) { # tests C code 378s + local({ 378s + X <- runifrect(10) 378s + Y <- runifrect(10) 378s + 378s + d <- pppdist(X, Y, type="ace", show.rprimal=TRUE) 378s + a <- matchingdist(d, type="ace") 378s + b <- matchingdist(d, type="mat") 378s + 378s + d2 <- pppdist(X, Y, type="spa", ccode=FALSE) 378s + d2 <- pppdist(X, Y, type="spa", ccode=TRUE, auction=FALSE) 378s + d3 <- pppdist(X, Y, type="mat", ccode=TRUE, auction=FALSE) 378s + d4 <- pppdist(X[FALSE], Y[FALSE], matching=TRUE, type="spa") 378s + d4 <- pppdist(X[FALSE], Y[FALSE], matching=FALSE, type="spa") 378s + d4 <- pppdist(X[FALSE], Y[FALSE], matching=TRUE, type="ace") 378s + d4 <- pppdist(X[FALSE], Y[FALSE], matching=FALSE, type="ace") 378s + 378s + m <- pppdist.mat(X, Y, q=Inf, cutoff=0.001) 378s + m2 <- pppdist.mat(X[FALSE], Y[FALSE], q=Inf, cutoff=0.001) 378s + m3 <- pppdist.mat(X[FALSE], Y[FALSE], q=2, cutoff=0.001) 378s + 378s + }) 378s + } 380s > 380s > 380s > 380s > #' 380s > #' tests/discarea.R 380s > #' 380s > #' $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 380s > #' 380s > 380s > if(ALWAYS) { 380s + local({ 380s + u <- c(0.5,0.5) 380s + B <- owin(poly=list(x=c(0.3, 0.5, 0.7, 0.4), y=c(0.3, 0.3, 0.6, 0.8))) 380s + areaGain(u, cells, 0.1, exact=TRUE) 380s + areaGain(u, cells, 0.1, W=NULL) 380s + areaGain(u, cells, 0.1, W=B) 380s + 380s + X <- cells[square(0.4)] 380s + areaLoss(X, 0.1, exact=TRUE) # -> areaLoss.diri 380s + areaLoss(X, 0.1, exact=FALSE) # -> areaLoss.grid 380s + areaLoss.poly(X, 0.1) 380s + 380s + areaLoss(X, 0.1, exact=FALSE, method="distmap") # -> areaLoss.grid 380s + areaLoss(X, c(0.1, 0.15), exact=FALSE, method="distmap") # -> areaLoss.grid 380s + }) 380s + } 380s Warning message: 380s In pppdist.mat(X, Y, q = Inf, cutoff = 0.001) : 380s distance with parameter q = Inf is approximated by distance with parameter q = 10 380s [,1] [,2] 380s [1,] 0.010449219 0.002197266 380s [2,] 0.025009766 0.016718750 380s [3,] 0.019658203 0.004248047 380s [4,] 0.004970703 0.000000000 380s [5,] 0.014111328 0.004951172 380s [6,] 0.014394531 0.000156250 380s [7,] 0.013779297 0.003691406 380s > #' 380s > #' tests/duplicity.R 380s > #' 380s > #' Tests of duplicated/multiplicity code 380s > #' 380s > #' $Revision: 1.8 $ $Date: 2020/04/28 12:58:26 $ 380s > 380s > if(ALWAYS) { 380s + local({ 380s + X <- ppp(c(1,1,0.5,1), c(2,2,1,2), window=square(3), check=FALSE) 380s + Y <- X %mark% factor(letters[c(3,2,4,3)]) 380s + ZC <- X %mark% letters[c(3,2,4,3)] 380s + ZM <- Y %mark% matrix(c(3,2,4,3), 4, 2) 380s + ZD <- Y %mark% as.data.frame(marks(ZM)) 380s + 380s + #' multiplicity 380s + m <- multiplicity(X) 380s + mf <- multiplicity(Y) 380s + mm <- multiplicity(ZM) 380s + mz <- multiplicity(ZD) 380s + mc <- multiplicity(ZC) 380s + ## default method 380s + kk <- c(1,2,3,1,1,2) 380s + mk <- multiplicity(kk) 380s + ml <- multiplicity(list(sin, cos, tan)[kk]) 380s + mc <- multiplicity(c("sin", "cos", "tan")[kk]) 380s + if(!identical(ml, mk)) 380s + stop("multiplicity.default() disagrees with multiplicityNumeric") 380s + if(!identical(mc, mk)) 381s + stop("multiplicity() disagrees with multiplicity()") 381s + ## data frame method 381s + df <- data.frame(x=c(1:4, 1,3,2,4, 0,0, 3,4), 381s + y=factor(rep(letters[1:4], 3))) 381s + md <- multiplicity(df) 381s + 381s + ## uniquemap.ppp 381s + checkum <- function(X, blurb) { 381s + a <- uniquemap(X) 381s + if(any(a > seq_along(a))) 381s + stop(paste("uniquemap", blurb, 381s + "does not respect sequential ordering")) 381s + return(invisible(NULL)) 381s + } 381s + checkum(X, "") 381s + checkum(Y, "") 381s + checkum(ZC, "") 381s + checkum(ZM, "") 381s + checkum(ZD, "") 381s + 381s + ## uniquemap.data.frame 381s + dfbase <- as.data.frame(replicate(3, sample(1:20, 10), simplify=FALSE)) 381s + df <- dfbase[sample(1:10, 30, replace=TRUE), , drop=FALSE] 381s + #' faster algorithm for numeric values 381s + checkum(df, "") 381s + a <- uniquemap(df) 381s + #' general algorithm using 'duplicated' and 'match' 381s + dfletters <- as.data.frame(matrix(letters[as.matrix(df)], nrow=nrow(df))) 381s + checkum(dfletters, "") 381s + b <- uniquemap(dfletters) 381s + if(!isTRUE(all.equal(a,b))) 381s + stop("inconsistency between algorithms in uniquemap.data.frame") 381s + 381s + ## uniquemap.matrix 381s + M0 <- matrix(1:12, 3, 4) 381s + ii <- sample(1:3, 5, replace=TRUE) 381s + M4 <- M0[ii, , drop=FALSE] 381s + checkum(M4, "") 381s + u4 <- uniquemap(M4) 381s + C4 <- matrix(letters[M4], 5, 4) 381s + uc4 <- uniquemap(C4) 381s + checkum(C4, "") 381s + if(!isTRUE(all.equal(u4, uc4))) 381s + stop("Inconsistency between algorithms in uniquemap.matrix") 381s + 381s + ## uniquemap.default 381s + a <- letters[c(1, 1:4, 3:2)] 381s + checkum(a, "") 381s + checkum(as.list(a), "") 381s + u1 <- uniquemap(a) 381s + u2 <- uniquemap(as.list(a)) 381s + if(!isTRUE(all.equal(u1, u2))) 381s + stop("Inconsistency between algorithms in uniquemap.default") 381s + }) 381s + } 381s > 381s END TEST testsD.R with result 0 381s BEGIN TEST testsEtoF.R 381s 381s R version 4.4.3 (2025-02-28) -- "Trophy Case" 381s Copyright (C) 2025 The R Foundation for Statistical Computing 381s Platform: aarch64-unknown-linux-gnu 381s 381s R is free software and comes with ABSOLUTELY NO WARRANTY. 381s You are welcome to redistribute it under certain conditions. 381s Type 'license()' or 'licence()' for distribution details. 381s 381s R is a collaborative project with many contributors. 381s Type 'contributors()' for more information and 381s 'citation()' on how to cite R or R packages in publications. 381s 381s Type 'demo()' for some demos, 'help()' for on-line help, or 381s 'help.start()' for an HTML browser interface to help. 381s Type 'q()' to quit R. 381s 381s > #' 381s > #' Header for all (concatenated) test files 381s > #' 381s > #' Require spatstat.geom 381s > #' Obtain environment variable controlling tests. 381s > #' 381s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 381s > 381s > require(spatstat.geom) 381s Loading required package: spatstat.geom 381s Loading required package: spatstat.data 383s Loading required package: spatstat.univar 383s spatstat.univar 3.1-1 383s spatstat.geom 3.3-5 383s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 383s > ALWAYS <- TRUE 383s > cat(paste("--------- Executing", 383s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 383s + "test code -----------\n")) 383s --------- Executing **RESTRICTED** subset of test code ----------- 383s > # tests/emptymarks.R 383s > # 383s > # test cases where there are no (rows or columns of) marks 383s > # 383s > # $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 383s > 383s > if(ALWAYS) { 383s + local({ 383s + n <- npoints(cells) 383s + df <- data.frame(x=1:n, y=factor(sample(letters, n, replace=TRUE))) 383s + nocolumns <- c(FALSE, FALSE) 383s + norows <- rep(FALSE, n) 383s + X <- cells 383s + marks(X) <- df 383s + marks(X) <- df[,1] 383s + marks(X) <- df[,nocolumns] 383s + Z <- Y <- X[integer(0)] 383s + marks(Y) <- df[norows,] 383s + stopifnot(is.marked(Y)) 383s + marks(Z) <- df[norows,nocolumns] 383s + stopifnot(!is.marked(Z)) 383s + }) 383s + } 383s > # 383s > # tests/factorbugs.R 383s > # 383s > # check for various bugs related to factor conversions 383s > # 383s > # $Revision: 1.8 $ $Date: 2023/01/30 00:51:42 $ 383s > # 383s > 383s > if(ALWAYS) { 383s + local({ 383s + ## make a factor image 383s + m <- factor(rep(letters[1:4], 4)) 383s + Z <- im(m, xcol=1:4, yrow=1:4) 383s + ## make a point pattern 383s + set.seed(42) 383s + X <- runifrect(20, win=as.owin(Z)) 383s + ## look up the image at the points of X 383s + ## (a) internal 383s + ans1 <- lookup.im(Z, X$x, X$y) 383s + stopifnot(is.factor(ans1)) 383s + ## (b) user level 383s + ans2 <- Z[X] 383s + stopifnot(is.factor(ans2)) 383s + ## (c) turn the image into a tessellation 383s + ## and apply quadratcount 383s + V <- tess(image = Z) 383s + quadratcount(X, tess=V) 383s + ## Pad image 383s + Y <- padimage(Z, factor("b", levels=levels(Z))) 383s + stopifnot(Y$type == "factor") 383s + U <- padimage(Z, "b") 383s + stopifnot(U$type == "factor") 383s + ## Manipulate factor levels 383s + Zb <- relevel(Z, "b") 383s + Zv <- mergeLevels(Z, vowel="a", consonant=c("b","c","d")) 383s + P <- X %mark% Z[X] 383s + Pv <- mergeLevels(P, vowel="a", consonant=c("b","c","d")) 383s + ## Harmonise factor levels - cases not covered 383s + Flat <- factor(sample(letters[1:3], 10, replace=TRUE)) 383s + Image <- gorillas.extra$slopetype 383s + oo <- harmoniseLevels() 383s + oo <- harmoniseLevels(Flat) 383s + oo <- harmoniseLevels(A=Image) 383s + oo <- harmoniseLevels(A=Flat,B=Image) 383s + }) 383s + } 383s > # 383s > # tests/func.R 383s > # 383s > # $Revision: 1.9 $ $Date: 2022/10/23 00:48:40 $ 383s > # 383s > # Tests of 'funxy' infrastructure etc 383s > 383s > if(FULLTEST) { 383s + local({ 383s + ## Check the peculiar function-building code in funxy 383s + W <- square(1) 383s + f1a <- function(x, y) sqrt(x^2 + y^2) 383s + F1a <- funxy(f1a, W) 383s + f1b <- function(x, y) { sqrt(x^2 + y^2) } 383s + f2a <- function(x, y) sin(x) 383s + f2b <- function(x, y) { sin(x) } 383s + f3a <- function(x, y) sin(x) + cos(x) 383s + f3b <- function(x, y) { sin(x) + cos(x) } 383s + f4a <- function(x, y) { z <- x + y ; z } 383s + f4b <- function(x, y) { x + y } 383s + F1b <- funxy(f1b, W) 383s + F2a <- funxy(f2a, W) 383s + F2b <- funxy(f2b, W) 383s + F3a <- funxy(f3a, W) 383s + F3b <- funxy(f3b, W) 383s + F4a <- funxy(f4a, W) 383s + F4b <- funxy(f4b, W) 383s + stopifnot(identical(F1a(cells), F1b(cells))) 383s + stopifnot(identical(F2a(cells), F2b(cells))) 383s + stopifnot(identical(F3a(cells), F3b(cells))) 383s + stopifnot(identical(F4a(cells), F4b(cells))) 383s + ## check coordinate extraction from objects 383s + X <- runifrect(9) 383s + Q <- quadscheme(X) 383s + a <- F1a(X) 383s + d <- F1a(Q) 383s + }) 383s + } 383s > 383s > 383s > 383s END TEST testsEtoF.R with result 0 383s BEGIN TEST testsGtoJ.R 383s 383s R version 4.4.3 (2025-02-28) -- "Trophy Case" 383s Copyright (C) 2025 The R Foundation for Statistical Computing 383s Platform: aarch64-unknown-linux-gnu 383s 383s R is free software and comes with ABSOLUTELY NO WARRANTY. 383s You are welcome to redistribute it under certain conditions. 383s Type 'license()' or 'licence()' for distribution details. 383s 383s R is a collaborative project with many contributors. 383s Type 'contributors()' for more information and 383s 'citation()' on how to cite R or R packages in publications. 383s 383s Type 'demo()' for some demos, 'help()' for on-line help, or 383s 'help.start()' for an HTML browser interface to help. 383s Type 'q()' to quit R. 383s 383s > #' 383s > #' Header for all (concatenated) test files 383s > #' 383s > #' Require spatstat.geom 383s > #' Obtain environment variable controlling tests. 383s > #' 383s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 383s > 383s > require(spatstat.geom) 383s Loading required package: spatstat.geom 383s Loading required package: spatstat.data 385s Loading required package: spatstat.univar 385s spatstat.univar 3.1-1 385s spatstat.geom 3.3-5 385s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 385s > ALWAYS <- TRUE 385s > cat(paste("--------- Executing", 385s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 385s + "test code -----------\n")) 385s --------- Executing **RESTRICTED** subset of test code ----------- 385s > # 385s > # tests/hyperframe.R 385s > # 385s > # test "[.hyperframe" etc 385s > # 385s > # $Revision: 1.11 $ $Date: 2023/02/03 06:17:16 $ 385s > # 385s > 385s > if(FULLTEST) { 385s + local({ 385s + lambda <- runif(4, min=50, max=100) 385s + X <- lapply(as.list(lambda), function(x) { runifrect(rpois(1, x)) }) 385s + h <- hyperframe(lambda=lambda, X=X) 385s + h$lambda2 <- lambda^2 385s + h[, "lambda3"] <- lambda^3 385s + h[, "Y"] <- X 385s + h[, "X"] <- lapply(X, flipxy) 385s + h[, c("X", "Y")] <- hyperframe(X=X, Y=X) 385s + 385s + names(h) <- LETTERS[1:5] 385s + print(h) 385s + 385s + summary(h) 385s + str(h) 385s + head(h) 385s + tail(h) 385s + 385s + rn <- rownames(h) 385s + r.n <- row.names(h) 385s + if(!identical(rn, r.n)) 385s + stop("rownames and row.names conflict for hyperframes") 385s + 385s + dn <- dimnames(h) 385s + dimnames(h) <- dn 385s + dimnames(h)[[2]][2] <- "copacetic" 385s + dimnames(h)[[1]][2] <- "second" 385s + 385s + #' hyperframe with a hyperatom 385s + H <- hyperframe(A=runif(3), B=1:3, D=runifrect(10)) 385s + H[,3] 385s + H[,3,drop=TRUE] 385s + #' special cases of [<- 385s + H$B <- H[,1] 385s + H[2:3,1] <- H[2:3,2] 385s + H[2:3,1] <- H[2,2] 385s + H[2,1:2] <- H[3,1:2] 385s + 385s + #' split 385s + f <- factor(c("a", "a", "b")) 385s + G <- split(H, f) 385s + G[["a"]]$B <- 42 385s + split(H, f) <- G 385s + 385s + #' [[ and [[<- 385s + junk <- pyramidal 385s + a <- junk[["group"]] 385s + junk[["group"]] <- sample(a) 385s + a <- junk[[2]] 385s + a <- junk[[15,2]] 385s + junk[[15,2]] <- "schizoaffective" 385s + junk[[15,2]] <- "z" # Warning given. 385s + a <- junk[[2]] # The warned-about NA appears as entry 15. 385s + junk[[10,1]] <- cells 385s + a <- junk[[10,1]] 385s + a <- junk[[10,"Neurons"]] 385s + }) 385s + } 385s > # 385s > # tests/imageops.R 385s > # 385s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 385s > # 385s > 385s > 385s > if(ALWAYS) { 385s + local({ 385s + #' Test of case 'CONNECT=24' in src/distmapbin.[ch] 385s + #' Distance transform with 24-connected neighbours 385s + A <- distmap(heather$coarse, connect=24) 385s + }) 385s + } 385s > 385s > if(FULLTEST) { 385s + local({ 385s + #' cases of 'im' data 385s + tab <- table(sample(factor(letters[1:10]), 30, replace=TRUE)) 385s + b <- im(tab, xrange=c(0,1), yrange=c(0,10)) 385s + b <- update(b) 385s + 385s + mat <- matrix(sample(0:4, 12, replace=TRUE), 3, 4) 385s + a <- im(mat) 385s + levels(a$v) <- 0:4 385s + a <- update(a) 385s + 385s + levels(mat) <- 0:4 385s + b <- im(mat) 385s + b <- update(b) 385s + 385s + D <- as.im(mat, letterR) 385s + df <- as.data.frame(D) 385s + DD <- as.im(df, step=c(D$xstep, D$ystep)) 385s + 385s + #' various manipulations 385s + AA <- A <- as.im(owin()) 385s + BB <- B <- as.im(owin(c(1.1, 1.9), c(0,1))) 385s + Z <- imcov(A, B) 385s + stopifnot(abs(max(Z) - 0.8) < 0.1) 385s + 385s + Frame(AA) <- Frame(B) 385s + Frame(BB) <- Frame(A) 385s + 385s + ## handling images with 1 row or column 385s + 385s + ycov <- function(x, y) y 385s + E <- as.im(ycov, owin(), dimyx = c(2,1)) 385s + G <- cut(E, 2) 385s + H <- as.tess(G) 385s + 385s + E12 <- as.im(ycov, owin(), dimyx = c(1,2)) 385s + G12 <- cut(E12, 2) 385s + H12 <- as.tess(G12) 385s + 385s + AAA <- as.array(AA) 385s + EEE <- as.array(E) 385s + AAD <- as.double(AA) 385s + EED <- as.double(E) 385s + aaa <- xtfrm(AAA) 385s + eee <- xtfrm(E) 385s + 385s + ## 385s + d <- distmap(cells, dimyx=32) 385s + D6 <- (d <= 0.06) 385s + Z <- connected(D6, method="interpreted") 385s + Z <- connected(D6, connect=4) 385s + Z <- connected(D6, method="interpreted", connect=4) 385s + 385s + a <- where.max(d, first=FALSE) 385s + a <- where.min(d, first=FALSE) 385s + 385s + dx <- raster.x(d) 385s + dy <- raster.y(d) 385s + dxy <- raster.xy(d) 385s + xyZ <- raster.xy(Z, drop=TRUE) 385s + 385s + horosho <- conform.imagelist(cells, list(d, Z)) 385s + 385s + #' split.im 385s + W <- square(1) 385s + X <- as.im(function(x,y){x}, W) 385s + Y <- dirichlet(runifrect(7, W)) 385s + Z <- split(X, as.im(Y)) 385s + 385s + ## ........... cases of "[.im" ........................ 385s + ## index window has zero overlap area with image window 385s + Out <- owin(c(-0.5, 0), c(0,1)) 385s + oo <- X[Out] 385s + oo <- X[Out, drop=FALSE] 385s + if(!is.im(oo)) stop("Wrong format in [.im with disjoint index window") 385s + oon <- X[Out, drop=TRUE, rescue=FALSE] 385s + if(is.im(oon)) stop("Expected a vector of values, not an image, from [.im") 385s + if(!all(is.na(oon))) stop("Expected a vector of NA values in [.im") 385s + ## 385s + Empty <- cells[FALSE] 385s + ff <- d[Empty] 385s + gg <- d[2,] 385s + gg <- d[,2] 385s + gg <- d[j=2] 385s + gg <- d[2:4, 3:5] 385s + hh <- d[2:4, 3:5, rescue=TRUE] 385s + if(!is.im(hh)) stop("rectangle was not rescued in [.im") 385s + ## factor and NA values 385s + f <- cut(d, breaks=4) 385s + f <- f[f != levels(f)[1], drop=FALSE] 385s + fff <- f[, , drop=FALSE] 385s + fff <- f[cells] 385s + fff <- f[cells, drop=FALSE] 385s + fff <- f[Empty] 385s + 385s + ## ........... cases of "[<-.im" ....................... 385s + d[,] <- d[] + 1 385s + d[Empty] <- 42 385s + ## smudge() and rasterfilter() 385s + dd <- smudge(d) 385s + 385s + ## rgb/hsv options 385s + X <- setcov(owin()) 385s + M <- Window(X) 385s + Y <- as.im(function(x,y) x, W=M) 385s + Z <- as.im(function(x,y) y, W=M) 385s + # convert after rescaling 385s + RGBscal <- rgbim(X, Y, Z, autoscale=TRUE, maxColorValue=1) 385s + HSVscal <- hsvim(X, Y, Z, autoscale=TRUE) 385s + 385s + #' cases of [.im 385s + Ma <- as.mask(M, dimyx=37) 385s + ZM <- Z[raster=Ma, drop=FALSE] 385s + ZM[solutionset(Y+Z > 0.4)] <- NA 385s + ZF <- cut(ZM, breaks=5) 385s + ZL <- (ZM > 0) 385s + P <- list(x=c(0.511, 0.774, 0.633, 0.248, 0.798), 385s + y=c(0.791, 0.608, 0.337, 0.613, 0.819)) 385s + zmp <- ZM[P, drop=TRUE] 385s + zfp <- ZF[P, drop=TRUE] 385s + zlp <- ZL[P, drop=TRUE] 385s + P <- as.ppp(P, owin()) 385s + zmp <- ZM[P, drop=TRUE] 385s + zfp <- ZF[P, drop=TRUE] 385s + zlp <- ZL[P, drop=TRUE] 385s + 385s + #' miscellaneous 385s + ZZ <- zapsmall.im(Z, digits=6) 385s + ZZ <- zapsmall.im(Z) 385s + 385s + ZS <- shift(Z, origin="centroid") 385s + ZS <- shift(Z, origin="bottomleft") 385s + 385s + ZA <- affine(Z, mat=diag(c(-1,-2))) 385s + 385s + U <- scaletointerval(Z) 385s + C <- as.im(1, W=U) 385s + U <- scaletointerval(C) 385s + 385s + #' hist.im 385s + h <- hist(Z) 385s + h <- hist(Z, probability=TRUE) 385s + h <- hist(Z, plot=FALSE) 385s + Zcut <- cut(Z, breaks=5) 385s + h <- hist(Zcut) # barplot 385s + hp <- hist(Zcut, probability=TRUE) # barplot 385s + plot(h) # plot.barplotdata 385s + 385s + #' plot.im code blocks 385s + plot(Z, ribside="left") 385s + plot(Z, ribside="top") 385s + plot(Z, riblab="value") 385s + plot(Z, clipwin=square(0.5)) 385s + plot(Z - mean(Z), log=TRUE) 385s + plot(Z, valuesAreColours=TRUE) # rejected with a warning 385s + IX <- as.im(function(x,y) { as.integer(round(3*x)) }, square(1)) 385s + co <- colourmap(rainbow(4), inputs=0:3) 385s + plot(IX, col=co) 385s + CX <- eval.im(col2hex(IX+1L)) 385s + plot(CX, valuesAreColours=TRUE) 385s + plot(CX, valuesAreColours=FALSE) 385s + 385s + #' plot.im contour code logarithmic case 385s + V0 <- setcov(owin()) 385s + V2 <- exp(2*V0+1) 385s + plot(V2, log=TRUE, addcontour=TRUE, contourargs=list(col="white")) 385s + plot(V2, log=TRUE, addcontour=TRUE, contourargs=list(col="white", nlevels=2)) 385s + plot(V2, log=TRUE, addcontour=TRUE, contourargs=list(col="white", nlevels=20)) 385s + V4 <- exp(4*V0+1) 385s + plot(V4, log=TRUE, addcontour=TRUE, contourargs=list(col="white")) 385s + plot(V4, log=TRUE, addcontour=TRUE, contourargs=list(col="white", nlevels=2)) 385s + plot(V4, log=TRUE, addcontour=TRUE, contourargs=list(col="white", nlevels=20)) 385s + 385s + #' pairs.im 385s + pairs(solist(Z)) 385s + pairs(solist(A=Z)) 385s + 385s + #' handling and plotting of character and factor images 385s + Afactor <- as.im(col2hex("green"), letterR, na.replace=col2hex("blue")) 385s + Acharacter <- as.im(col2hex("green"), letterR, na.replace=col2hex("blue"), 385s + stringsAsFactors=FALSE) 385s + plot(Afactor) 385s + plot(Acharacter, valuesAreColours=TRUE) 385s + print(summary(Afactor)) 385s + print(summary(Acharacter)) 385s + 385s + #' substitute for runifpoint 385s + rup <- function(n, W) { runifrect(n, Frame(W))[W] } 385s + #' safelookup (including extrapolation case) 385s + Z <- as.im(function(x,y) { x - y }, letterR) 385s + Zcut <- cut(Z, breaks=4) 385s + B <- grow.rectangle(Frame(letterR), 1) 385s + X <- superimpose(rup(10, letterR), 385s + rup(20, setminus.owin(B, letterR)), 385s + vertices(Frame(B)), 385s + W=B) 385s + a <- safelookup(Z, X) 385s + aa <- safelookup(Z, X, factor=100) 385s + b <- safelookup(Zcut, X) 385s + bb <- safelookup(Zcut, X, factor=100) 385s + cc <- lookup.im(Z, X) 385s + 385s + #' im.apply 385s + Z <- im.apply(bei.extra, sd) 385s + 385s + #' Math.imlist, Ops.imlist, Complex.imlist 385s + U <- Z+2i 385s + B <- U * (2+1i) 385s + print(summary(B)) 385s + V <- solist(A=U, B=B) 385s + negV <- -V 385s + E <- Re(V) 385s + negE <- -E 385s + 385s + }) 385s + } 385s > 385s > if(ALWAYS) { 385s + local({ 385s + #' check nearest.valid.pixel 385s + W <- Window(demopat) 385s + set.seed(911911) 385s + X <- runifrect(1000, Frame(W))[W] 385s + Z <- quantess(W, function(x,y) { x }, 9)$image 385s + nearest.valid.pixel(numeric(0), numeric(0), Z) 385s + x <- X$x 385s + y <- X$y 385s + a <- nearest.valid.pixel(x, y, Z, method="interpreted") 385s + b <- nearest.valid.pixel(x, y, Z, method="C") 385s + if(!isTRUE(all.equal(a,b))) 385s + stop("Unequal results in nearest.valid.pixel") 385s + if(!identical(a,b)) 385s + stop("Equal, but not identical, results in nearest.valid.pixel") 385s + }) 385s + } 385s > 385s > 385s > 385s END TEST testsGtoJ.R with result 0 385s BEGIN TEST testsK.R 385s 385s R version 4.4.3 (2025-02-28) -- "Trophy Case" 385s Copyright (C) 2025 The R Foundation for Statistical Computing 385s Platform: aarch64-unknown-linux-gnu 385s 385s R is free software and comes with ABSOLUTELY NO WARRANTY. 385s You are welcome to redistribute it under certain conditions. 385s Type 'license()' or 'licence()' for distribution details. 385s 385s R is a collaborative project with many contributors. 385s Type 'contributors()' for more information and 385s 'citation()' on how to cite R or R packages in publications. 385s 385s Type 'demo()' for some demos, 'help()' for on-line help, or 385s 'help.start()' for an HTML browser interface to help. 385s Type 'q()' to quit R. 385s 385s > #' 385s > #' Header for all (concatenated) test files 385s > #' 385s > #' Require spatstat.geom 385s > #' Obtain environment variable controlling tests. 385s > #' 385s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 385s > 385s > require(spatstat.geom) 385s Loading required package: spatstat.geom 385s Loading required package: spatstat.data 387s Loading required package: spatstat.univar 387s spatstat.univar 3.1-1 387s spatstat.geom 3.3-5 387s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 387s > ALWAYS <- TRUE 387s > cat(paste("--------- Executing", 387s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 387s + "test code -----------\n")) 387s --------- Executing **RESTRICTED** subset of test code ----------- 387s > 387s END TEST testsK.R with result 0 387s BEGIN TEST testsL.R 387s 387s R version 4.4.3 (2025-02-28) -- "Trophy Case" 387s Copyright (C) 2025 The R Foundation for Statistical Computing 387s Platform: aarch64-unknown-linux-gnu 387s 387s R is free software and comes with ABSOLUTELY NO WARRANTY. 387s You are welcome to redistribute it under certain conditions. 387s Type 'license()' or 'licence()' for distribution details. 387s 387s R is a collaborative project with many contributors. 387s Type 'contributors()' for more information and 387s 'citation()' on how to cite R or R packages in publications. 387s 387s Type 'demo()' for some demos, 'help()' for on-line help, or 387s 'help.start()' for an HTML browser interface to help. 387s Type 'q()' to quit R. 387s 387s > #' 387s > #' Header for all (concatenated) test files 387s > #' 387s > #' Require spatstat.geom 387s > #' Obtain environment variable controlling tests. 387s > #' 387s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 387s > 387s > require(spatstat.geom) 387s Loading required package: spatstat.geom 387s Loading required package: spatstat.data 389s Loading required package: spatstat.univar 389s spatstat.univar 3.1-1 389s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 389s > ALWAYS <- TRUE 389s > cat(paste("--------- Executing", 389s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 389s + "test code -----------\n")) 389s --------- Executing **RESTRICTED** subset of test code ----------- 389s > #' 389s > #' tests/layered.R 389s > #' 389s > #' Tests of 'layered' class 389s > #' 389s > #' $Revision: 1.2 $ $Date: 2020/04/29 08:55:17 $ 389s > #' 389s > if(FULLTEST) { 389s + local({ 389s + D <- distmap(cells) 389s + L <- layered(D, cells, 389s + plotargs=list(list(ribbon=FALSE), list(pch=16))) 389s + #' 389s + plot(L, which=2, plotargs=list(list(pch=3))) 389s + plot(L, plotargs=list(list(pch=3))) 389s + #' 389s + W <- as.owin(L) 389s + V <- domain(L) 389s + #' methods 389s + L2 <- L[square(0.5)] 389s + Lr <- reflect(L) 389s + Lf <- flipxy(L) 389s + Ls <- scalardilate(L, 2) 389s + La <- shift(L, origin="midpoint") 389s spatstat.geom 3.3-5 389s + Lo <- rotate(L, pi/3, origin="bottomleft") 389s + Lu <- rescale(L, 0.1, "parsec") 389s + #' as.layered 389s + M <- as.layered(finpines) 389s + M2 <- as.layered(split(amacrine)) 389s + }) 389s + } 389s > 389s END TEST testsL.R with result 0 389s BEGIN TEST testsM.R 389s 389s R version 4.4.3 (2025-02-28) -- "Trophy Case" 389s Copyright (C) 2025 The R Foundation for Statistical Computing 389s Platform: aarch64-unknown-linux-gnu 389s 389s R is free software and comes with ABSOLUTELY NO WARRANTY. 389s You are welcome to redistribute it under certain conditions. 389s Type 'license()' or 'licence()' for distribution details. 389s 389s R is a collaborative project with many contributors. 389s Type 'contributors()' for more information and 389s 'citation()' on how to cite R or R packages in publications. 389s 389s Type 'demo()' for some demos, 'help()' for on-line help, or 389s 'help.start()' for an HTML browser interface to help. 389s Type 'q()' to quit R. 389s 389s > #' 389s > #' Header for all (concatenated) test files 389s > #' 389s > #' Require spatstat.geom 389s > #' Obtain environment variable controlling tests. 389s > #' 389s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 389s > 389s > require(spatstat.geom) 389s Loading required package: spatstat.geom 389s Loading required package: spatstat.data 391s Loading required package: spatstat.univar 391s spatstat.univar 3.1-1 391s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 391s > ALWAYS <- TRUE 391s > cat(paste("--------- Executing", 391s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 391s + "test code -----------\n")) 391s --------- Executing **RESTRICTED** subset of test code ----------- 391s > #' tests/morpho.R 391s > #' 391s > #' morphology code blocks 391s > #' 391s > #' $Revision: 1.3 $ $Date: 2020/04/30 02:18:23 $ 391s > 391s > local({ 391s + if(ALWAYS) { # depends on C code etc 391s + #' owin 391s + a <- erosion(letterR, 0.1, polygonal=FALSE) 391s + b <- dilation(letterR, 0.1, polygonal=FALSE) 391s + at <- erosion(letterR, 0.1, polygonal=FALSE, strict=TRUE) 391s + bt <- dilation(letterR, 0.1, polygonal=FALSE, tight=FALSE) 391s + #' psp 391s + S <- edges(letterR) 391s + dm <- dilation(S, 0.1, polygonal=FALSE) 391s + dt <- dilation(S, 0.1, polygonal=FALSE, tight=FALSE) 391s + op <- spatstat.options(old.morpho.psp=TRUE) 391s + dn <- dilation(S, 0.1, polygonal=TRUE) 391s + spatstat.options(op) 391s + cS <- closing(S, 0.1, polygonal=FALSE) 391s + eS <- erosion(S, 0) 391s + oS <- opening(S, 0) 391s + #' ppp 391s + dc <- dilation(cells, 0.06, polygonal=FALSE) 391s + ec <- erosion(cells, 0) 391s + oc <- opening(cells, 0) 391s + #' 391s + reset.spatstat.options() 391s + } 391s + }) 391s spatstat.geom 3.3-5 391s > 391s > 391s END TEST testsM.R with result 0 391s BEGIN TEST testsNtoO.R 391s 391s R version 4.4.3 (2025-02-28) -- "Trophy Case" 391s Copyright (C) 2025 The R Foundation for Statistical Computing 391s Platform: aarch64-unknown-linux-gnu 391s 391s R is free software and comes with ABSOLUTELY NO WARRANTY. 391s You are welcome to redistribute it under certain conditions. 391s Type 'license()' or 'licence()' for distribution details. 391s 391s R is a collaborative project with many contributors. 391s Type 'contributors()' for more information and 391s 'citation()' on how to cite R or R packages in publications. 391s 391s Type 'demo()' for some demos, 'help()' for on-line help, or 391s 'help.start()' for an HTML browser interface to help. 391s Type 'q()' to quit R. 391s 392s > #' 392s > #' Header for all (concatenated) test files 392s > #' 392s > #' Require spatstat.geom 392s > #' Obtain environment variable controlling tests. 392s > #' 392s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 392s > 392s > require(spatstat.geom) 392s Loading required package: spatstat.geom 392s Loading required package: spatstat.data 393s Loading required package: spatstat.univar 393s > spatstat.univar 3.1-1 393s spatstat.geom 3.3-5 393s FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 393s > ALWAYS <- TRUE 393s > cat(paste("--------- Executing", 393s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 393s + "test code -----------\n")) 393s --------- Executing **RESTRICTED** subset of test code ----------- 393s > # 393s > # tests/nndist.R 393s > # 393s > # Check that nndist and nnwhich give 393s > # results consistent with direct calculation from pairdist 393s > # 393s > # Similarly for nncross and distfun 393s > # 393s > # Also test whether minnndist(X) == min(nndist(X)) 393s > # 393s > # $Revision: 1.39 $ $Date: 2021/05/20 09:31:23 $ 393s > # 393s > 393s > 393s > local({ 393s + eps <- sqrt(.Machine$double.eps) 393s + f <- function(mat,k) { apply(mat, 1, function(z,n) { sort(z)[n] }, n=k+1) } 393s + g <- function(mat,k) { apply(mat, 1, function(z,n) { order(z)[n] }, n=k+1) } 393s + 393s + ## ....... Two dimensions ................ 393s + if(ALWAYS) { 393s + X <- runifrect(24) 393s + 393s + nn <- nndist(X) 393s + nnP <- f(pairdist(X), 1) 393s + if(any(abs(nn - nnP) > eps)) 393s + stop("nndist.ppp does not agree with pairdist") 393s + 393s + nn5 <- nndist(X, k=5) 393s + nn5P <- f(pairdist(X), 5) 393s + if(any(abs(nn5 - nn5P) > eps)) 393s + stop("nndist.ppp(k=5) does not agree with pairdist") 393s + 393s + nw <- nnwhich(X) 393s + nwP <- g(pairdist(X), 1) 393s + if(any(nw != nwP)) 393s + stop("nnwhich.ppp does not agree with pairdist") 393s + 393s + nw5 <- nnwhich(X, k=5) 393s + nw5P <- g(pairdist(X), 5) 393s + if(any(nw5 != nw5P)) 393s + stop("nnwhich.ppp(k=5) does not agree with pairdist") 393s + } 393s + 393s + if(FULLTEST) { 393s + a <- nndist(X, method="test") 393s + b <- nnwhich(X, method="test") 393s + a <- nndist(X, method="test", k=1:2) 393s + b <- nnwhich(X, method="test", k=1:2) 393s + a2 <- nndist(cells[1:3], k=1:3) 393s + b2 <- nnwhich(cells[1:3], k=1:3) 393s + a3 <- nndist(cells[1]) 393s + b3 <- nnwhich(cells[1]) 393s + m <- factor((1:npoints(X)) %% 2 == 0) 393s + a4 <- nndist.default(X, by=m, k=2) 393s + b4 <- nnwhich.default(X, by=m, k=2) 393s + } 393s + 393s + if(ALWAYS) { 393s + ## nncross.ppp without options 393s + Y <- runifrect(30) 393s + Y <- Y[nndist(Y) > 0.02] 393s + nc <- nncross(X,Y) 393s + ncd <- nc$dist 393s + ncw <- nc$which 393s + cd <- crossdist(X,Y) 393s + cdd <- apply(cd, 1, min) 393s + cdw <- apply(cd, 1, which.min) 393s + if(any(abs(ncd - cdd) > eps)) 393s + stop("nncross()$dist does not agree with apply(crossdist(), 1, min)") 393s + if(any(ncw != cdw)) 393s + stop("nncross()$which does not agree with apply(crossdist(), 1, which.min)") 393s + 393s + ## nncross with sort on x 393s + nc <- nncross(X,Y, sortby="x") 393s + ncd <- nc$dist 393s + ncw <- nc$which 393s + if(any(abs(ncd - cdd) > eps)) 393s + stop("nncross(sortby=x)$dist does not agree with apply(crossdist(), 1, min)") 393s + if(any(ncw != cdw)) 393s + stop("nncross(sortby=x)$which does not agree with apply(crossdist(), 1, which.min)") 393s + 393s + ## nncross with data pre-sorted on x 393s + Y <- Y[order(Y$x)] 393s + nc <- nncross(X,Y, is.sorted.Y=TRUE, sortby="x") 393s + ncd <- nc$dist 393s + ncw <- nc$which 393s + cd <- crossdist(X,Y) 393s + cdd <- apply(cd, 1, min) 393s + cdw <- apply(cd, 1, which.min) 393s + if(any(abs(ncd - cdd) > eps)) 393s + stop("For sorted data, nncross()$dist does not agree with apply(crossdist(), 1, min)") 393s + if(any(ncw != cdw)) 393s + stop("For sorted data, nncross()$which does not agree with apply(crossdist(), 1, which.min)") 393s + 393s + ## sanity check for nncross with k > 1 393s + ndw <- nncross(X, Y, k=1:4, what="which") 393s + if(any(is.na(ndw))) 393s + stop("NA's returned by nncross.ppp(k > 1, what='which')") 393s + nnc4 <- nncross(X, Y, k=1:4) 393s + iswhich <- (substr(colnames(nnc4), 1, nchar("which")) == "which") 393s + ndw <- nnc4[,iswhich] 393s + if(any(is.na(ndw))) 393s + stop("NA's returned by nncross.ppp(k > 1)$which") 393s + 393s + ## test of correctness for nncross with k > 1 393s + flipcells <- flipxy(cells) 393s + calcwhich <- nncross(cells, flipcells, k=1:4, what="which") 393s + truewhich <- t(apply(crossdist(cells,flipcells), 1, order))[,1:4] 393s + if(any(calcwhich != truewhich)) 393s + stop("nncross(k > 1) gives wrong answer") 393s + } 393s + 393s + if(FULLTEST) { 393s + ## example from Hank Stevens 393s + A <- data.frame( 393s + m= c("K", "K", "A1", "A2", "G", "A2", "A3"), 393s + x=c(4.85, 6.76, 10.58, 19.18, 15.74, 19.08, 12.27), 393s + y=c(5.60, 12.92, 11.14, 17.22, 5.74, 1.24, 2.20), 393s + stringsAsFactors=TRUE 393s + ) 393s + X <- with(A, ppp(x, y, marks=m, window=bounding.box.xy(x, y))) 393s + suspect <- nncross(X, X[7], iX=1:7, iY=7L)$dist 393s + correct <- c(pairdist(X)[1:6, 7], Inf) 393s + maxer <- max(abs(suspect[1:6] - correct[1:6])) 393s + if(maxer > 0.001) 393s + stop("Error in nncross (Inf values) in Hank Stevens example") 393s + if(suspect[7] != Inf) 393s + stop("Error in nncross (finite values) in Hank Stevens example") 393s + M <- as.matrix(minnndist(X, by=marks(X))) 393s + M[is.infinite(M)] <- 0 393s + maxer <- max(abs(M - t(M))) 393s + if(maxer > 0.001) 393s + stop("Error in minnndist(by) in Hank Stevens example") 393s + } 393s + 393s + if(ALWAYS) { 393s + #' cover some C code blocks 393s + Z <- runifrect(50) 393s + X <- Z[1:30] 393s + Y <- Z[20:50] 393s + iX <- 1:30 393s + iY <- 20:50 393s + Ndw <- nncross(X,Y, iX, iY, k=3) 393s + Nw <- nncross(X,Y, iX, iY, k=3, what="which") 393s + Nd <- nncross(X,Y, iX, iY, k=3, what="dist") 393s + } 393s + 393s + if(FULLTEST) { 393s + ## special cases 393s + nndist(X[FALSE]) 393s + nndist(X[1]) 393s + nndist(X[1:3], k=4) 393s + nndist(X[1:3], k=1:4) 393s + nnwhich(X[FALSE]) 393s + nnwhich(X[1]) 393s + nnwhich(X[1:3], k=4) 393s + nnwhich(X[1:3], k=1:4) 393s + nncross(X[1:3], Y[FALSE]) 393s + nncross(X[1:3], Y[1]) 393s + nncross(X[1:3], Y[1:3], k=4) 393s + nncross(X[1:3], Y[1:3], k=1:4) 393s + } 393s + 393s + ## ....... Three dimensions ................ 393s + 393s + if(ALWAYS) { 393s + rthree <- function(n) { pp3(runif(n), runif(n), runif(n), box3(c(0,1))) } 393s + XX <- rthree(42) 393s + X <- XX[1:20] 393s + nn <- nndist(X) 393s + nnP <- f(pairdist(X), 1) 393s + if(any(abs(nn - nnP) > eps)) 393s + stop("nndist.pp3 does not agree with pairdist") 393s + 393s + nn5 <- nndist(X, k=5) 393s + nn5P <- f(pairdist(X), 5) 393s + if(any(abs(nn5 - nn5P) > eps)) 393s + stop("nndist.pp3(k=5) does not agree with pairdist") 393s + 393s + nw <- nnwhich(X) 393s + nwP <- g(pairdist(X), 1) 393s + if(any(nw != nwP)) 393s + stop("nnwhich.pp3 does not agree with pairdist") 393s + 393s + nw5 <- nnwhich(X, k=5) 393s + nw5P <- g(pairdist(X), 5) 393s + if(any(nw5 != nw5P)) 393s + stop("nnwhich.pp3(k=5) does not agree with pairdist") 393s + 393s + ff <- function(mat,k) { apply(mat, 1, function(z,n) { sort(z)[n] }, n=k) } 393s + gg <- function(mat,k) { apply(mat, 1, function(z,n) { order(z)[n] }, n=k) } 393s + 393s + Y <- rthree(20) 393s + Y <- Y[nndist(Y) > 0.02] 393s + DXY <- crossdist(X,Y) 393s + a <- nncross(X,Y) 393s + a <- nncross(X,Y, what="dist") 393s + a <- nncross(X,Y, what="which") 393s + if(any(a != gg(DXY, 1))) 393s + stop("incorrect result from nncross.pp3(what='which')") 393s + a2 <- nncross(X,Y, k=2) 393s + a2 <- nncross(X,Y, what="dist", k=2) 393s + a2 <- nncross(X,Y, what="which", k=2) 393s + if(any(a2 != gg(DXY, 2))) 393s + stop("incorrect result from nncross.pp3(k=2, what='which')") 393s + } 393s + 393s + if(FULLTEST) { 393s + X <- XX 393s + iX <- 1:42 393s + iZ <- 30:42 393s + Z <- X[iZ] 393s + b <- nncross(X, Z, iX=iX, iY=iZ) 393s + b <- nncross(X, Z, iX=iX, iY=iZ, what="which") 393s + b <- nncross(X, Z, iX=iX, iY=iZ, what="dist") 393s + b2 <- nncross(X, Z, iX=iX, iY=iZ, k=2) 393s + b2 <- nncross(X, Z, iX=iX, iY=iZ, what="which", k=2) 393s + b2 <- nncross(X, Z, iX=iX, iY=iZ, what="dist", k=2) 393s + e1 <- nncross(X, Y[1:3], k=2:4) 393s + c1 <- nncross(X, Y, sortby="var") 393s + c2 <- nncross(X, Y, sortby="x") 393s + c3 <- nncross(X, Y, sortby="y") 393s + c4 <- nncross(X, Y, sortby="z") 393s + Xsort <- X[order(coords(X)$x)] 393s + c5 <- nncross(Xsort, Y, is.sorted.X=TRUE, sortby="x") 393s + Ysort <- Y[order(coords(Y)$x)] 393s + c6 <- nncross(Xsort, Ysort, is.sorted.X=TRUE, is.sorted.Y=TRUE, sortby="x") 393s + } 393s + 393s + if(FULLTEST) { 393s + ## special cases 393s + nndist(X[FALSE]) 393s + nndist(X[1]) 393s + nndist(X[1:3], k=4) 393s + nndist(X[1:3], k=1:4) 393s + nnwhich(X[FALSE]) 393s + nnwhich(X[1]) 393s + nnwhich(X[1:3], k=4) 393s + nnwhich(X[1:3], k=1:4) 393s + nncross(X[1:3], Y[FALSE]) 393s + nncross(X[1:3], Y[1]) 393s + nncross(X[1:3], Y[1:3], k=4) 393s + nncross(X[1:3], Y[1:3], k=1:4) 393s + } 393s + 393s + ## ....... m dimensions ................ 393s + 393s + if(ALWAYS) { 393s + rx <- function(n) { 393s + B <- boxx(c(0,1),c(0,1),c(0,1),c(0,1)) 393s + df <- replicate(4, runif(n), simplify=FALSE) 393s + names(df) <- letters[23:26] 393s + ppx(as.data.frame(df), B) 393s + } 393s + ## X <- runifpointx(42, B) 393s + ## Y <- runifpointx(50, B) 393s + X <- rx(42) 393s + Y <- rx(50) 393s + Y <- Y[nndist(Y) > 0.02] 393s + DXY <- crossdist(X,Y) 393s + 393s + nn <- nndist(X) 393s + nnP <- f(pairdist(X), 1) 393s + if(any(abs(nn - nnP) > eps)) 393s + stop("nndist.ppx does not agree with pairdist") 393s + 393s + nn5 <- nndist(X, k=5) 393s + nn5P <- f(pairdist(X), 5) 393s + if(any(abs(nn5 - nn5P) > eps)) 393s + stop("nndist.ppx(k=5) does not agree with pairdist") 393s + 393s + nw <- nnwhich(X) 393s + nwP <- g(pairdist(X), 1) 393s + if(any(nw != nwP)) 393s + stop("nnwhich.ppx does not agree with pairdist") 393s + 393s + nw5 <- nnwhich(X, k=5) 393s + nw5P <- g(pairdist(X), 5) 393s + if(any(nw5 != nw5P)) 393s + stop("nnwhich.ppx(k=5) does not agree with pairdist") 393s + 393s + a <- nncross(X,Y) 393s + ncd <- nncross(X,Y, what="dist") 393s + ncw <- nncross(X,Y, what="which") 393s + if(any(ncw != gg(DXY, 1))) 393s + stop("incorrect result from nncross.ppx(what='which')") 393s + a2 <- nncross(X,Y, k=2) 393s + ncd <- nncross(X,Y, what="dist", k=2) 393s + ncw <- nncross(X,Y, what="which", k=2) 393s + if(any(ncw != gg(DXY, 2))) 393s + stop("incorrect result from nncross.ppx(k=2, what='which')") 393s + } 393s + 393s + if(FULLTEST) { 393s + ## special cases 393s + nndist(X[FALSE]) 393s + nndist(X[1]) 393s + nndist(X[1:3], k=4) 393s + nndist(X[1:3], k=1:4) 393s + nnwhich(X[FALSE]) 393s + nnwhich(X[1]) 393s + nnwhich(X[1:3], k=4) 393s + nnwhich(X[1:3], k=1:4) 393s + nncross(X[1:3], Y[FALSE]) 393s + nncross(X[1:3], Y[1]) 393s + nncross(X[1:3], Y[1:3], k=4) 393s + nncross(X[1:3], Y[1:3], k=1:4) 393s + } 393s + 393s + if(ALWAYS) { 393s + ## test of agreement between nngrid.h and knngrid.h 393s + ## dimyx=23 (found by trial-and-error) ensures that there are no ties 393s + a <- as.matrix(nnmap(cells, what="which", dimyx=23)) 393s + b <- as.matrix(nnmap(cells, what="which", dimyx=23, k=1:2)[[1]]) 393s + if(any(a != b)) 393s + stop("algorithms in nngrid.h and knngrid.h disagree") 393s + 393s + ## minnndist correctness 393s + X <- redwood3 393s + eps <- sqrt(.Machine$double.eps) 393s + mfast <- minnndist(X) 393s + mslow <- min(nndist(X)) 393s + if(abs(mfast-mslow) > eps) 393s + stop("minnndist(X) disagrees with min(nndist(X))") 393s + 393s + ## maxnndist correctness 393s + mfast <- maxnndist(X) 393s + mslow <- max(nndist(X)) 393s + if(abs(mfast-mslow) > eps) 393s + stop("maxnndist(X) disagrees with max(nndist(X))") 393s + } 393s + 393s + if(ALWAYS) { 393s + ## minnndist, maxnndist code blocks 393s + Y <- superimpose(amacrine, amacrine[10:20]) 393s + a <- maxnndist(Y, positive=TRUE) 393s + u <- maxnndist(Y, positive=TRUE, by=marks(Y)) 393s + b <- minnndist(Y, positive=TRUE) 393s + v <- minnndist(Y, positive=TRUE, by=marks(Y)) 393s + 393s + ## nnmap code blocks 393s + A <- nnmap(cells[FALSE]) 393s + A <- nnmap(cells, sortby="var") 393s + A <- nnmap(cells, sortby="x") 393s + A <- nnmap(cells, sortby="y") 393s + B <- nnmap(cells[1:3], k=4) 393s + B <- nnmap(cells[1:3], k=2:4) 393s + D <- nnmap(cells, outputarray=TRUE) 393s + } 393s + 393s + if(ALWAYS) { 393s + #' tests for has.close() 393s + #' (the default method uses nndist or pairdist, and can be trusted!) 393s + a <- has.close(redwood, 0.05) 393s + b <- has.close.default(redwood, 0.05) 393s + if(any(a != b)) stop("Incorrect result for has.close(X, r)") 393s + 393s + a <- has.close(redwood, 0.05, periodic=TRUE) 393s + a <- has.close.default(redwood, 0.05, periodic=TRUE) 393s + if(any(a != b)) stop("Incorrect result for has.close(X, r, periodic=TRUE)") 393s + 393s + Y <- split(amacrine) 393s + a <- with(Y, has.close(on, 0.05, off)) 393s + b <- with(Y, has.close.default(on, 0.05, off)) 393s + if(any(a != b)) stop("Incorrect result for has.close(X, r, Y)") 393s + 393s + a <- with(Y, has.close(on, 0.05, off, periodic=TRUE)) 393s + b <- with(Y, has.close.default(on, 0.05, off, periodic=TRUE)) 393s + if(any(a != b)) stop("Incorrect result for has.close(X, r, Y, periodic=TRUE)") 393s + } 393s + 393s + if(ALWAYS) { 393s + b <- bdist.pixels(letterR, style="coords") 393s + d <- bdist.pixels(letterR, dimyx=64, method="interpreted") 393s + } 393s + 393s + if(FULLTEST) { 393s + ## nnfun.ppp 393s + h <- nnfun(cells) 393s + Z <- as.im(h) 393s + d <- domain(h) 393s + h <- nnfun(amacrine, value="mark") 393s + d <- domain(h) 393s + Z <- as.im(h) 393s + h <- nnfun(longleaf, value="mark") 393s + d <- domain(h) 393s + Z <- as.im(h) 393s + } 393s + 393s + }) 394s > 394s > 394s Warning message: 394s data contain duplicated points 394s END TEST testsNtoO.R with result 0 394s BEGIN TEST testsP1.R 394s 394s R version 4.4.3 (2025-02-28) -- "Trophy Case" 394s Copyright (C) 2025 The R Foundation for Statistical Computing 394s Platform: aarch64-unknown-linux-gnu 394s 394s R is free software and comes with ABSOLUTELY NO WARRANTY. 394s You are welcome to redistribute it under certain conditions. 394s Type 'license()' or 'licence()' for distribution details. 394s 394s R is a collaborative project with many contributors. 394s Type 'contributors()' for more information and 394s 'citation()' on how to cite R or R packages in publications. 394s 394s Type 'demo()' for some demos, 'help()' for on-line help, or 394s 'help.start()' for an HTML browser interface to help. 394s Type 'q()' to quit R. 394s 394s > #' 394s > #' Header for all (concatenated) test files 394s > #' 394s > #' Require spatstat.geom 394s > #' Obtain environment variable controlling tests. 394s > #' 394s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 394s > 394s > require(spatstat.geom) 394s Loading required package: spatstat.geom 394s Loading required package: spatstat.data 395s Loading required package: spatstat.univar 395s spatstat.univar 3.1-1 396s spatstat.geom 3.3-5 396s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 396s > ALWAYS <- TRUE 396s > cat(paste("--------- Executing", 396s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 396s + "test code -----------\n")) 396s --------- Executing **RESTRICTED** subset of test code ----------- 396s > #' tests/perspim.R 396s > #' 396s > #' Check persp.im handling of NA, etc 396s > #' 396s > #' $Revision: 1.3 $ $Date: 2020/12/04 04:05:54 $ 396s > 396s > if(FULLTEST) { 396s + local({ 396s + set.seed(42) 396s + Z <- distmap(letterR, invert=TRUE)[letterR, drop=FALSE] 396s + X <- runifrect(100, Frame(Z)) 396s + M <- persp(Z, colin=Z, visible=TRUE, phi=50) 396s + perspPoints(X, Z=Z, M=M) 396s + P <- psp(c(2.360, 3.079, 2.211), 396s + c(0.934, 1.881, 2.184), 396s + c(2.337, 3.654, 3.274), 396s + c(1.829, 0.883, 2.093), window=letterR) 396s + perspSegments(P, Z=Z, M=M) 396s + 396s + persp(Z, colmap=rainbow) 396s + persp(Z, colmap=beachcolours, sealevel=mean(Z)) 396s + persp(Z, colin=as.im(Z, dimyx=dim(Z)/4)) 396s + }) 396s + } 396s > ## 396s > ## tests/pixelgripes.R 396s > ## Problems related to pixellation of windows 396s > ## 396s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 396s > 396s > if(FULLTEST) { 396s + local({ 396s + 396s + 396s + ## pixellate.ppp includes mapping from (x,y) to (row, col) 396s + Z <- pixellate(cells, savemap=TRUE) 396s + ind <- attr(Z, "map") 396s + m <- (as.matrix(Z))[ind] 396s + if(!all(m == 1)) stop("Coordinate mismatch in pixellate.ppp") 396s + }) 396s + } 396s > ## 396s > ## tests/polygons.R 396s > ## 396s > ## $Revision: 1.5 $ $Date: 2020/04/30 05:23:52 $ 396s > ## 396s > if(ALWAYS) { # involves C code 396s + local({ 396s + co <- as.ppp(corners(letterR), letterR, check=FALSE) 396s + co[letterR] 396s + 396s + b <- letterR$bdry 396s + a <- sapply(b, xypolyselfint, yesorno=TRUE) 396s + a <- lapply(b, xypolyselfint, proper=TRUE) 396s + 396s + ## Simple example of self-crossing polygon 396s + x <- read.table("selfcross.txt", header=TRUE) 396s + y <- xypolyselfint(x) 396s + }) 396s + } 396s > 396s END TEST testsP1.R with result 0 396s BEGIN TEST testsP2.R 396s 396s R version 4.4.3 (2025-02-28) -- "Trophy Case" 396s Copyright (C) 2025 The R Foundation for Statistical Computing 396s Platform: aarch64-unknown-linux-gnu 396s 396s R is free software and comes with ABSOLUTELY NO WARRANTY. 396s You are welcome to redistribute it under certain conditions. 396s Type 'license()' or 'licence()' for distribution details. 396s 396s R is a collaborative project with many contributors. 396s Type 'contributors()' for more information and 396s 'citation()' on how to cite R or R packages in publications. 396s 396s Type 'demo()' for some demos, 'help()' for on-line help, or 396s 'help.start()' for an HTML browser interface to help. 396s Type 'q()' to quit R. 396s 396s > #' 396s > #' Header for all (concatenated) test files 396s > #' 396s > #' Require spatstat.geom 396s > #' Obtain environment variable controlling tests. 396s > #' 396s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 396s > 396s > require(spatstat.geom) 396s Loading required package: spatstat.geom 396s Loading required package: spatstat.data 397s Loading required package: spatstat.univar 397s spatstat.univar 3.1-1 397s spatstat.geom 3.3-5 397s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 397s > ALWAYS <- TRUE 397s > cat(paste("--------- Executing", 397s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 397s + "test code -----------\n")) 397s --------- Executing **RESTRICTED** subset of test code ----------- 397s > #' 397s > #' tests/ppp.R 397s > #' 397s > #' $Revision: 1.14 $ $Date: 2022/08/27 04:49:32 $ 397s > #' 397s > #' Untested cases in ppp() or associated code 397s > 397s > local({ 397s + ## X <- runifpoint(10, letterR) 397s + ## Y <- runifpoint(10, complement.owin(letterR)) 397s + Bin <- owin(c(2.15, 2.45), c(0.85, 3.0)) 397s + Bout <- owin(c(2.75, 2.92), c(0.85, 1.4)) 397s + X <- runifrect(10, Bin)[letterR] 397s + Y <- runifrect(10, Bout)[complement.owin(letterR)] 397s + 397s + if(FULLTEST) { 397s + #' test handling of points out-of-bounds 397s + df <- rbind(as.data.frame(X), as.data.frame(Y)) 397s + A <- ppp(df$x, df$y, window=letterR, marks=1:20) 397s + #' test handling of points with bad coordinates 397s + df$x[1:3] <- c(Inf, NA, NaN) 397s + df$y[18:20] <- c(Inf, NA, NaN) 397s + B <- ppp(df$x, df$y, window=letterR, marks=1:20) 397s + D <- ppp(df$x, df$y, window=letterR, marks=data.frame(id=1:20, u=runif(20))) 397s + 397s + #' test print/summary/plot methods on these bad objects 397s + print(A) 397s + print(B) 397s + print(D) 397s + print(summary(A)) 397s + print(summary(B)) 397s + print(summary(D)) 397s + plot(A) 397s + plot(B) 397s + plot(D) 397s + plot(attr(A, "rejects")) 397s + plot(attr(B, "rejects")) 397s + plot(attr(D, "rejects")) 397s + 397s + #' subset operator --- cases not covered elsewhere 397s + #' subset index is a logical image 397s + Z <- distmap(letterR, invert=TRUE) 397s + V <- (Z > 0.2) 397s + XV <- X[V] 397s + #' multiple columns of marks 397s + fun3 <- finpines[1:3] 397s + #' multiple columns of marks, one of which is a factor 397s + U <- finpines 397s + marks(U)[,2] <- factor(c(rep("A", 60), rep("B", npoints(U)-60))) 397s + UU <- U[1:3, drop=TRUE] 397s + 397s + #' cut.ppp 397s + CU <- cut(U, "height") 397s + CU <- cut(U, breaks=3) 397s + 397s + #' cases of [<-.ppp 397s + set.seed(999) 397s + X <- cells 397s + B <- square(0.2) 397s + X[B] <- runifrect(3, B) 397s + #' checking 'value' 397s + Y <- flipxy(X) 397s + X[B] <- Y[square(0.3)] 397s + ## deprecated use of second argument 397s + X[,1:4] <- runifrect(3) # deprecated 397s + X[,B] <- runifrect(3, B) # deprecated 397s + X[1:3, B] <- runifrect(20) 397s + A <- superimpose(cells, X, W="convex") 397s + A <- superimpose(cells, X, W=ripras) 397s + B <- superimpose(concatxy(cells), concatxy(X), W=NULL) 397s + ## superimpose.splitppp 397s + Y <- superimpose(split(amacrine)) 397s + 397s + ## catch outdated usage of scanpp 397s + d <- system.file("rawdata", "amacrine", package="spatstat.data") 397s + if(nzchar(d)) { 397s + W <- owin(c(0, 1060/662), c(0, 1)) 397s + Y <- scanpp("amacrine.txt", dir=d, window=W, multitype=TRUE) 397s + print(Y) 397s + } 397s + ## (bad) usage of cobble.xy 397s + xx <- runif(10) 397s + yy <- runif(10) 397s + W1 <- cobble.xy(xx, yy) 397s + W2 <- cobble.xy(xx, yy, boundingbox) 397s + Wnope <- cobble.xy(xx, yy, function(x,y) {cbind(x,y)}, fatal=FALSE) 397s + 397s + ## as.data.frame.ppplist 397s + Z <- runifrect(3, nsim=4) 397s + Z[[2]] <- Z[[2]][1] 397s + Z[[3]] <- Z[[3]][FALSE] 397s + d <- as.data.frame(Z) 397s + } 397s + }) 397s > 397s > # 397s > # tests/ppx.R 397s > # 397s > # Test operations for ppx objects 397s > # 397s > # $Revision: 1.9 $ $Date: 2020/12/04 04:49:40 $ 397s > # 397s > 397s > local({ 397s + if(ALWAYS) { 397s + ## make data 397s + df <- data.frame(x=c(1,2,2,1)/4, y=c(1,2,3,1)/4, z=c(2,3,4,3)/5) 397s + X <- ppx(data=df, coord.type=rep("s", 3), domain=box3()) 397s + } 397s + if(ALWAYS) { 397s + #' methods involving C code 397s + unique(X) 397s + duplicated(X) 397s + anyDuplicated(X) 397s + multiplicity(X) 397s + uniquemap(X) 397s + } 397s + if(FULLTEST) { 397s + #' general tests 397s + print(X) 397s + summary(X) 397s + plot(X) 397s + domain(X) 397s + unitname(X) <- c("metre", "metres") 397s + unitname(X) 397s + 397s + #' subset operator 397s + X[integer(0)] 397s + Y <- X %mark% data.frame(a=df$x, b=1:4) 397s + Y[1:2] 397s + Y[FALSE] 397s + marks(Y) <- as.data.frame(marks(Y)) 397s + Y[integer(0)] 397s + Y[1:2] 397s + Y[FALSE] 397s + } 397s + 397s + if(FULLTEST) { 397s + #' two dimensional 397s + A <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=square(1)) 397s + plot(A) 397s + B <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=NULL) 397s + plot(B) 397s + #' one dimensional 397s + E <- ppx(data=data.frame(x=runif(10))) 397s + plot(E) 397s + 397s + #' bug 397s + stopifnot(identical(unmark(chicago[1]), 397s + unmark(chicago)[1])) 397s + 397s + #' ppx with zero points 397s + U <- chicago[integer(0)] 397s + V <- U %mark% 1 397s + V <- U %mark% factor("a") 397s + 397s + #' simplify lower-dimensional patterns 397s + X3 <- ppx(data=df, coord.type=rep("s", 3), domain=box3(), simplify=TRUE) 397s + stopifnot(is.pp3(X3)) 397s + X2 <- ppx(data=df[,1:2], coord.type=rep("s", 2), domain=square(1), simplify=TRUE) 397s + stopifnot(is.ppp(X2)) 397s + 397s + #' marks<-.ppx 397s + M <- as.matrix(X) 397s + marks(X) <- df[,1] 397s + marks(X) <- df[,integer(0)] 397s + } 397s + 397s + if(FULLTEST) { 397s + ## ............ from Ege .......................... 397s + ## Tests for shift: 397s + ## Check ppp and ppx shift are the same 397s + X <- cells 397s + Y <- ppx(coords(cells), domain = boxx(0:1,0:1)) 397s + Xs <- shift(X, vec = c(1,1)) 397s + Ys <- shift(Y, vec = c(1,1)) 397s + stopifnot(all.equal(coords(Xs), coords(Ys), 397s + check.attributes = FALSE)) 397s + stopifnot(all.equal(domain(Xs), as.owin(domain(Ys)), 397s + check.attributes = FALSE)) 397s + ## Check a single numeric for vec in shift.ppx 397s + stopifnot(identical(Ys, shift(Y, vec = 1))) 397s + 397s + ## Tests for scale: 397s + dat <- data.frame(x=1:3, y=1:3, m=letters[1:3]) 397s + xrange <- yrange <- c(0,4) 397s + cent <- c(2,2) 397s + scal <- c(5,5) 397s + X <- as.ppp(dat, W = owin(xrange, yrange)) 397s + Xscaled <- affine(shift(X, vec = -cent), mat = diag(1/scal)) 397s + ## Check ppx without domain: 397s + Y <- ppx(dat, coord.type = c("spatial", "spatial", "mark")) 397s + Yscaled <- scale(Y, center = cent, scale = scal) 397s + stopifnot(all.equal(coords(Xscaled), 397s + coords(Yscaled), 397s + check.attributes = FALSE)) 397s + ## Check ppx with domain: 397s + Y$domain <- boxx(xrange, yrange) 397s + Yscaled <- scale(Y, center = cent, scale = scal) 397s + stopifnot(all.equal(as.boxx(Window(Xscaled)), 397s + domain(Yscaled), 397s + check.attributes = FALSE)) 397s + 397s + ## Tests for intersect.boxx: 397s + ## Should be unit 2D box: 397s + A <- intersect.boxx(boxx(c(-1,1),c(0,2)), boxx(c(0,3),c(0,1))) 397s + stopifnot(identical(A, boxx(c(0,1),c(0,1)))) 397s + ## Should be empty (NULL) 397s + B <- intersect.boxx(boxx(c(-1,1),c(0,2)), 397s + boxx(c(0,3),c(0,1)), 397s + boxx(c(1,2), c(-1,1))) 397s + stopifnot(is.null(B)) 397s + ## Should be unit 3D box: 397s + C <- intersect.boxx(boxx(c(-1,1),c(0,2),c(-1,1)), 397s + boxx(c(0,3),c(0,1),c(0,4))) 397s + stopifnot(identical(C, boxx(c(0,1),c(0,1),c(0,1)))) 397s + ## Should be empty (NULL) 397s + D <- intersect.boxx(boxx(c(-1,1),c(0,2),c(-1,1)), 397s + boxx(c(0,3),c(0,1),c(0,4)), NULL) 397s + stopifnot(is.null(D)) 397s + 397s + ## Tests for [.boxx with clip: 397s + ## Check ppp and ppx subset with clip are the same 397s + X <- cells 397s + WX <- shift(domain(X), vec = c(.5,.5)) 397s + X2 <- X[WX, clip=TRUE] 397s + Y <- ppx(coords(X), domain = boxx(c(0,1),c(0,1))) 397s + WY <- shift(domain(Y), vec = c(.5,.5)) 397s + Y2 <- Y[WY, clip=TRUE] 397s + stopifnot(all.equal(coords(X2), coords(Y2), check.attributes = FALSE)) 397s + stopifnot(all.equal(domain(X2), as.owin(domain(Y2)))) 397s + } 397s + 397s + }) 397s > 397s END TEST testsP2.R with result 0 397s BEGIN TEST testsQ.R 398s 398s R version 4.4.3 (2025-02-28) -- "Trophy Case" 398s Copyright (C) 2025 The R Foundation for Statistical Computing 398s Platform: aarch64-unknown-linux-gnu 398s 398s R is free software and comes with ABSOLUTELY NO WARRANTY. 398s You are welcome to redistribute it under certain conditions. 398s Type 'license()' or 'licence()' for distribution details. 398s 398s R is a collaborative project with many contributors. 398s Type 'contributors()' for more information and 398s 'citation()' on how to cite R or R packages in publications. 398s 398s Type 'demo()' for some demos, 'help()' for on-line help, or 398s 'help.start()' for an HTML browser interface to help. 398s Type 'q()' to quit R. 398s 398s > #' 398s > #' Header for all (concatenated) test files 398s > #' 398s > #' Require spatstat.geom 398s > #' Obtain environment variable controlling tests. 398s > #' 398s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 398s > 398s > require(spatstat.geom) 398s Loading required package: spatstat.geom 398s Loading required package: spatstat.data 399s Loading required package: spatstat.univar 399s spatstat.univar 3.1-1 399s spatstat.geom 3.3-5 399s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 399s > ALWAYS <- TRUE 399s > cat(paste("--------- Executing", 399s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 399s + "test code -----------\n")) 399s --------- Executing **RESTRICTED** subset of test code ----------- 399s > #' 399s > #' tests/quadschemes.R 399s > #' 399s > #' Quadrature schemes, dummy points etc 399s > #' 399s > #' $Revision: 1.8 $ $Date: 2020/12/04 04:56:26 $ 399s > #' 399s > 399s > if(FULLTEST) { 399s + local({ 399s + ## class 'quad' 399s + qu <- quadscheme(cells) 399s + qm <- quadscheme(amacrine) 399s + plot(qu) 399s + plot(qm) 399s + is.multitype(qu) 399s + is.multitype(qm) 399s + a <- param.quad(qu) 399s + a <- param.quad(qm) 399s + a <- equals.quad(qu) 399s + a <- equals.quad(qm) 399s + a <- domain(qu) 399s + unitname(qu) <- c("Furlong", "Furlongs") 399s + 399s + ## utilities 399s + b <- cellmiddles(square(1), 3, 4) 399s + b <- cellmiddles(letterR, 3, 4, distances=FALSE) 399s + b <- cellmiddles(letterR, 3, 4, distances=TRUE) 399s + v <- tilecentroids(square(1), 3, 4) 399s + v <- tilecentroids(letterR, 3, 4) 399s + n <- default.n.tiling(cells) 399s + n <- default.n.tiling(cells, nd=4) 399s + n <- default.n.tiling(cells, ntile=4) 399s + n <- default.n.tiling(cells, ntile=4, quasi=TRUE) 399s + 399s + ## quadrature weights - special cases 399s + ## X <- runifpoint(10, as.mask(letterR)) 399s + X <- runifrect(10, Frame(letterR))[as.mask(letterR)] 399s + gr <- gridweights(X, ntile=12, npix=7) # causes warnings about zero digital area 399s + 399s + ## plot.quad 399s + plot(quadscheme(cells, method="dirichlet", nd=7), tiles=TRUE) 399s + plot(quadscheme(cells, method="dirichlet", nd=7, exact=FALSE), tiles=TRUE) 399s + 399s + ## logistic 399s + d <- quadscheme.logi(cells, logi.dummy(cells, "binomial")) 399s + print(summary(d)) 399s + d <- quadscheme.logi(cells, logi.dummy(cells, "poisson")) 399s + print(summary(d)) 399s + d <- quadscheme.logi(cells, logi.dummy(cells, "grid")) 399s + print(summary(d)) 399s + d <- quadscheme.logi(cells, logi.dummy(cells, "transgrid")) 399s + print(summary(d)) 399s + d <- quadscheme.logi(amacrine, 399s + logi.dummy(amacrine, "binomial", mark.repeat=TRUE)) 399s + print(summary(d)) 399s + d <- quadscheme.logi(amacrine, 399s + logi.dummy(amacrine, "poisson", mark.repeat=FALSE)) 399s + print(summary(d)) 399s + }) 399s + } 399s > # 399s > # tests/quadcount.R 399s > # 399s > # Tests of quadrat counting code 399s > # 399s > # $Revision: 1.3 $ $Date: 2023/08/15 13:28:31 $ 399s > 399s > local({ 399s + if(FULLTEST) { 399s + ## from Jordan Adamson 399s + Te <- quadrats(unit.square(), 4) 399s + X <- runifrect(8) 399s + Q <- quadratcount(X, tess=Te) 399s + ## from M. Gimond 399s + A <- quadratcount(humberside, 2, 3) 399s + nA <- as.integer(t(A)) 399s + if(!all(nA == c(2, 20, 13, 11, 34, 123))) 399s + stop("Incorrect quadrat count (2,3)") 399s + ## execute intensity.quadratcount 399s + lamA <- intensity(A, image=TRUE) 399s + ## check sum 1/lambda equals area 399s + vA <- sum(1/lamA[humberside]) 399s + aA <- area(Window(humberside)) 399s + if(abs(1 - vA/aA) > 0.05) 399s + stop("Incorrect sum of 1/lambda (2,3)") 399s + ## 399s + B <- quadratcount(humberside, 5, 3) 399s + nB <- as.integer(t(B)) 399s + if(!all(nB == c(0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3))) 399s + stop("Incorrect quadrat count (5,3)") 399s + lamB <- intensity(B, image=TRUE) 399s + vB <- sum(1/lamB[humberside]) 399s + aaB <- tile.areas(as.tess(B)) 399s + aB <- sum(aaB[nB > 0]) 399s + if(abs(1 - vB/aB) > 0.05) 399s + stop("Incorrect sum of 1/lambda (5,3)") 399s + } 399s + }) 399s > reset.spatstat.options() 399s > 399s END TEST testsQ.R with result 0 399s BEGIN TEST testsR.R 399s 399s R version 4.4.3 (2025-02-28) -- "Trophy Case" 399s Copyright (C) 2025 The R Foundation for Statistical Computing 399s Platform: aarch64-unknown-linux-gnu 399s 399s R is free software and comes with ABSOLUTELY NO WARRANTY. 399s You are welcome to redistribute it under certain conditions. 399s Type 'license()' or 'licence()' for distribution details. 399s 399s R is a collaborative project with many contributors. 399s Type 'contributors()' for more information and 399s 'citation()' on how to cite R or R packages in publications. 399s 399s Type 'demo()' for some demos, 'help()' for on-line help, or 399s 'help.start()' for an HTML browser interface to help. 399s Type 'q()' to quit R. 399s 400s > #' 400s > #' Header for all (concatenated) test files 400s > #' 400s > #' Require spatstat.geom 400s > #' Obtain environment variable controlling tests. 400s > #' 400s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 400s > 400s > require(spatstat.geom) 400s Loading required package: spatstat.geom 400s Loading required package: spatstat.data 401s Loading required package: spatstat.univar 401s spatstat.univar 3.1-1 401s spatstat.geom 3.3-5 401s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 401s > ALWAYS <- TRUE 401s > cat(paste("--------- Executing", 401s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 401s + "test code -----------\n")) 401s --------- Executing **RESTRICTED** subset of test code ----------- 401s > #' tests/randbasic.R 401s > #' Tests of basic random generation code 401s > #' $Revision: 1.1 $ $Date: 2021/09/09 09:59:23 $ 401s > 401s > 401s > local({ 401s + if(FULLTEST) { 401s + #' cases not covered in examples 401s + A <- runifrect(6, nsim=2) 401s + A <- rsyst(nx=4, nsim=2) 401s + A <- rjitter(cells, nsim=2, retry=FALSE) 401s + A <- rjitter(cells, nndist(cells)/2) 401s + A <- rjitter(cells[FALSE]) 401s + } 401s + }) 401s > 401s > 401s > 401s END TEST testsR.R with result 0 401s BEGIN TEST testsS.R 401s 401s R version 4.4.3 (2025-02-28) -- "Trophy Case" 401s Copyright (C) 2025 The R Foundation for Statistical Computing 401s Platform: aarch64-unknown-linux-gnu 401s 401s R is free software and comes with ABSOLUTELY NO WARRANTY. 401s You are welcome to redistribute it under certain conditions. 401s Type 'license()' or 'licence()' for distribution details. 401s 401s R is a collaborative project with many contributors. 401s Type 'contributors()' for more information and 401s 'citation()' on how to cite R or R packages in publications. 401s 401s Type 'demo()' for some demos, 'help()' for on-line help, or 401s 'help.start()' for an HTML browser interface to help. 401s Type 'q()' to quit R. 401s 402s > #' 402s > #' Header for all (concatenated) test files 402s > #' 402s > #' Require spatstat.geom 402s > #' Obtain environment variable controlling tests. 402s > #' 402s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 402s > 402s > require(spatstat.geom) 402s Loading required package: spatstat.geom 402s Loading required package: spatstat.data 403s Loading required package: spatstat.univar 403s spatstat.univar 3.1-1 403s spatstat.geom 3.3-5 403s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 403s > ALWAYS <- TRUE 403s > cat(paste("--------- Executing", 403s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 403s + "test code -----------\n")) 403s --------- Executing **RESTRICTED** subset of test code ----------- 403s > ## 403s > ## tests/segments.R 403s > ## Tests of psp class and related code 403s > ## [SEE ALSO: tests/xysegment.R] 403s > ## 403s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 403s > 403s > 403s > local({ 403s + 403s + if(ALWAYS) { # depends on platform 403s + ## pointed out by Jeff Laake 403s + W <- owin() 403s + X <- psp(x0=.25,x1=.25,y0=0,y1=1,window=W) 403s + X[W] 403s + } 403s + 403s + X <- psp(runif(10),runif(10),runif(10),runif(10), window=owin()) 403s + 403s + if(FULLTEST) { 403s + Z <- as.mask.psp(X) 403s + Z <- pixellate(X) 403s + } 403s + 403s + if(ALWAYS) { # platform dependent 403s + ## add short segment 403s + Shorty <- psp(0.5, 0.6, 0.5001, 0.6001, window=Window(X)) 403s + XX <- superimpose(X[1:5], Shorty, X[6:10]) 403s + ZZ <- as.mask.psp(XX) 403s + ZZ <- pixellate(XX) 403s + } 403s + 403s + if(FULLTEST) { 403s + #' misc 403s + PX <- periodify(X, 2) 403s + } 403s + 403s + if(ALWAYS) { # C code 403s + ## tests of pixellate.psp -> seg2pixL 403s + ns <- 50 403s + out <- numeric(ns) 403s + for(i in 1:ns) { 403s + X <- psp(runif(1), runif(1), runif(1), runif(1), window=owin()) 403s + len <- lengths_psp(X) 403s + dlen <- sum(pixellate(X)$v) 403s + out[i] <- if(len > 1e-7) dlen/len else 1 403s + } 403s + if(diff(range(out)) > 0.01) stop(paste( 403s + "pixellate.psp test 1: relative error [", 403s + paste(diff(range(out)), collapse=", "), 403s + "]")) 403s + 403s + ## Michael Sumner's test examples 403s + set.seed(33) 403s + n <- 2001 403s + co <- cbind(runif(n), runif(n)) 403s + ow <- owin() 403s + X <- psp(co[-n,1], co[-n,2], co[-1,1], co[-1,2], window=ow) 403s + s1 <- sum(pixellate(X)) 403s + s2 <- sum(lengths_psp(X)) 403s + if(abs(s1 - s2)/s2 > 0.01) { 403s + stop(paste("pixellate.psp test 2:", 403s + "sum(pixellate(X)) = ", s1, 403s + "!=", s2, "= sum(lengths_psp(X))")) 403s + } 403s + 403s + wts <- 1/(lengths_psp(X) * X$n) 403s + s1 <- sum(pixellate(X, weights=wts)) 403s + if(abs(s1-1) > 0.01) { 403s + stop(paste("pixellate.psp test 3:", 403s + "sum(pixellate(X, weights))=", s1, 403s + " (should be 1)")) 403s + } 403s + 403s + X <- psp(0, 0, 0.01, 0.001, window=owin()) 403s + s1 <- sum(pixellate(X)) 403s + s2 <- sum(lengths_psp(X)) 403s + if(abs(s1 - s2)/s2 > 0.01) { 403s + stop(paste("pixellate.psp test 4:", 403s + "sum(pixellate(X)) = ", s1, 403s + "!=", s2, "= sum(lengths_psp(X))")) 403s + } 403s + 403s + X <- psp(0, 0, 0.001, 0.001, window=owin()) 403s + s1 <- sum(pixellate(X)) 403s + s2 <- sum(lengths_psp(X)) 403s + if(abs(s1 - s2)/s2 > 0.01) { 403s + stop(paste("pixellate.psp test 5:", 403s + "sum(pixellate(X)) = ", s1, 403s + "!=", s2, "= sum(lengths_psp(X))")) 403s + } 403s + } 403s + 403s + if(FULLTEST) { 403s + #' cases of superimpose.psp 403s + A <- as.psp(matrix(runif(40), 10, 4), window=owin()) 403s + B <- as.psp(matrix(runif(40), 10, 4), window=owin()) 403s + superimpose(A, B, W=ripras) 403s + superimpose(A, B, W="convex") 403s + } 403s + 403s + if(FULLTEST) { 403s + #' as.psp.data.frame 403s + df <- as.data.frame(matrix(runif(40), ncol=4)) 403s + A <- as.psp(df, window=square(1)) 403s + colnames(df) <- c("x0","y0","x1","y1") 403s + df <- cbind(df, data.frame(marks=1:nrow(df))) 403s + B <- as.psp(df, window=square(1)) 403s + colnames(df) <- c("xmid", "ymid", "length", "angle", "marks") 403s + E <- as.psp(df, window=square(c(-1,2))) 403s + G <- E %mark% factor(sample(letters[1:3], nsegments(E), replace=TRUE)) 403s + H <- E %mark% runif(nsegments(E)) 403s + 403s + #' print and summary methods 403s + A 403s + B 403s + E 403s + G 403s + H 403s + summary(B) 403s + summary(G) 403s + summary(H) 403s + M <- B 403s + marks(M) <- data.frame(id=marks(B), len=lengths_psp(B)) 403s + M 403s + summary(M) 403s + subset(M, select=len) 403s + 403s + #' plot method cases 403s + spatstat.options(monochrome=TRUE) 403s + plot(B) 403s + plot(G) 403s + plot(M) 403s + spatstat.options(monochrome=FALSE) 403s + plot(B) 403s + plot(G) 403s + plot(M) 403s + #' misuse of 'col' argument - several cases 403s + plot(G, col="grey") # discrete 403s + plot(B, col="grey") 403s + plot(unmark(B), col="grey") 403s + plot(M, col="grey") 403s + 403s + #' miscellaneous class support cases 403s + marks(M) <- marks(M)[1,,drop=FALSE] 403s + 403s + #' undocumented 403s + as.ppp(B) 403s + } 403s + 403s + if(ALWAYS) { # C code 403s + #' segment crossing code 403s + X <- psp(runif(30),runif(30),runif(30),runif(30), window=owin()) 403s + A <- selfcut.psp(X, eps=1e-11) 403s + B <- selfcut.psp(X[1]) 403s + #' 403s + Y <- psp(runif(30),runif(30),runif(30),runif(30), window=owin()) 403s + Z <- edges(letterR)[c(FALSE,TRUE)] 403s + spatstat.options(selfcrossing.psp.useCall=FALSE, crossing.psp.useCall=FALSE) 403s + A <- selfcrossing.psp(X) 403s + B <- selfcrossing.psp(Z) 403s + D <- crossing.psp(X,Y,details=TRUE) 403s + spatstat.options(selfcrossing.psp.useCall=TRUE, crossing.psp.useCall=TRUE) 403s + A <- selfcrossing.psp(X) 403s + B <- selfcrossing.psp(Z) 403s + D <- crossing.psp(X,Y,details=TRUE) 403s + reset.spatstat.options() 403s + } 403s + 403s + if(FULLTEST) { 403s + #' geometry 403s + m <- data.frame(A=1:10, B=letters[1:10]) 403s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 403s + Z <- rotate(X, angle=pi/3, centre=c(0.5, 0.5)) 403s + Y <- endpoints.psp(X, which="lower") 403s + Y <- endpoints.psp(X, which="upper") 403s + Y <- endpoints.psp(X, which="right") 403s + U <- flipxy(X) 403s + } 403s + 403s + if(ALWAYS) { 403s + ## nnfun.psp 403s + P <- psp(runif(10), runif(10), runif(10), runif(10), 403s + window=square(1), marks=runif(10)) 403s + f <- nnfun(P) 403s + f <- nnfun(P, value="mark") 403s + d <- domain(f) 403s + Z <- as.im(f) 403s + } 403s + 403s + }) 403s > 403s > reset.spatstat.options() 403s > 403s > 403s > 403s > 403s > 403s > #' 403s > #' tests/simplepan.R 403s > #' 403s > #' Tests of user interaction in simplepanel 403s > #' Handled by spatstatLocator() 403s > #' 403s dev.new(): using pdf(file="Rplots1.pdf") 403s > #' $Revision: 1.3 $ $Date: 2020/05/01 09:59:59 $ 403s > #' 403s > 403s > if(ALWAYS) { # may depend on platform 403s + local({ 403s + ## Adapted from example(simplepanel) 403s + ## make boxes 403s + outerbox <- owin(c(0,4), c(0,1)) 403s + buttonboxes <- layout.boxes(outerbox, 4, horizontal=TRUE, aspect=1) 403s + ## make environment containing an integer count 403s + myenv <- new.env() 403s + assign("answer", 0, envir=myenv) 403s + ## what to do when finished: return the count. 403s + myexit <- function(e) { return(get("answer", envir=e)) } 403s + ## button clicks 403s + ## decrement the count 403s + Cminus <- function(e, xy) { 403s + ans <- get("answer", envir=e) 403s + assign("answer", ans - 1, envir=e) 403s + return(TRUE) 403s + } 403s + ## display the count (clicking does nothing) 403s + Cvalue <- function(...) { TRUE } 403s + ## increment the count 403s + Cplus <- function(e, xy) { 403s + ans <- get("answer", envir=e) 403s + assign("answer", ans + 1, envir=e) 403s + return(TRUE) 403s + } 403s + ## 'Clear' button 403s + Cclear <- function(e, xy) { 403s + assign("answer", 0, envir=e) 403s + return(TRUE) 403s + } 403s + ## quit button 403s + Cdone <- function(e, xy) { return(FALSE) } 403s + 403s + myclicks <- list("-"=Cminus, 403s + value=Cvalue, 403s + "+"=Cplus, 403s + done=Cdone) 403s + ## redraw the button that displays the current value of the count 403s + Rvalue <- function(button, nam, e) { 403s + plot(button, add=TRUE) 403s + ans <- get("answer", envir=e) 403s + text(centroid.owin(button), labels=ans) 403s + return(TRUE) 403s + } 403s + ## make the panel 403s + P <- simplepanel("Counter", 403s + B=outerbox, boxes=buttonboxes, 403s + clicks=myclicks, 403s + redraws = list(NULL, Rvalue, NULL, NULL), 403s + exit=myexit, env=myenv) 403s + ## queue up a sequence of inputs 403s + boxcentres <- do.call(concatxy, unname(lapply(buttonboxes[c(3,3,1,3,2,4)], 403s + centroid.owin))) 403s + spatstat.utils::queueSpatstatLocator(boxcentres$x, boxcentres$y) 403s + ## go 403s + run.simplepanel(P) 403s + }) 403s + } 403s [1] 2 403s > # 403s > # tests/splitpea.R 403s > # 403s > # Check behaviour of split.ppp etc 403s > # 403s > # Thanks to Marcelino de la Cruz 403s > # 403s > # $Revision: 1.17 $ $Date: 2021/04/15 06:19:51 $ 403s > # 403s > 403s > local({ 403s + W <- square(8) 403s + X <- ppp(c(2.98, 4.58, 7.27, 1.61, 7.19), 403s + c(7.56, 5.29, 5.03, 0.49, 1.65), 403s + window=W, check=FALSE) 403s + Z <- quadrats(W, 4, 4) 403s + Yall <- split(X, Z, drop=FALSE) 403s + Ydrop <- split(X, Z, drop=TRUE) 403s + 403s + if(ALWAYS) { # may depend on platform 403s + P <- Yall[[1]] 403s + if(!all(inside.owin(P$x, P$y, P$window))) 403s + stop("Black hole detected when drop=FALSE") 403s + P <- Ydrop[[1]] 403s + if(!all(inside.owin(P$x, P$y, P$window))) 403s + stop("Black hole detected when drop=TRUE") 403s + Ydrop[[1]] <- P[1] 403s + split(X, Z, drop=TRUE) <- Ydrop 403s + } 403s + 403s + ## test NA handling 403s + Zbad <- quadrats(square(4), 2, 2) 403s + Ybdrop <- split(X, Zbad, drop=TRUE) 403s + Yball <- split(X, Zbad, drop=FALSE) 403s + 403s + if(FULLTEST) { 403s + ## other bugs/ code blocks in split.ppp, split<-.ppp, [<-.splitppp 403s + flog <- rep(c(TRUE,FALSE), 21) 403s + fimg <- as.im(dirichlet(runifrect(5, Window(cells))), dimyx=32) 403s + A <- split(cells, flog) 403s + B <- split(cells, square(0.5)) 403s + D <- split(cells, fimg) 403s + E <- split(cells, logical(42), drop=TRUE) 403s + Cellules <- cells 403s + split(Cellules, flog) <- solapply(A, rjitter) 403s + split(Cellules, fimg) <- solapply(D, rjitter) 403s + D[[2]] <- rjitter(D[[2]]) 403s + Funpines <- finpines 403s + marks(Funpines)[,"diameter"] <- factor(marks(Funpines)[,"diameter"]) 403s + G <- split(Funpines) 403s + H <- split(Funpines, "diameter") 403s + split(Funpines) <- solapply(G, rjitter) 403s + split(Funpines, "diameter") <- solapply(H, rjitter) 403s + 403s + ## From Marcelino 403s + set.seed(1) 403s + W<- square(10) # the big window 403s + ## puntos<- rpoispp(0.5, win=W) 403s + puntos<- runifrect(rpois(1, 0.5 * area(W)), win=W) 403s + r00 <- letterR 403s + r05 <- shift(letterR,c(0,5)) 403s + r50 <- shift(letterR,c(5,0)) 403s + r55 <- shift(letterR,c(5,5)) 403s + tessr4 <- tess(tiles=list(r00, r05,r50,r55)) 403s + puntosr4 <- split(puntos, tessr4, drop=TRUE) 403s + split(puntos, tessr4, drop=TRUE) <- puntosr4 403s + 403s + ## More headaches with mark format 403s + A <- runifrect(10) 403s + B <- runifrect(10) 403s + AB <- split(superimpose(A=A, B=B)) 403s + 403s + #' check that split<- respects ordering where possible 403s + X <- amacrine 403s + Y <- split(X) 403s + split(X) <- Y 403s + stopifnot(identical(X, amacrine)) 403s + 403s + #' split.ppx 403s + df <- data.frame(x=runif(4),y=runif(4),t=runif(4), 403s + age=rep(c("old", "new"), 2), 403s + mineral=factor(rep(c("Au","Cu"), each=2), 403s + levels=c("Au", "Cu", "Pb")), 403s + size=runif(4)) 403s + X <- ppx(data=df, coord.type=c("s","s","t","m", "m","m")) 403s + Y <- split(X, "age") 403s + Y <- split(X, "mineral", drop=TRUE) 403s + Y <- split(X, "mineral") 403s + print(Y) 403s + print(summary(Y)) 403s + Y[c(TRUE,FALSE,TRUE)] 403s + Y[1:2] 403s + Y[3] <- Y[1] 403s + } 403s + }) 403s > 403s > ## 403s > ## tests/symbolmaps.R 403s > ## 403s > ## Quirks associated with symbolmaps, etc. 403s > ## 403s > ## $Revision: 1.6 $ $Date: 2024/04/08 04:22:25 $ 403s > 403s > if(FULLTEST) { 403s + local({ 403s + set.seed(100) 403s + X <- runifrect(8) 403s + 403s + ## symbolmap for numeric values 403s + g1 <- symbolmap(range=c(0,100), size=function(x) x/50) 403s + invoke.symbolmap(g1, 50, x=numeric(0), y=numeric(0), add=TRUE) 403s + plot(g1, labelmap=100) 403s + ## symbolmap for discrete categories 403s + g2 <- symbolmap(inputs=letters[1:5], chars=1:5) 403s + invoke.symbolmap(g2, "a", x=numeric(0), y=numeric(0), add=TRUE) 403s + plot(g2) 403s + ## constant/trivial 403s + a <- symbolmap(pch=16) 403s + print(a) 403s + plot(a) 403s + symbolmapdomain(a) 403s + b <- symbolmap() 403s + print(b) 403s + ## graphical arguments with mixed types (function, constant) 403s + f <- function(x) { ifelse(x %in% letters[1:3], "circles", "squares")} 403s + g3 <- symbolmap(inputs=letters[1:5], size=0.7, shape=f) 403s + invoke.symbolmap(g3, "a", x=numeric(0), y=numeric(0), add=TRUE) 403s + plot(g3) 403s + 403s + ## textureplot 403s + V <- as.im(dirichlet(X)) 403s + tmap <- textureplot(V) 403s + textureplot(V, textures=tmap, legend=TRUE, leg.side="left") 403s + textureplot(V, leg.side="bottom") 403s + textureplot(V, leg.side="top") 403s + ## spacing too large for tiles - upsets various pieces of code 403s + textureplot(V, spacing=2) 403s + 403s + ## plot.texturemap 403s + plot(tmap, vertical=TRUE) 403s + plot(tmap, vertical=TRUE, xlim=c(0,1)) 403s + plot(tmap, vertical=TRUE, ylim=c(0,1)) 403s + plot(tmap, vertical=FALSE, xlim=c(0,1)) 403s + plot(tmap, vertical=FALSE, ylim=c(0,1)) 403s + 403s + ## infrastructure 403s + plan.legend.layout(owin(), side="top", started=TRUE) 403s + }) 403s + } 403s > 403s END TEST testsS.R with result 0 403s BEGIN TEST testsT.R 404s 404s R version 4.4.3 (2025-02-28) -- "Trophy Case" 404s Copyright (C) 2025 The R Foundation for Statistical Computing 404s Platform: aarch64-unknown-linux-gnu 404s 404s R is free software and comes with ABSOLUTELY NO WARRANTY. 404s You are welcome to redistribute it under certain conditions. 404s Type 'license()' or 'licence()' for distribution details. 404s 404s R is a collaborative project with many contributors. 404s Type 'contributors()' for more information and 404s 'citation()' on how to cite R or R packages in publications. 404s 404s Type 'demo()' for some demos, 'help()' for on-line help, or 404s 'help.start()' for an HTML browser interface to help. 404s Type 'q()' to quit R. 404s 404s > #' 404s > #' Header for all (concatenated) test files 404s > #' 404s > #' Require spatstat.geom 404s > #' Obtain environment variable controlling tests. 404s > #' 404s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 404s > 404s > require(spatstat.geom) 404s Loading required package: spatstat.geom 404s Loading required package: spatstat.data 405s Loading required package: spatstat.univar 405s spatstat.univar 3.1-1 405s spatstat.geom 3.3-5 405s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 405s > ALWAYS <- TRUE 405s > cat(paste("--------- Executing", 405s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 405s + "test code -----------\n")) 405s --------- Executing **RESTRICTED** subset of test code ----------- 405s > #' tests/tessera.R 405s > #' Tessellation code, not elsewhere tested 405s > #' $Revision: 1.9 $ $Date: 2020/12/04 08:04:38 $ 405s > #' 405s > if(FULLTEST) { 405s + local({ 405s + W <- owin() 405s + Wsub <- square(0.5) 405s + X <- runifrect(7, W) 405s + A <- dirichlet(X) 405s + marks(A) <- 1:nobjects(A) 405s + Z <- distmap(letterR, invert=TRUE)[letterR, drop=FALSE] 405s + H <- tess(xgrid=0:2, ygrid=0:3) 405s + #' discretisation of tiles 405s + V <- as.im(A) 405s + B <- tess(window=as.mask(W), tiles=tiles(A)) 405s + #' logical images 405s + D <- tess(image=(Z > 0.2)) 405s + U <- (Z > -0.2) # TRUE or NA 405s + E <- tess(image=U, keepempty=TRUE) 405s + G <- tess(image=U, keepempty=FALSE) 406s + #' methods 406s + flay <- function(op, ..., Rect=H, Poly=A, Img=E) { 406s + a <- do.call(op, list(Rect, ...)) 406s + b <- do.call(op, list(Poly, ...)) 406s + e <- do.call(op, list(Img, ...)) 406s + } 406s + flay(reflect) 406s + flay(flipxy) 406s + flay(shift, vec=c(1,2)) 406s + flay(scalardilate, f=2) 406s + flay(rotate, angle=pi/3, centre=c(0, 0)) 406s + flay(rotate, angle=pi/2) 406s + flay(affine, mat=matrix(c(1,2,0,1), 2, 2), vec=c(1,2)) 406s + flay(affine, mat=diag(c(1,2))) 406s + flay(as.data.frame) 406s + ## 406s + unitname(A) <- "km" 406s + unitname(B) <- c("metre", "metres") 406s + unitname(B) 406s + print(B) 406s + Bsub <- B[c(3,5,7)] 406s + print(Bsub) 406s + tilenames(H) <- letters[seq_along(tilenames(H))] 406s + G <- tess(xgrid=(0:3)/3, ygrid=(0:3)/3) 406s + tilenames(G) <- letters[1:9] 406s + h <- tilenames(G) 406s + GG <- as.tess(tiles(G)) 406s + #' 406s + Pe <- intersect.tess(A, Wsub, keepmarks=TRUE) 406s + Pm <- intersect.tess(A, as.mask(Wsub), keepmarks=TRUE) 406s + H <- dirichlet(runifrect(4, W)) 406s + AxH <- intersect.tess(A, H, keepmarks=TRUE) # A is marked, H is not 406s + HxA <- intersect.tess(H, A, keepmarks=TRUE) # A is marked, H is not 406s + 406s + b <- bdist.tiles(D) 406s + b <- bdist.tiles(A[c(3,5,7)]) 406s + #' 406s + Eim <- as.im(E, W=letterR) 406s + #' 406s + #' chop.tess 406s + #' horiz/vert lines 406s + W <- square(1) 406s + H <- infline(h=(2:4)/5) 406s + V <- infline(v=(3:4)/5) 406s + WH <- chop.tess(W, H) 406s + WV <- chop.tess(W, V) 406s + #' polygonal tessellation 406s + D <- dirichlet(runifrect(4)) 406s + DH <- chop.tess(D, H) 406s + DV <- chop.tess(D, V) 406s + #' image-based tessellation 406s + f <- function(x,y){factor(round(4* (x^2 + y^2)))} 406s + A <- tess(image=as.im(f, W=W)) 406s + L <- infline(p=(1:3)/3, theta=pi/4) 406s + AL <- chop.tess(A, L) 406s + AH <- chop.tess(A, H) 406s + AV <- chop.tess(A, V) 406s + #' 406s + #' quantess 406s + #' quantess.owin 406s + a <- quantess(square(1), "x", 3) 406s + a <- quantess(square(1), "y", 3) 406s + a <- quantess(square(1), "rad", 5, origin=c(1/2, 1/3)) 406s + a <- quantess(square(1), "ang", 7, origin=c(1/2, 1/3)) 406s + ZFUN <- function(x,y){y-x} 406s + a <- quantess(square(1), ZFUN, 3) 406s + b <- quantess(letterR, "y", 3) 406s + #' quantess.ppp 406s + d <- quantess(cells, "y", 4) 406s + g <- quantess(demopat, "x", 5) 406s + g <- quantess(demopat, "y", 5) 406s + g <- quantess(demopat, "rad", 5, origin=c(4442, 4214)) 406s + g <- quantess(demopat, "ang", 5, origin=c(4442, 4214)) 406s + g <- quantess(demopat, ZFUN, 7) 406s + #' quantess.im 406s + D <- distmap(demopat) 406s + h <- quantess(D, "y", 4) 406s + h <- quantess(D, ZFUN, 5) 406s + g <- quantess(D, "rad", 5, origin=c(4442, 4214)) 406s + g <- quantess(D, "ang", 5, origin=c(4442, 4214)) 406s + #' 406s + X <- shift(chorley, vec = c(1e6, 0)) 406s + tes <- quantess(X, "x", 4) 406s + if(anyDuplicated(tilenames(tes))) 406s + stop("quantess produced non-unique tilenames") 406s + ## 406s + ## 406s + XR <- runifrect(40, Frame(letterR))[letterR] 406s + da <- dirichletAreas(discretise(XR)) 406s + }) 406s + } 406s > #' tests/trigraph.R 406s > #' 406s > #' Tests for C code in trigraf.c 406s > #' 406s > #' $Revision: 1.5 $ $Date: 2020/06/12 00:35:44 $ 406s > #' 406s > if(ALWAYS) { # depends on C code 406s + local({ 406s + #' called from deldir.R 406s + spatstat.deldir.setopt(FALSE, TRUE) 406s + A <- delaunay(redwood) 406s + spatstat.deldir.setopt(FALSE, FALSE) 406s + B <- delaunay(redwood) 406s + spatstat.deldir.setopt(TRUE, TRUE) 406s + #' called from edges2triangles.R 406s + tryangles <- function(iedge, jedge, nt=0) { 406s + spatstat.options(fast.trigraph=FALSE) 406s + A <- edges2triangles(iedge, jedge) 406s + spatstat.options(fast.trigraph=TRUE) 406s + B <- edges2triangles(iedge, jedge) 406s + if(!all(dim(A) == dim(B)) || !all(A == B)) 406s + stop(paste("Discrepancy in edges2triangles (with", nt, "triangles)")) 406s + } 406s + ## ii <- simplenet$from 406s + ## jj <- simplenet$to 406s + ii <- c(1, 3, 4, 2, 4, 5, 5, 6, 7, 8) 406s + jj <- c(4, 4, 5, 6, 6, 8, 9, 10, 10, 10) 406s + tryangles(ii, jj, 0) 406s + tryangles(c(ii, 1), c(jj, 5), 1) 406s + tryangles(c(ii, 1, 8), c(jj, 5, 9), 2) 406s + }) 406s + } 406s > reset.spatstat.options() 406s > 406s > 406s > 406s END TEST testsT.R with result 0 406s BEGIN TEST testsUtoZ.R 406s 406s R version 4.4.3 (2025-02-28) -- "Trophy Case" 406s Copyright (C) 2025 The R Foundation for Statistical Computing 406s Platform: aarch64-unknown-linux-gnu 406s 406s R is free software and comes with ABSOLUTELY NO WARRANTY. 406s You are welcome to redistribute it under certain conditions. 406s Type 'license()' or 'licence()' for distribution details. 406s 406s R is a collaborative project with many contributors. 406s Type 'contributors()' for more information and 406s 'citation()' on how to cite R or R packages in publications. 406s 406s Type 'demo()' for some demos, 'help()' for on-line help, or 406s 'help.start()' for an HTML browser interface to help. 406s Type 'q()' to quit R. 406s 406s > #' 406s > #' Header for all (concatenated) test files 406s > #' 406s > #' Require spatstat.geom 406s > #' Obtain environment variable controlling tests. 406s > #' 406s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 406s > 406s > require(spatstat.geom) 406s Loading required package: spatstat.geom 406s Loading required package: spatstat.data 408s Loading required package: spatstat.univar 408s spatstat.univar 3.1-1 408s spatstat.geom 3.3-5 408s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 408s > ALWAYS <- TRUE 408s > cat(paste("--------- Executing", 408s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 408s + "test code -----------\n")) 408s --------- Executing **RESTRICTED** subset of test code ----------- 408s > # 408s > # tests/utils.R 408s > # 408s > # Tests of miscellaneous utilities 408s > # 408s > # $Revision: 1.1 $ $Date: 2023/05/07 08:59:32 $ 408s > 408s > local({ 408s + if(FULLTEST) { 408s + ## test code blocks in 'progressreport' 408s + pstate <- list() 408s + for(i in 1:10) { 408s + Sys.sleep(1) 408s + pstate <- progressreport(i, 10, 408s + formula = (time ~ i + I(i^2) + I(i^3)), 408s + showtime=TRUE, 408s + savehistory=TRUE, 408s + state=pstate) 408s + } 408s + } 408s + }) 408s > 408s > # 408s > # tests/windows.R 408s > # 408s > # Tests of owin geometry code 408s > # 408s > # $Revision: 1.18 $ $Date: 2023/07/11 06:21:37 $ 408s > 408s > local({ 408s + if(ALWAYS) { # C code 408s + ## Ege Rubak spotted this problem in 1.28-1 408s + A <- as.owin(ants) 408s + B <- dilation(A, 140) 408s + if(!is.subset.owin(A, B)) 408s + stop("is.subset.owin fails in polygonal case") 408s + 408s + ## thanks to Tom Rosenbaum 408s + A <- shift(square(3), origin="midpoint") 408s + B <- shift(square(1), origin="midpoint") 408s + AB <- setminus.owin(A, B) 408s + D <- shift(square(2), origin="midpoint") 408s + if(is.subset.owin(D,AB)) 408s + stop("is.subset.owin fails for polygons with holes") 408s + 408s + ## thanks to Brian Ripley / SpatialVx 408s + M <- as.mask(letterR) 408s + stopifnot(area(bdry.mask(M)) > 0) 408s + stopifnot(area(convexhull(M)) > 0) 408s + R <- as.mask(square(1)) 408s + stopifnot(area(bdry.mask(R)) > 0) 408s + stopifnot(area(convexhull(R)) > 0) 408s + } 408s + 408s + if(FULLTEST) { 408s + RR <- convexify(as.mask(letterR)) 408s + CC <- covering(letterR, 0.05, eps=0.1) 408s + 408s + #' as.owin.data.frame 408s + V <- as.mask(letterR, eps=0.2) 408s + Vdf <- as.data.frame(V) 408s + Vnew <- as.owin(Vdf) 408s + zz <- mask2df(V) 408s + } 408s + 408s + if(ALWAYS) { # C code 408s + RM <- owinpoly2mask(letterR, as.mask(Frame(letterR)), check=TRUE) 408s + } 408s + 408s + if(FULLTEST) { 408s + #' as.owin 408s + U <- as.owin(quadscheme(cells)) 408s + U2 <- as.owin(list(xmin=0, xmax=1, ymin=0, ymax=1)) 408s + } 408s + 408s + if(ALWAYS) { 408s + #' validity of as.mask applied to rectangles with additional raster info 408s + Z <- as.im(unit.square()) 408s + R <- square(0.5) 408s + aR <- area(R) 408s + a <- area(as.mask(R, xy=Z)) 408s + if(abs(a-aR) > aR/20) 408s + stop("Problem with as.mask(rectangle, xy=image)") 408s + a <- area(as.mask(R, xy=list(x=Z$xcol, y=Z$yrow))) 408s + if(abs(a-aR) > aR/20) 408s + stop("Problem with as.mask(rectangle, xy=list(x,y))") 408s + } 408s + 408s + if(FULLTEST) { 408s + #' intersections involving masks 408s + B1 <- square(1) 408s + B2 <- as.mask(shift(B1, c(0.2, 0.3))) 408s + o12 <- overlap.owin(B1, B2) 408s + o21 <- overlap.owin(B2, B1) 408s + i12 <- intersect.owin(B1, B2, eps=0.01) 408s + i21 <- intersect.owin(B2, B1, eps=0.01) 408s + E2 <- emptywindow(square(2)) 408s + e12 <- intersect.owin(B1, E2) 408s + e21 <- intersect.owin(E2, B1) 408s + 408s + #' geometry 408s + inradius(B1) 408s + inradius(B2) 408s + inradius(letterR) 408s + inpoint(B1) 408s + inpoint(B2) 408s + inpoint(letterR) 408s + is.convex(B1) 408s + is.convex(B2) 408s + is.convex(letterR) 408s + volume(letterR) 408s + perimeter(as.mask(letterR)) 408s + boundingradius(cells) 408s + 408s + boundingbox(letterR) 408s + boundingbox(letterR, NULL) 408s + boundingbox(solist(letterR)) 408s + 408s + } 408s + 408s + if(ALWAYS) { # C code 408s + spatstat.options(Cbdrymask=FALSE) 408s + bb <- bdry.mask(letterR) 408s + spatstat.options(Cbdrymask=TRUE) 408s + } 408s + 408s + if(FULLTEST) { 408s + X <- longleaf[square(50)] 408s + marks(X) <- marks(X)/8 408s + D <- discs(X) 408s + D <- discs(X, delta=5, separate=TRUE) 408s + } 408s + 408s + if(ALWAYS) { # C code 408s + AD <- dilated.areas(cells, 408s + r=0.01 * matrix(1:10, 10,1), 408s + constrained=FALSE, exact=FALSE) 408s + } 408s + 408s + if(FULLTEST) { 408s + periodify(B1, 2) 408s + periodify(union.owin(B1, B2), 2) 408s + periodify(letterR, 2) 408s + } 408s + 408s + if(ALWAYS) { 408s + #' Ancient bug in inside.owin 408s + W5 <- owin(poly=1e5*cbind(c(-1,1,1,-1),c(-1,-1,1,1))) 408s + W6 <- owin(poly=1e6*cbind(c(-1,1,1,-1),c(-1,-1,1,1))) 408s + i5 <- inside.owin(0,0,W5) 408s + i6 <- inside.owin(0,0,W6) 408s + if(!i5) stop("Wrong answer from inside.owin") 408s + if(i5 != i6) stop("Results from inside.owin are scale-dependent") 408s + } 408s + 408s + if(FULLTEST) { 408s + #' miscellaneous utilities 408s + thrash <- function(f) { 408s + f(letterR) 408s + f(Frame(letterR)) 408s + f(as.mask(letterR)) 408s + } 408s + thrash(meanX.owin) 408s + thrash(meanY.owin) 408s + thrash(intX.owin) 408s + thrash(intY.owin) 408s + 408s + interpretAsOrigin("right", letterR) 408s + interpretAsOrigin("bottom", letterR) 408s + interpretAsOrigin("bottomright", letterR) 408s + interpretAsOrigin("topleft", letterR) 408s + interpretAsOrigin("topright", letterR) 408s + } 408s + 408s + if(ALWAYS) { # depends on polyclip 408s + A <- break.holes(letterR) 408s + B <- break.holes(letterR, splitby="y") 408s + plot(letterR, col="blue", use.polypath=FALSE) 408s + } 408s + 408s + if(ALWAYS) { # C code 408s + #' mask conversion 408s + M <- as.mask(letterR) 408s + D2 <- as.data.frame(M) # two-column 408s + D3 <- as.data.frame(M, drop=FALSE) # three-column 408s + M2 <- as.owin(D2) 408s + M3 <- as.owin(D3) 408s + W2 <- owin(mask=D2) 408s + W3 <- owin(mask=D3) 408s + } 408s + 408s + if(FULLTEST) { 408s + #' void/empty cases 408s + nix <- nearest.raster.point(numeric(0), numeric(0), M) 408s + E <- emptywindow(Frame(letterR)) 408s + print(E) 408s + #' cases of summary.owin 408s + print(summary(E)) # empty 408s + print(summary(Window(humberside))) # single polygon 408s + #' additional cases of owin() 408s + B <- owin(mask=M$m) # no pixel size or coordinate info 408s + xy <- as.data.frame(letterR) 408s + xxyy <- split(xy[,1:2], xy$id) 408s + spatstat.options(checkpolygons=TRUE) 408s + H <- owin(poly=xxyy, check=TRUE) 408s + } 408s + 408s + #' Code for/using intersection and union of windows 408s + 408s + if(FULLTEST) { 408s + Empty <- emptywindow(Frame(letterR)) 408s + a <- intersect.owin() 408s + a <- intersect.owin(Empty) 408s + a <- intersect.owin(Empty, letterR) 408s + a <- intersect.owin(letterR, Empty) 408s + b <- intersect.owin() 408s + b <- intersect.owin(Empty) 408s + b <- intersect.owin(Empty, letterR) 408s + b <- intersect.owin(letterR, Empty) 408s + d <- union.owin(as.mask(square(1)), as.mask(square(2))) 408s + #' [.owin 408s + A <- erosion(letterR, 0.2) 408s + Alogi <- as.im(TRUE, W=A) 408s + B <- letterR[A] 408s + B <- letterR[Alogi] 408s + #' miscellaneous 408s + D <- convexhull(Alogi) 408s + } 408s + }) 408s > 408s > reset.spatstat.options() 408s > ## 408s > ## tests/xysegment.R 408s > ## [SEE ALSO tests/segments.R] 408s > ## 408s > ## Test weird problems and boundary cases for line segment code 408s > ## 408s > ## $Version$ $Date: 2022/10/23 01:21:09 $ 408s > ## 408s > 408s > local({ 408s + if(FULLTEST) { 408s + ## segment of length zero 408s + B <- psp(1/2, 1/2, 1/2, 1/2, window=square(1)) 408s + BB <- angles.psp(B) 408s + A <- runifrect(3) 408s + AB <- project2segment(A,B) 408s + 408s + ## mark inheritance 408s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin()) 408s + marks(X) <- 1:10 408s + Y <- selfcut.psp(X) 408s + marks(X) <- data.frame(A=1:10, B=factor(letters[1:10])) 408s + Z <- selfcut.psp(X) 408s + #' psp class support 408s + S <- unmark(X) 408s + marks(S) <- sample(factor(c("A","B")), nobjects(S), replace=TRUE) 408s + intensity(S) 408s + intensity(S, weights=runif(nsegments(S))) 408s + } 408s + }) 408s > 408s > 408s > 408s END TEST testsUtoZ.R with result 0 409s autopkgtest [16:04:16]: test run-unit-test: -----------------------] 409s autopkgtest [16:04:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 409s run-unit-test PASS 410s autopkgtest [16:04:17]: test pkg-r-autopkgtest: preparing testbed 929s autopkgtest [16:12:56]: testbed dpkg architecture: arm64 929s autopkgtest [16:12:56]: testbed apt version: 2.9.33 929s autopkgtest [16:12:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 930s autopkgtest [16:12:57]: testbed release detected to be: plucky 930s autopkgtest [16:12:57]: updating testbed package index (apt update) 931s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 931s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 931s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates 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man-db (2.13.0-1) ... 966s Processing triggers for systemd (257.3-1ubuntu3) ... 967s Reading package lists... 967s Building dependency tree... 967s Reading state information... 968s Starting pkgProblemResolver with broken count: 0 968s Starting 2 pkgProblemResolver with broken count: 0 968s Done 968s Solving dependencies... 969s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 969s autopkgtest [16:13:36]: rebooting testbed after setup commands that affected boot 996s Reading package lists... 996s Building dependency tree... 996s Reading state information... 996s Starting pkgProblemResolver with broken count: 0 997s Starting 2 pkgProblemResolver with broken count: 0 997s Done 997s The following NEW packages will be installed: 997s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 997s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 997s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 997s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 997s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 997s libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 997s libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev 997s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 997s libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 997s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4 997s liblsan0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0 997s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 997s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 997s libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 997s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 997s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 997s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind 997s r-cran-deldir r-cran-goftest r-cran-lattice r-cran-matrix r-cran-mgcv 997s r-cran-nlme r-cran-polyclip r-cran-rpart r-cran-spatial r-cran-spatstat 997s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 997s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 997s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 997s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip zlib1g-dev 998s 0 upgraded, 120 newly installed, 0 to remove and 0 not upgraded. 998s Need to get 174 MB of archives. 998s After this operation, 467 MB of additional disk space will be used. 998s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 998s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 999s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [10.6 MB] 1010s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-17ubuntu3 [1028 B] 1010s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 1010s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 1010s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 15-20250222-0ubuntu1 [44.2 kB] 1010s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 1010s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 15-20250222-0ubuntu1 [28.0 kB] 1010s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 15-20250222-0ubuntu1 [2924 kB] 1013s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 15-20250222-0ubuntu1 [1319 kB] 1015s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 15-20250222-0ubuntu1 [2694 kB] 1018s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 15-20250222-0ubuntu1 [1178 kB] 1020s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 15-20250222-0ubuntu1 [1642 kB] 1022s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-17ubuntu3 [2593 kB] 1025s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [20.9 MB] 1052s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-17ubuntu3 [526 kB] 1052s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 1052s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 1052s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-17ubuntu3 [2499 kB] 1055s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [12.1 MB] 1069s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-17ubuntu3 [21.8 kB] 1069s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 1069s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 1069s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 1069s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 1069s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 1070s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 1071s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 1071s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 1071s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig arm64 2.15.0-2ubuntu1 [191 kB] 1071s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 1072s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran-14-dev arm64 14.2.0-17ubuntu3 [498 kB] 1072s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17ubuntu3 [11.4 MB] 1086s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-14 arm64 14.2.0-17ubuntu3 [13.6 kB] 1086s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 1086s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 1086s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 1086s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 1086s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 1086s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 1086s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 1087s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 1087s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 1087s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 1087s Get:46 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 1087s Get:47 http://ftpmaster.internal/ubuntu plucky/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 1087s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 1087s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 1087s Get:50 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 1088s Get:51 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 1088s Get:52 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 1088s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 1088s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 1102s Get:55 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 1102s Get:56 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 1103s Get:57 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 1103s Get:58 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 1103s Get:59 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 1103s Get:60 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 1105s Get:61 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 1110s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 1111s Get:63 http://ftpmaster.internal/ubuntu plucky/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 1111s Get:64 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 1111s Get:65 http://ftpmaster.internal/ubuntu plucky/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 1111s Get:66 http://ftpmaster.internal/ubuntu plucky/main arm64 libpango-1.0-0 arm64 1.56.2-1 [237 kB] 1112s Get:67 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangoft2-1.0-0 arm64 1.56.2-1 [49.5 kB] 1112s Get:68 http://ftpmaster.internal/ubuntu plucky/main arm64 libpangocairo-1.0-0 arm64 1.56.2-1 [27.6 kB] 1112s Get:69 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 1112s Get:70 http://ftpmaster.internal/ubuntu plucky/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 1112s Get:71 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 1112s Get:72 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 1112s Get:73 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 1112s Get:74 http://ftpmaster.internal/ubuntu plucky/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 1113s Get:75 http://ftpmaster.internal/ubuntu plucky/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 1113s Get:76 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 1114s Get:77 http://ftpmaster.internal/ubuntu plucky/main arm64 libpng-dev arm64 1.6.47-1 [269 kB] 1115s Get:78 http://ftpmaster.internal/ubuntu plucky/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 1115s Get:79 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 1115s Get:80 http://ftpmaster.internal/ubuntu plucky/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 1115s Get:81 http://ftpmaster.internal/ubuntu plucky/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 1116s Get:82 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 1116s Get:83 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 1116s Get:84 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 1116s Get:85 http://ftpmaster.internal/ubuntu plucky/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 1117s Get:86 http://ftpmaster.internal/ubuntu plucky/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 1117s Get:87 http://ftpmaster.internal/ubuntu plucky/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 1117s Get:88 http://ftpmaster.internal/ubuntu plucky/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 1118s Get:89 http://ftpmaster.internal/ubuntu plucky/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 1118s Get:90 http://ftpmaster.internal/ubuntu plucky/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 1118s Get:91 http://ftpmaster.internal/ubuntu plucky/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 1118s Get:92 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 1147s Get:93 http://ftpmaster.internal/ubuntu plucky/main arm64 liblzma-dev arm64 5.6.4-1 [180 kB] 1147s Get:94 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 1147s Get:95 http://ftpmaster.internal/ubuntu plucky/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 1147s Get:96 http://ftpmaster.internal/ubuntu plucky/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 1147s Get:97 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 1147s Get:98 http://ftpmaster.internal/ubuntu plucky/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 1147s Get:99 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 1147s Get:100 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 1147s Get:101 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 1148s Get:102 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 1149s Get:103 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 1153s Get:104 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-nlme arm64 3.1.167-1 [2311 kB] 1155s Get:105 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 1159s Get:106 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 1159s Get:107 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 1167s Get:108 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 1168s Get:109 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 1168s Get:110 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.utils arm64 3.1-2-1 [381 kB] 1168s Get:111 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.data all 3.1-4-1 [4047 kB] 1172s Get:112 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.univar arm64 3.1-1-1build1 [308 kB] 1173s Get:113 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.geom arm64 3.3-5-1 [3929 kB] 1177s Get:114 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.random arm64 3.3-2-1 [1159 kB] 1178s Get:115 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 1178s Get:116 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 1178s Get:117 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 1181s Get:118 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 1185s Get:119 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 1186s Get:120 http://ftpmaster.internal/ubuntu plucky/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 1191s Preconfiguring packages ... 1191s Fetched 174 MB in 3min 13s (902 kB/s) 1191s Selecting previously unselected package libisl23:arm64. 1191s (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.) 1191s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ... 1191s Unpacking libisl23:arm64 (0.27-1) ... 1191s Selecting previously unselected package libmpc3:arm64. 1191s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ... 1191s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 1191s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 1191s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1191s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1191s Selecting previously unselected package cpp-14. 1191s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_arm64.deb ... 1191s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 1192s Selecting previously unselected package cpp-aarch64-linux-gnu. 1192s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1192s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1192s Selecting previously unselected package cpp. 1192s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 1192s Unpacking cpp (4:14.2.0-1ubuntu1) ... 1192s Selecting previously unselected package libcc1-0:arm64. 1192s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libcc1-0:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libgomp1:arm64. 1192s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libitm1:arm64. 1192s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libitm1:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libasan8:arm64. 1192s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libasan8:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package liblsan0:arm64. 1192s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking liblsan0:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libtsan2:arm64. 1192s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libtsan2:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libubsan1:arm64. 1192s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libubsan1:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libhwasan0:arm64. 1192s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_arm64.deb ... 1192s Unpacking libhwasan0:arm64 (15-20250222-0ubuntu1) ... 1192s Selecting previously unselected package libgcc-14-dev:arm64. 1192s Preparing to unpack .../014-libgcc-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1192s Unpacking libgcc-14-dev:arm64 (14.2.0-17ubuntu3) ... 1192s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 1192s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1192s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1193s Selecting previously unselected package gcc-14. 1193s Preparing to unpack .../016-gcc-14_14.2.0-17ubuntu3_arm64.deb ... 1193s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 1193s Selecting previously unselected package gcc-aarch64-linux-gnu. 1193s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1193s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1193s Selecting previously unselected package gcc. 1193s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 1193s Unpacking gcc (4:14.2.0-1ubuntu1) ... 1193s Selecting previously unselected package libstdc++-14-dev:arm64. 1193s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1193s Unpacking libstdc++-14-dev:arm64 (14.2.0-17ubuntu3) ... 1193s Selecting previously unselected package g++-14-aarch64-linux-gnu. 1193s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1193s Unpacking g++-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1193s Selecting previously unselected package g++-14. 1193s Preparing to unpack .../021-g++-14_14.2.0-17ubuntu3_arm64.deb ... 1193s Unpacking g++-14 (14.2.0-17ubuntu3) ... 1193s Selecting previously unselected package g++-aarch64-linux-gnu. 1193s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1193s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1193s Selecting previously unselected package g++. 1193s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 1193s Unpacking g++ (4:14.2.0-1ubuntu1) ... 1193s Selecting previously unselected package build-essential. 1193s Preparing to unpack .../024-build-essential_12.10ubuntu1_arm64.deb ... 1193s Unpacking build-essential (12.10ubuntu1) ... 1193s Selecting previously unselected package dctrl-tools. 1193s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ... 1193s Unpacking dctrl-tools (2.24-3build3) ... 1193s Selecting previously unselected package fonts-dejavu-mono. 1193s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... 1193s Unpacking fonts-dejavu-mono (2.37-8) ... 1193s Selecting previously unselected package fonts-dejavu-core. 1194s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb 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.../032-libgfortran-14-dev_14.2.0-17ubuntu3_arm64.deb ... 1194s Unpacking libgfortran-14-dev:arm64 (14.2.0-17ubuntu3) ... 1194s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 1194s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-17ubuntu3_arm64.deb ... 1194s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17ubuntu3) ... 1194s Selecting previously unselected package gfortran-14. 1194s Preparing to unpack .../034-gfortran-14_14.2.0-17ubuntu3_arm64.deb ... 1194s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 1195s Selecting previously unselected package gfortran-aarch64-linux-gnu. 1195s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 1195s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 1195s Selecting previously unselected package gfortran. 1195s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 1195s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 1195s Selecting previously unselected package icu-devtools. 1195s Preparing to unpack .../037-icu-devtools_76.1-1ubuntu2_arm64.deb ... 1195s Unpacking icu-devtools (76.1-1ubuntu2) ... 1195s Selecting previously unselected package libblas3:arm64. 1195s Preparing to unpack .../038-libblas3_3.12.1-2_arm64.deb ... 1195s Unpacking libblas3:arm64 (3.12.1-2) ... 1195s Selecting previously unselected package libblas-dev:arm64. 1195s Preparing to unpack .../039-libblas-dev_3.12.1-2_arm64.deb ... 1195s Unpacking libblas-dev:arm64 (3.12.1-2) ... 1195s Selecting previously unselected package libbz2-dev:arm64. 1195s Preparing to unpack .../040-libbz2-dev_1.0.8-6_arm64.deb ... 1195s Unpacking libbz2-dev:arm64 (1.0.8-6) ... 1195s Selecting previously unselected package libpixman-1-0:arm64. 1195s Preparing to unpack .../041-libpixman-1-0_0.44.0-3_arm64.deb ... 1195s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 1195s Selecting previously unselected package libxcb-render0:arm64. 1195s Preparing to unpack .../042-libxcb-render0_1.17.0-2_arm64.deb ... 1195s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 1195s Selecting previously unselected package libxcb-shm0:arm64. 1195s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_arm64.deb ... 1195s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 1195s Selecting previously unselected package libxrender1:arm64. 1195s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 1195s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 1195s Selecting previously unselected package libcairo2:arm64. 1195s Preparing to unpack .../045-libcairo2_1.18.2-2_arm64.deb ... 1195s Unpacking libcairo2:arm64 (1.18.2-2) ... 1195s Selecting previously unselected package libdatrie1:arm64. 1195s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_arm64.deb ... 1195s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 1195s Selecting previously unselected package libdeflate0:arm64. 1195s Preparing to unpack .../047-libdeflate0_1.23-1_arm64.deb ... 1195s Unpacking libdeflate0:arm64 (1.23-1) ... 1195s Selecting previously unselected package libdeflate-dev:arm64. 1195s Preparing to unpack .../048-libdeflate-dev_1.23-1_arm64.deb ... 1195s Unpacking libdeflate-dev:arm64 (1.23-1) ... 1195s Selecting previously unselected package libgraphite2-3:arm64. 1195s Preparing to unpack .../049-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 1195s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 1195s Selecting previously unselected package libharfbuzz0b:arm64. 1195s Preparing to unpack .../050-libharfbuzz0b_10.2.0-1_arm64.deb ... 1195s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 1195s Selecting previously unselected package x11-common. 1195s Preparing to unpack .../051-x11-common_1%3a7.7+23ubuntu3_all.deb ... 1195s Unpacking x11-common (1:7.7+23ubuntu3) ... 1195s Selecting previously unselected package libice6:arm64. 1195s Preparing to unpack .../052-libice6_2%3a1.1.1-1_arm64.deb ... 1195s Unpacking libice6:arm64 (2:1.1.1-1) ... 1195s Selecting previously unselected package libicu-dev:arm64. 1195s Preparing to unpack .../053-libicu-dev_76.1-1ubuntu2_arm64.deb ... 1195s Unpacking libicu-dev:arm64 (76.1-1ubuntu2) ... 1196s Selecting previously unselected package libjpeg-turbo8:arm64. 1196s Preparing to unpack .../054-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 1196s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 1196s Selecting previously unselected package libjpeg-turbo8-dev:arm64. 1196s Preparing to unpack .../055-libjpeg-turbo8-dev_2.1.5-3ubuntu2_arm64.deb ... 1196s Unpacking libjpeg-turbo8-dev:arm64 (2.1.5-3ubuntu2) ... 1196s Selecting previously unselected package libjpeg8:arm64. 1196s Preparing to unpack .../056-libjpeg8_8c-2ubuntu11_arm64.deb ... 1196s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 1196s Selecting previously unselected package libjpeg8-dev:arm64. 1196s Preparing to unpack .../057-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 1196s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 1196s Selecting previously unselected package libjpeg-dev:arm64. 1196s Preparing to unpack .../058-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 1196s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 1196s Selecting previously unselected package liblapack3:arm64. 1196s Preparing to unpack .../059-liblapack3_3.12.1-2_arm64.deb ... 1196s Unpacking liblapack3:arm64 (3.12.1-2) ... 1196s Selecting previously unselected package liblapack-dev:arm64. 1196s Preparing to unpack .../060-liblapack-dev_3.12.1-2_arm64.deb ... 1196s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 1196s Selecting previously unselected package liblerc4:arm64. 1196s Preparing to unpack .../061-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 1196s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 1196s Selecting previously unselected package libncurses-dev:arm64. 1196s Preparing to unpack .../062-libncurses-dev_6.5+20250216-2_arm64.deb ... 1196s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 1196s Selecting previously unselected package libthai-data. 1196s Preparing to unpack .../063-libthai-data_0.1.29-2build1_all.deb ... 1196s Unpacking libthai-data (0.1.29-2build1) ... 1196s Selecting previously unselected package libthai0:arm64. 1196s Preparing to unpack .../064-libthai0_0.1.29-2build1_arm64.deb ... 1196s Unpacking libthai0:arm64 (0.1.29-2build1) ... 1196s Selecting previously unselected package libpango-1.0-0:arm64. 1196s Preparing to unpack .../065-libpango-1.0-0_1.56.2-1_arm64.deb ... 1196s Unpacking libpango-1.0-0:arm64 (1.56.2-1) ... 1196s Selecting previously unselected package libpangoft2-1.0-0:arm64. 1196s Preparing to unpack .../066-libpangoft2-1.0-0_1.56.2-1_arm64.deb ... 1196s Unpacking libpangoft2-1.0-0:arm64 (1.56.2-1) ... 1196s Selecting previously unselected package libpangocairo-1.0-0:arm64. 1196s Preparing to unpack .../067-libpangocairo-1.0-0_1.56.2-1_arm64.deb ... 1196s Unpacking libpangocairo-1.0-0:arm64 (1.56.2-1) ... 1196s Selecting previously unselected package libpaper2:arm64. 1196s Preparing to unpack .../068-libpaper2_2.2.5-0.3_arm64.deb ... 1196s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 1196s Selecting previously unselected package libpaper-utils. 1196s Preparing to unpack .../069-libpaper-utils_2.2.5-0.3_arm64.deb ... 1196s Unpacking libpaper-utils (2.2.5-0.3) ... 1196s Selecting previously unselected package libpcre2-16-0:arm64. 1196s Preparing to unpack .../070-libpcre2-16-0_10.45-1_arm64.deb ... 1196s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 1196s Selecting previously unselected package libpcre2-32-0:arm64. 1196s Preparing to unpack .../071-libpcre2-32-0_10.45-1_arm64.deb ... 1196s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 1196s Selecting previously unselected package libpcre2-posix3:arm64. 1197s Preparing to unpack .../072-libpcre2-posix3_10.45-1_arm64.deb ... 1197s Unpacking libpcre2-posix3:arm64 (10.45-1) ... 1197s Selecting previously unselected package libpcre2-dev:arm64. 1197s Preparing to unpack .../073-libpcre2-dev_10.45-1_arm64.deb ... 1197s Unpacking libpcre2-dev:arm64 (10.45-1) ... 1197s Selecting previously unselected package libpkgconf3:arm64. 1197s Preparing to unpack .../074-libpkgconf3_1.8.1-4_arm64.deb ... 1197s Unpacking libpkgconf3:arm64 (1.8.1-4) ... 1197s Selecting previously unselected package zlib1g-dev:arm64. 1197s Preparing to unpack .../075-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 1197s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 1197s Selecting previously unselected package libpng-dev:arm64. 1197s Preparing to unpack .../076-libpng-dev_1.6.47-1_arm64.deb ... 1197s Unpacking libpng-dev:arm64 (1.6.47-1) ... 1197s Selecting previously unselected package libreadline-dev:arm64. 1197s Preparing to unpack .../077-libreadline-dev_8.2-6_arm64.deb ... 1197s Unpacking libreadline-dev:arm64 (8.2-6) ... 1197s Selecting previously unselected package libsharpyuv0:arm64. 1197s Preparing to unpack .../078-libsharpyuv0_1.5.0-0.1_arm64.deb ... 1197s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 1197s Selecting previously unselected package libsm6:arm64. 1197s Preparing to unpack .../079-libsm6_2%3a1.2.4-1_arm64.deb ... 1197s Unpacking libsm6:arm64 (2:1.2.4-1) ... 1197s Selecting previously unselected package libtcl8.6:arm64. 1197s Preparing to unpack .../080-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 1197s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 1197s Selecting previously unselected package libjbig0:arm64. 1197s Preparing to unpack .../081-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 1197s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 1197s Selecting previously unselected package libwebp7:arm64. 1197s Preparing to unpack .../082-libwebp7_1.5.0-0.1_arm64.deb ... 1197s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 1197s Selecting previously unselected package libtiff6:arm64. 1197s Preparing to unpack .../083-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 1197s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 1197s Selecting previously unselected package libxft2:arm64. 1197s Preparing to unpack .../084-libxft2_2.3.6-1build1_arm64.deb ... 1197s Unpacking libxft2:arm64 (2.3.6-1build1) ... 1197s Selecting previously unselected package libxss1:arm64. 1197s Preparing to unpack .../085-libxss1_1%3a1.2.3-1build3_arm64.deb ... 1197s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 1197s Selecting previously unselected package libtk8.6:arm64. 1197s Preparing to unpack .../086-libtk8.6_8.6.16-1_arm64.deb ... 1197s Unpacking libtk8.6:arm64 (8.6.16-1) ... 1197s Selecting previously unselected package libxt6t64:arm64. 1197s Preparing to unpack .../087-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 1197s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 1197s Selecting previously unselected package zip. 1197s Preparing to unpack .../088-zip_3.0-14ubuntu2_arm64.deb ... 1197s Unpacking zip (3.0-14ubuntu2) ... 1197s Selecting previously unselected package unzip. 1197s Preparing to unpack .../089-unzip_6.0-28ubuntu6_arm64.deb ... 1197s Unpacking unzip (6.0-28ubuntu6) ... 1197s Selecting previously unselected package xdg-utils. 1197s Preparing to unpack .../090-xdg-utils_1.2.1-2ubuntu1_all.deb ... 1197s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 1197s Selecting previously unselected package r-base-core. 1197s Preparing to unpack .../091-r-base-core_4.4.3-1_arm64.deb ... 1197s Unpacking r-base-core (4.4.3-1) ... 1198s Selecting previously unselected package liblzma-dev:arm64. 1198s Preparing to unpack .../092-liblzma-dev_5.6.4-1_arm64.deb ... 1198s Unpacking liblzma-dev:arm64 (5.6.4-1) ... 1198s Selecting previously unselected package pkgconf-bin. 1198s Preparing to unpack .../093-pkgconf-bin_1.8.1-4_arm64.deb ... 1198s Unpacking pkgconf-bin (1.8.1-4) ... 1198s Selecting previously unselected package pkgconf:arm64. 1198s Preparing to unpack .../094-pkgconf_1.8.1-4_arm64.deb ... 1198s Unpacking pkgconf:arm64 (1.8.1-4) ... 1198s Selecting previously unselected package libtirpc-dev:arm64. 1198s Preparing to unpack .../095-libtirpc-dev_1.3.4+ds-1.3_arm64.deb ... 1198s Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.3) ... 1198s Selecting previously unselected package r-base-dev. 1198s Preparing to unpack .../096-r-base-dev_4.4.3-1_all.deb ... 1198s Unpacking r-base-dev (4.4.3-1) ... 1198s Selecting previously unselected package pkg-r-autopkgtest. 1198s Preparing to unpack .../097-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 1198s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 1198s Selecting previously unselected package r-cran-abind. 1198s Preparing to unpack .../098-r-cran-abind_1.4-8-1_all.deb ... 1198s Unpacking r-cran-abind (1.4-8-1) ... 1198s Selecting previously unselected package r-cran-deldir. 1198s Preparing to unpack .../099-r-cran-deldir_2.0-4-1build1_arm64.deb ... 1198s Unpacking r-cran-deldir (2.0-4-1build1) ... 1198s Selecting previously unselected package r-cran-goftest. 1198s Preparing to unpack .../100-r-cran-goftest_1.2-3-1_arm64.deb ... 1198s Unpacking r-cran-goftest (1.2-3-1) ... 1198s Selecting previously unselected package r-cran-lattice. 1198s Preparing to unpack .../101-r-cran-lattice_0.22-6-1_arm64.deb ... 1198s Unpacking r-cran-lattice (0.22-6-1) ... 1198s Selecting previously unselected package r-cran-matrix. 1198s Preparing to unpack .../102-r-cran-matrix_1.7-3-1_arm64.deb ... 1198s Unpacking r-cran-matrix (1.7-3-1) ... 1198s Selecting previously unselected package r-cran-nlme. 1198s Preparing to unpack .../103-r-cran-nlme_3.1.167-1_arm64.deb ... 1198s Unpacking r-cran-nlme (3.1.167-1) ... 1198s Selecting previously unselected package r-cran-mgcv. 1198s Preparing to unpack .../104-r-cran-mgcv_1.9-1-1_arm64.deb ... 1198s Unpacking r-cran-mgcv (1.9-1-1) ... 1198s Selecting previously unselected package r-cran-polyclip. 1198s Preparing to unpack .../105-r-cran-polyclip_1.10-7-1_arm64.deb ... 1198s Unpacking r-cran-polyclip (1.10-7-1) ... 1198s Selecting previously unselected package r-cran-survival. 1198s Preparing to unpack .../106-r-cran-survival_3.8-3-1_arm64.deb ... 1198s Unpacking r-cran-survival (3.8-3-1) ... 1199s Selecting previously unselected package r-cran-rpart. 1199s Preparing to unpack .../107-r-cran-rpart_4.1.24-1_arm64.deb ... 1199s Unpacking r-cran-rpart (4.1.24-1) ... 1199s Selecting previously unselected package r-cran-spatial. 1199s Preparing to unpack .../108-r-cran-spatial_7.3-18-1_arm64.deb ... 1199s Unpacking r-cran-spatial (7.3-18-1) ... 1199s Selecting previously unselected package r-cran-spatstat.utils. 1199s Preparing to unpack .../109-r-cran-spatstat.utils_3.1-2-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.utils (3.1-2-1) ... 1199s Selecting previously unselected package r-cran-spatstat.data. 1199s Preparing to unpack .../110-r-cran-spatstat.data_3.1-4-1_all.deb ... 1199s Unpacking r-cran-spatstat.data (3.1-4-1) ... 1199s Selecting previously unselected package r-cran-spatstat.univar. 1199s Preparing to unpack .../111-r-cran-spatstat.univar_3.1-1-1build1_arm64.deb ... 1199s Unpacking r-cran-spatstat.univar (3.1-1-1build1) ... 1199s Selecting previously unselected package r-cran-spatstat.geom. 1199s Preparing to unpack .../112-r-cran-spatstat.geom_3.3-5-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.geom (3.3-5-1) ... 1199s Selecting previously unselected package r-cran-spatstat.random. 1199s Preparing to unpack .../113-r-cran-spatstat.random_3.3-2-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.random (3.3-2-1) ... 1199s Selecting previously unselected package r-cran-tensor. 1199s Preparing to unpack .../114-r-cran-tensor_1.5-4_all.deb ... 1199s Unpacking r-cran-tensor (1.5-4) ... 1199s Selecting previously unselected package r-cran-spatstat.sparse. 1199s Preparing to unpack .../115-r-cran-spatstat.sparse_3.1-0-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.sparse (3.1-0-1) ... 1199s Selecting previously unselected package r-cran-spatstat.explore. 1199s Preparing to unpack .../116-r-cran-spatstat.explore_3.3-4-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.explore (3.3-4-1) ... 1199s Selecting previously unselected package r-cran-spatstat.model. 1199s Preparing to unpack .../117-r-cran-spatstat.model_3.3-4-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.model (3.3-4-1) ... 1199s Selecting previously unselected package r-cran-spatstat.linnet. 1199s Preparing to unpack .../118-r-cran-spatstat.linnet_3.2-5-1_arm64.deb ... 1199s Unpacking r-cran-spatstat.linnet (3.2-5-1) ... 1199s Selecting previously unselected package r-cran-spatstat. 1199s Preparing to unpack .../119-r-cran-spatstat_3.3-1-1_arm64.deb ... 1199s Unpacking r-cran-spatstat (3.3-1-1) ... 1199s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 1199s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 1199s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 1199s Setting up libncurses-dev:arm64 (6.5+20250216-2) ... 1199s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 1199s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 1199s Setting up libdatrie1:arm64 (0.2.13-3build1) ... 1199s Setting up libxcb-render0:arm64 (1.17.0-2) ... 1199s 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1202s Setting up r-cran-spatstat.sparse (3.1-0-1) ... 1202s Setting up r-cran-mgcv (1.9-1-1) ... 1202s Setting up g++ (4:14.2.0-1ubuntu1) ... 1202s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1202s Setting up build-essential (12.10ubuntu1) ... 1202s Setting up r-cran-survival (3.8-3-1) ... 1202s Setting up gfortran (4:14.2.0-1ubuntu1) ... 1202s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 1202s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 1202s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 1202s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 1202s Setting up r-cran-spatstat.data (3.1-4-1) ... 1202s Setting up r-cran-spatstat.geom (3.3-5-1) ... 1202s Setting up r-base-dev (4.4.3-1) ... 1202s Setting up r-cran-rpart (4.1.24-1) ... 1202s Setting up r-cran-spatstat.random (3.3-2-1) ... 1202s Setting up r-cran-spatstat.explore (3.3-4-1) ... 1202s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 1202s Setting up r-cran-spatstat.model (3.3-4-1) ... 1202s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 1202s Setting up r-cran-spatstat (3.3-1-1) ... 1202s Processing triggers for install-info (7.1.1-1) ... 1203s Processing triggers for libc-bin (2.41-1ubuntu2) ... 1203s Processing triggers for man-db (2.13.0-1) ... 1209s autopkgtest [16:17:36]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 1209s autopkgtest [16:17:36]: test pkg-r-autopkgtest: [----------------------- 1210s Test: Try to load the R library spatstat.geom 1210s 1210s R version 4.4.3 (2025-02-28) -- "Trophy Case" 1210s Copyright (C) 2025 The R Foundation for Statistical Computing 1210s Platform: aarch64-unknown-linux-gnu 1210s 1210s R is free software and comes with ABSOLUTELY NO WARRANTY. 1210s You are welcome to redistribute it under certain conditions. 1210s Type 'license()' or 'licence()' for distribution details. 1210s 1210s R is a collaborative project with many contributors. 1210s Type 'contributors()' for more information and 1210s 'citation()' on how to cite R or R packages in publications. 1210s 1210s Type 'demo()' for some demos, 'help()' for on-line help, or 1210s 'help.start()' for an HTML browser interface to help. 1210s Type 'q()' to quit R. 1210s 1210s > library('spatstat.geom') 1210s Loading required package: spatstat.data 1211s Loading required package: spatstat.univar 1211s spatstat.univar 3.1-1 1211s spatstat.geom 3.3-5 1211s > 1211s > 1211s Other tests are currently unsupported! 1211s They will be progressively added. 1211s autopkgtest [16:17:38]: test pkg-r-autopkgtest: -----------------------] 1212s autopkgtest [16:17:39]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1212s pkg-r-autopkgtest PASS 1212s autopkgtest [16:17:39]: @@@@@@@@@@@@@@@@@@@@ summary 1212s run-unit-test PASS 1212s pkg-r-autopkgtest PASS 1231s nova [W] Using flock in prodstack6-arm64 1231s Creating nova instance adt-plucky-arm64-r-cran-spatstat.geom-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-a63e14f4-a5ce-4fa0-8e11-71e5178b5118 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1231s nova [W] Timed out waiting for 4ab0b2ef-9481-4293-a91d-2785d4b82923 to get deleted. 1231s nova [W] Using flock in prodstack6-arm64 1231s Creating nova instance adt-plucky-arm64-r-cran-spatstat.geom-20250315-155727-juju-7f2275-prod-proposed-migration-environment-2-a63e14f4-a5ce-4fa0-8e11-71e5178b5118 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 1231s nova [W] nova quota exceeded (attempt #0) 1231s nova [W] Timed out waiting for ecd6316d-a0fa-4583-bb16-c8ecaf1674bf to get deleted.