0s autopkgtest [02:31:24]: starting date and time: 2025-05-03 02:31:24+0000 0s autopkgtest [02:31:24]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [02:31:24]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ml1abpc5/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:nlme --apt-upgrade r-cran-spatstat.model --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=nlme/3.1.168-1 -- lxd -r lxd-armhf-10.145.243.61 lxd-armhf-10.145.243.61:autopkgtest/ubuntu/questing/armhf 20s autopkgtest [02:31:44]: testbed dpkg architecture: armhf 22s autopkgtest [02:31:46]: testbed apt version: 3.0.0 25s autopkgtest [02:31:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [02:31:51]: testbed release detected to be: None 35s autopkgtest [02:31:59]: updating testbed package index (apt update) 36s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 37s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 37s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 37s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 37s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.3 kB] 37s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 37s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1920 kB] 37s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [204 kB] 37s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1378 kB] 37s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.5 kB] 37s Get:11 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 37s Get:12 http://ftpmaster.internal/ubuntu questing/main Sources [1395 kB] 37s Get:13 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 38s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 38s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [14.9 MB] 38s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 41s Fetched 43.3 MB in 5s (8363 kB/s) 42s Reading package lists... 48s autopkgtest [02:32:12]: upgrading testbed (apt dist-upgrade and autopurge) 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 51s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 51s Starting 2 pkgProblemResolver with broken count: 0 51s Done 52s Entering ResolveByKeep 52s 52s Calculating upgrade... 53s The following packages will be upgraded: 53s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 53s libftdi1-2 libfwupd3 libnpth0t64 libnvme1t64 libsensors-config libsensors5 53s liburcu8t64 motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n 53s usb.ids 53s 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 5431 kB of archives. 53s After this operation, 3722 kB disk space will be freed. 53s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 53s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 53s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 53s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 53s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 53s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 53s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 53s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 53s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 53s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 53s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 53s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 53s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 53s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 53s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 53s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 53s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 53s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 53s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 53s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libnvme1t64 armhf 1.13-2 [74.3 kB] 54s Fetched 5431 kB in 1s (6806 kB/s) 54s (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 ... 63953 files and directories currently installed.) 54s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 54s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 54s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 54s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 54s Setting up base-files (13.7ubuntu1) ... 54s Installing new version of config file /etc/issue ... 54s Installing new version of config file /etc/issue.net ... 54s Installing new version of config file /etc/lsb-release ... 55s motd-news.service is a disabled or a static unit not running, not starting it. 55s (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 ... 63953 files and directories currently installed.) 55s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 55s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 55s Setting up dpkg (1.22.18ubuntu3) ... 55s (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 ... 63953 files and directories currently installed.) 55s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 55s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 55s Setting up libnpth0t64:armhf (1.8-3) ... 56s (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 ... 63953 files and directories currently installed.) 56s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 56s Unpacking distro-info-data (0.64) over (0.63) ... 56s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 56s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 56s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 56s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 56s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 56s Unpacking ed (1.21.1-1) over (1.21-1) ... 56s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 56s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 56s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 56s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 56s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 56s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 56s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 56s Unpacking nano (8.4-1) over (8.3-1) ... 56s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 56s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 56s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 56s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 56s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 56s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 56s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 56s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 57s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 57s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 57s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 57s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 57s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 57s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 57s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 57s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 57s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 57s Setting up motd-news-config (13.7ubuntu1) ... 57s Setting up liburcu8t64:armhf (0.15.2-2) ... 57s Setting up distro-info-data (0.64) ... 57s Setting up htop (3.4.1-4) ... 57s Setting up libsensors-config (1:3.6.2-2) ... 57s Installing new version of config file /etc/sensors3.conf ... 57s Setting up libfwupd3:armhf (2.0.8-3) ... 57s Setting up libftdi1-2:armhf (1.5-10) ... 57s Setting up libnvme1t64 (1.13-2) ... 57s Setting up ed (1.21.1-1) ... 57s Setting up usb.ids (2025.04.01-1) ... 57s Setting up libsensors5:armhf (1:3.6.2-2) ... 57s Setting up libdpkg-perl (1.22.18ubuntu3) ... 57s Setting up nano (8.4-1) ... 57s Installing new version of config file /etc/nanorc ... 57s Setting up ubuntu-pro-client (35.1ubuntu0) ... 57s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 57s 57s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 57s 57s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 57s 58s Setting up fwupd (2.0.8-3) ... 59s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 59s fwupd.service is a disabled or a static unit not running, not starting it. 59s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 59s Setting up dpkg-dev (1.22.18ubuntu3) ... 59s Processing triggers for dbus (1.16.2-2ubuntu1) ... 59s Processing triggers for install-info (7.1.1-1) ... 59s Processing triggers for libc-bin (2.41-6ubuntu1) ... 59s Processing triggers for man-db (2.13.0-1) ... 61s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 61s Processing triggers for initramfs-tools (0.147ubuntu1) ... 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 64s Starting pkgProblemResolver with broken count: 0 64s Starting 2 pkgProblemResolver with broken count: 0 64s Done 64s Solving dependencies... 65s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [02:32:30]: rebooting testbed after setup commands that affected boot 106s autopkgtest [02:33:10]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 131s autopkgtest [02:33:35]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.model 140s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.model 3.3-4-1 (dsc) [2601 B] 140s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.model 3.3-4-1 (tar) [808 kB] 140s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.model 3.3-4-1 (diff) [3508 B] 141s gpgv: Signature made Fri Jan 31 08:13:11 2025 UTC 141s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 141s gpgv: issuer "plessy@debian.org" 141s gpgv: Can't check signature: No public key 141s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.model_3.3-4-1.dsc: no acceptable signature found 141s autopkgtest [02:33:45]: testing package r-cran-spatstat.model version 3.3-4-1 143s autopkgtest [02:33:47]: build not needed 147s autopkgtest [02:33:51]: test run-unit-test: preparing testbed 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 150s The following NEW packages will be installed: 150s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 150s fonts-mathjax libblas3 libcairo2 libdatrie1 libdeflate0 libfontconfig1 150s libfreetype6 libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 150s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-mathjax 150s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 150s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 150s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 150s libxft2 libxrender1 libxss1 libxt6t64 littler r-base-core r-cran-abind 150s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 150s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-locfit 150s r-cran-matrix r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten 150s r-cran-polyclip r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape 150s r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 150s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 150s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 150s r-cran-spatstat.univar r-cran-spatstat.utils r-cran-survival r-cran-tensor 150s unzip x11-common xdg-utils zip 150s 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 97.8 MB of archives. 150s After this operation, 199 MB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 151s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 151s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 152s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 152s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 152s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig armhf 2.15.0-2.2ubuntu1 [190 kB] 152s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 153s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 153s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 153s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 153s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 153s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 153s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 153s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 153s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 153s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 153s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 153s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 153s Get:19 http://ftpmaster.internal/ubuntu questing/universe armhf libgslcblas0 armhf 2.8+dfsg-5ubuntu1 [84.4 kB] 153s Get:20 http://ftpmaster.internal/ubuntu questing/universe armhf libgsl28 armhf 2.8+dfsg-5ubuntu1 [876 kB] 153s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 153s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 153s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 153s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 153s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 153s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 154s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 154s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libthai-data all 0.1.29-2build1 [158 kB] 154s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 154s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libpango-1.0-0 armhf 1.56.3-1 [216 kB] 154s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf libpangoft2-1.0-0 armhf 1.56.3-1 [44.1 kB] 154s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libpangocairo-1.0-0 armhf 1.56.3-1 [25.0 kB] 154s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 154s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 154s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 154s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 154s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 154s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 154s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 154s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 154s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 154s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 154s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 154s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 154s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 154s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 154s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 154s Get:48 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 156s Get:49 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 156s Get:50 http://ftpmaster.internal/ubuntu questing/universe armhf littler all 0.3.20-2 [2554 B] 156s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 156s Get:52 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-codetools all 0.2-20-1 [90.5 kB] 156s Get:53 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-deldir armhf 2.0-4-1build1 [268 kB] 156s Get:54 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-iterators all 1.0.14-1 [336 kB] 156s Get:55 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-foreach all 1.5.2-1 [124 kB] 156s Get:56 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 156s Get:57 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 156s Get:58 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 156s Get:59 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 156s Get:60 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 156s Get:61 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 156s Get:62 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 156s Get:63 http://ftpmaster.internal/ubuntu questing/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 156s Get:64 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-glmnet armhf 4.1-8-1 [1881 kB] 156s Get:65 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-goftest armhf 1.2-3-1 [58.6 kB] 156s Get:66 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-gsl armhf 2.1-8-1build1 [481 kB] 156s Get:67 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-locfit armhf 1.5-9.12-1 [495 kB] 156s Get:68 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 156s Get:69 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 157s Get:70 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-nleqslv armhf 3.3.5-1 [97.2 kB] 157s Get:71 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-polyclip armhf 1.10-7-1 [109 kB] 157s Get:72 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 157s Get:73 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-sm armhf 2.2-6.0-1 [787 kB] 157s Get:74 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatial armhf 7.3-18-1 [131 kB] 157s Get:75 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.utils armhf 3.1-3-1 [384 kB] 157s Get:76 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.data all 3.1-6-1 [4153 kB] 157s Get:77 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.univar armhf 3.1-2-1 [310 kB] 157s Get:78 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.geom armhf 3.3-6-1 [3923 kB] 157s Get:79 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.random armhf 3.3-3-1 [1155 kB] 157s Get:80 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-tensor all 1.5-4 [15.7 kB] 157s Get:81 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.sparse armhf 3.1-0-1 [216 kB] 157s Get:82 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.explore armhf 3.3-4-1 [3271 kB] 157s Get:83 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.model armhf 3.3-4-1 [3397 kB] 157s Get:84 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.linnet armhf 3.2-5-1 [1505 kB] 157s Get:85 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat armhf 3.3-1-1 [4121 kB] 158s Preconfiguring packages ... 158s Fetched 97.8 MB in 7s (14.2 MB/s) 158s Selecting previously unselected package libfreetype6:armhf. 158s (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 ... 63951 files and directories currently installed.) 158s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 158s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 158s Selecting previously unselected package fonts-dejavu-mono. 158s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-mono (2.37-8) ... 158s Selecting previously unselected package fonts-dejavu-core. 158s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 158s Unpacking fonts-dejavu-core (2.37-8) ... 158s Selecting previously unselected package fontconfig-config. 158s Preparing to unpack .../03-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 158s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 158s Selecting previously unselected package libfontconfig1:armhf. 158s Preparing to unpack .../04-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 158s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 158s Selecting previously unselected package fontconfig. 158s Preparing to unpack .../05-fontconfig_2.15.0-2.2ubuntu1_armhf.deb ... 158s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 158s Selecting previously unselected package fonts-mathjax. 158s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 158s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 158s Selecting previously unselected package libblas3:armhf. 158s Preparing to unpack .../07-libblas3_3.12.1-2_armhf.deb ... 158s Unpacking libblas3:armhf (3.12.1-2) ... 158s Selecting previously unselected package libpixman-1-0:armhf. 158s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_armhf.deb ... 158s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 158s Selecting previously unselected package libxcb-render0:armhf. 158s Preparing to unpack .../09-libxcb-render0_1.17.0-2_armhf.deb ... 158s Unpacking libxcb-render0:armhf (1.17.0-2) ... 158s Selecting previously unselected package libxcb-shm0:armhf. 158s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_armhf.deb ... 158s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 158s Selecting previously unselected package libxrender1:armhf. 158s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 158s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 158s Selecting previously unselected package libcairo2:armhf. 158s Preparing to unpack .../12-libcairo2_1.18.4-1_armhf.deb ... 158s Unpacking libcairo2:armhf (1.18.4-1) ... 159s Selecting previously unselected package libdatrie1:armhf. 159s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_armhf.deb ... 159s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 159s Selecting previously unselected package libdeflate0:armhf. 159s Preparing to unpack .../14-libdeflate0_1.23-1_armhf.deb ... 159s Unpacking libdeflate0:armhf (1.23-1) ... 159s Selecting previously unselected package libgfortran5:armhf. 159s Preparing to unpack .../15-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 159s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 159s Selecting previously unselected package libgomp1:armhf. 159s Preparing to unpack .../16-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 159s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 159s Selecting previously unselected package libgraphite2-3:armhf. 159s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 159s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 159s Selecting previously unselected package libgslcblas0:armhf. 159s Preparing to unpack .../18-libgslcblas0_2.8+dfsg-5ubuntu1_armhf.deb ... 159s Unpacking libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 159s Selecting previously unselected package libgsl28:armhf. 159s Preparing to unpack .../19-libgsl28_2.8+dfsg-5ubuntu1_armhf.deb ... 159s Unpacking libgsl28:armhf (2.8+dfsg-5ubuntu1) ... 159s Selecting previously unselected package libharfbuzz0b:armhf. 159s Preparing to unpack .../20-libharfbuzz0b_10.2.0-1_armhf.deb ... 159s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 159s Selecting previously unselected package x11-common. 159s Preparing to unpack .../21-x11-common_1%3a7.7+23ubuntu4_all.deb ... 159s Unpacking x11-common (1:7.7+23ubuntu4) ... 159s Selecting previously unselected package libice6:armhf. 159s Preparing to unpack .../22-libice6_2%3a1.1.1-1_armhf.deb ... 159s Unpacking libice6:armhf (2:1.1.1-1) ... 159s Selecting previously unselected package libjpeg-turbo8:armhf. 159s Preparing to unpack .../23-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 159s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 159s Selecting previously unselected package libjpeg8:armhf. 159s Preparing to unpack .../24-libjpeg8_8c-2ubuntu11_armhf.deb ... 159s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 159s Selecting previously unselected package liblapack3:armhf. 159s Preparing to unpack .../25-liblapack3_3.12.1-2_armhf.deb ... 159s Unpacking liblapack3:armhf (3.12.1-2) ... 159s Selecting previously unselected package liblerc4:armhf. 159s Preparing to unpack .../26-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 159s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 159s Selecting previously unselected package libthai-data. 159s Preparing to unpack .../27-libthai-data_0.1.29-2build1_all.deb ... 159s Unpacking libthai-data (0.1.29-2build1) ... 159s Selecting previously unselected package libthai0:armhf. 159s Preparing to unpack .../28-libthai0_0.1.29-2build1_armhf.deb ... 159s Unpacking libthai0:armhf (0.1.29-2build1) ... 159s Selecting previously unselected package libpango-1.0-0:armhf. 159s Preparing to unpack .../29-libpango-1.0-0_1.56.3-1_armhf.deb ... 159s Unpacking libpango-1.0-0:armhf (1.56.3-1) ... 159s Selecting previously unselected package libpangoft2-1.0-0:armhf. 159s Preparing to unpack .../30-libpangoft2-1.0-0_1.56.3-1_armhf.deb ... 159s Unpacking libpangoft2-1.0-0:armhf (1.56.3-1) ... 159s Selecting previously unselected package libpangocairo-1.0-0:armhf. 159s Preparing to unpack .../31-libpangocairo-1.0-0_1.56.3-1_armhf.deb ... 159s Unpacking libpangocairo-1.0-0:armhf (1.56.3-1) ... 159s Selecting previously unselected package libpaper2:armhf. 159s Preparing to unpack .../32-libpaper2_2.2.5-0.3_armhf.deb ... 159s Unpacking libpaper2:armhf (2.2.5-0.3) ... 159s Selecting previously unselected package libpaper-utils. 159s Preparing to unpack .../33-libpaper-utils_2.2.5-0.3_armhf.deb ... 159s Unpacking libpaper-utils (2.2.5-0.3) ... 159s Selecting previously unselected package libsharpyuv0:armhf. 159s Preparing to unpack .../34-libsharpyuv0_1.5.0-0.1_armhf.deb ... 159s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 159s Selecting previously unselected package libsm6:armhf. 159s Preparing to unpack .../35-libsm6_2%3a1.2.4-1_armhf.deb ... 159s Unpacking libsm6:armhf (2:1.2.4-1) ... 159s Selecting previously unselected package libtcl8.6:armhf. 159s Preparing to unpack .../36-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 159s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 159s Selecting previously unselected package libjbig0:armhf. 159s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 159s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 159s Selecting previously unselected package libwebp7:armhf. 159s Preparing to unpack .../38-libwebp7_1.5.0-0.1_armhf.deb ... 159s Unpacking libwebp7:armhf (1.5.0-0.1) ... 160s Selecting previously unselected package libtiff6:armhf. 160s Preparing to unpack .../39-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 160s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 160s Selecting previously unselected package libxft2:armhf. 160s Preparing to unpack .../40-libxft2_2.3.6-1build1_armhf.deb ... 160s Unpacking libxft2:armhf (2.3.6-1build1) ... 160s Selecting previously unselected package libxss1:armhf. 160s Preparing to unpack .../41-libxss1_1%3a1.2.3-1build3_armhf.deb ... 160s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 160s Selecting previously unselected package libtk8.6:armhf. 160s Preparing to unpack .../42-libtk8.6_8.6.16-1_armhf.deb ... 160s Unpacking libtk8.6:armhf (8.6.16-1) ... 160s Selecting previously unselected package libxt6t64:armhf. 160s Preparing to unpack .../43-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 160s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 160s Selecting previously unselected package zip. 160s Preparing to unpack .../44-zip_3.0-14ubuntu2_armhf.deb ... 160s Unpacking zip (3.0-14ubuntu2) ... 160s Selecting previously unselected package unzip. 160s Preparing to unpack .../45-unzip_6.0-28ubuntu6_armhf.deb ... 160s Unpacking unzip (6.0-28ubuntu6) ... 160s Selecting previously unselected package xdg-utils. 160s Preparing to unpack .../46-xdg-utils_1.2.1-2ubuntu1_all.deb ... 160s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 160s Selecting previously unselected package r-base-core. 160s Preparing to unpack .../47-r-base-core_4.4.3-1_armhf.deb ... 160s Unpacking r-base-core (4.4.3-1) ... 160s Selecting previously unselected package r-cran-littler. 160s Preparing to unpack .../48-r-cran-littler_0.3.20-2_armhf.deb ... 160s Unpacking r-cran-littler (0.3.20-2) ... 160s Selecting previously unselected package littler. 160s Preparing to unpack .../49-littler_0.3.20-2_all.deb ... 160s Unpacking littler (0.3.20-2) ... 160s Selecting previously unselected package r-cran-abind. 160s Preparing to unpack .../50-r-cran-abind_1.4-8-1_all.deb ... 160s Unpacking r-cran-abind (1.4-8-1) ... 160s Selecting previously unselected package r-cran-codetools. 160s Preparing to unpack .../51-r-cran-codetools_0.2-20-1_all.deb ... 160s Unpacking r-cran-codetools (0.2-20-1) ... 160s Selecting previously unselected package r-cran-deldir. 160s Preparing to unpack .../52-r-cran-deldir_2.0-4-1build1_armhf.deb ... 160s Unpacking r-cran-deldir (2.0-4-1build1) ... 160s Selecting previously unselected package r-cran-iterators. 160s Preparing to unpack .../53-r-cran-iterators_1.0.14-1_all.deb ... 160s Unpacking r-cran-iterators (1.0.14-1) ... 160s Selecting previously unselected package r-cran-foreach. 160s Preparing to unpack .../54-r-cran-foreach_1.5.2-1_all.deb ... 160s Unpacking r-cran-foreach (1.5.2-1) ... 160s Selecting previously unselected package r-cran-lattice. 160s Preparing to unpack .../55-r-cran-lattice_0.22-6-1_armhf.deb ... 160s Unpacking r-cran-lattice (0.22-6-1) ... 161s Selecting previously unselected package r-cran-matrix. 161s Preparing to unpack .../56-r-cran-matrix_1.7-3-1_armhf.deb ... 161s Unpacking r-cran-matrix (1.7-3-1) ... 161s Selecting previously unselected package r-cran-shape. 161s Preparing to unpack .../57-r-cran-shape_1.4.6.1-1_all.deb ... 161s Unpacking r-cran-shape (1.4.6.1-1) ... 161s Selecting previously unselected package r-cran-survival. 161s Preparing to unpack .../58-r-cran-survival_3.8-3-1_armhf.deb ... 161s Unpacking r-cran-survival (3.8-3-1) ... 161s Selecting previously unselected package r-cran-pkgkitten. 161s Preparing to unpack .../59-r-cran-pkgkitten_0.2.4-1_all.deb ... 161s Unpacking r-cran-pkgkitten (0.2.4-1) ... 161s Selecting previously unselected package r-cran-rcpp. 161s Preparing to unpack .../60-r-cran-rcpp_1.0.14-1_armhf.deb ... 161s Unpacking r-cran-rcpp (1.0.14-1) ... 161s Selecting previously unselected package r-cran-rcppeigen. 161s Preparing to unpack .../61-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 161s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 161s Selecting previously unselected package libjs-mathjax. 161s Preparing to unpack .../62-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 161s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 162s Selecting previously unselected package r-cran-glmnet. 162s Preparing to unpack .../63-r-cran-glmnet_4.1-8-1_armhf.deb ... 162s Unpacking r-cran-glmnet (4.1-8-1) ... 162s Selecting previously unselected package r-cran-goftest. 162s Preparing to unpack .../64-r-cran-goftest_1.2-3-1_armhf.deb ... 162s Unpacking r-cran-goftest (1.2-3-1) ... 162s Selecting previously unselected package r-cran-gsl. 162s Preparing to unpack .../65-r-cran-gsl_2.1-8-1build1_armhf.deb ... 162s Unpacking r-cran-gsl (2.1-8-1build1) ... 162s Selecting previously unselected package r-cran-locfit. 162s Preparing to unpack .../66-r-cran-locfit_1.5-9.12-1_armhf.deb ... 162s Unpacking r-cran-locfit (1.5-9.12-1) ... 162s Selecting previously unselected package r-cran-nlme. 162s Preparing to unpack .../67-r-cran-nlme_3.1.168-1_armhf.deb ... 162s Unpacking r-cran-nlme (3.1.168-1) ... 162s Selecting previously unselected package r-cran-mgcv. 162s Preparing to unpack .../68-r-cran-mgcv_1.9-1-1_armhf.deb ... 162s Unpacking r-cran-mgcv (1.9-1-1) ... 162s Selecting previously unselected package r-cran-nleqslv. 162s Preparing to unpack .../69-r-cran-nleqslv_3.3.5-1_armhf.deb ... 162s Unpacking r-cran-nleqslv (3.3.5-1) ... 162s Selecting previously unselected package r-cran-polyclip. 162s Preparing to unpack .../70-r-cran-polyclip_1.10-7-1_armhf.deb ... 162s Unpacking r-cran-polyclip (1.10-7-1) ... 162s Selecting previously unselected package r-cran-rpart. 162s Preparing to unpack .../71-r-cran-rpart_4.1.24-1_armhf.deb ... 162s Unpacking r-cran-rpart (4.1.24-1) ... 162s Selecting previously unselected package r-cran-sm. 162s Preparing to unpack .../72-r-cran-sm_2.2-6.0-1_armhf.deb ... 162s Unpacking r-cran-sm (2.2-6.0-1) ... 162s Selecting previously unselected package r-cran-spatial. 162s Preparing to unpack .../73-r-cran-spatial_7.3-18-1_armhf.deb ... 162s Unpacking r-cran-spatial (7.3-18-1) ... 162s Selecting previously unselected package r-cran-spatstat.utils. 162s Preparing to unpack .../74-r-cran-spatstat.utils_3.1-3-1_armhf.deb ... 162s Unpacking r-cran-spatstat.utils (3.1-3-1) ... 162s Selecting previously unselected package r-cran-spatstat.data. 162s Preparing to unpack .../75-r-cran-spatstat.data_3.1-6-1_all.deb ... 162s Unpacking r-cran-spatstat.data (3.1-6-1) ... 162s Selecting previously unselected package r-cran-spatstat.univar. 162s Preparing to unpack .../76-r-cran-spatstat.univar_3.1-2-1_armhf.deb ... 162s Unpacking r-cran-spatstat.univar (3.1-2-1) ... 162s Selecting previously unselected package r-cran-spatstat.geom. 162s Preparing to unpack .../77-r-cran-spatstat.geom_3.3-6-1_armhf.deb ... 162s Unpacking r-cran-spatstat.geom (3.3-6-1) ... 162s Selecting previously unselected package r-cran-spatstat.random. 162s Preparing to unpack .../78-r-cran-spatstat.random_3.3-3-1_armhf.deb ... 162s Unpacking r-cran-spatstat.random (3.3-3-1) ... 162s Selecting previously unselected package r-cran-tensor. 162s Preparing to unpack .../79-r-cran-tensor_1.5-4_all.deb 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... 174s autopkgtest [02:34:18]: test run-unit-test: [----------------------- 176s BEGIN TEST testsAtoC.R 176s 176s R version 4.4.3 (2025-02-28) -- "Trophy Case" 176s Copyright (C) 2025 The R Foundation for Statistical Computing 176s Platform: arm-unknown-linux-gnueabihf (32-bit) 176s 176s R is free software and comes with ABSOLUTELY NO WARRANTY. 176s You are welcome to redistribute it under certain conditions. 176s Type 'license()' or 'licence()' for distribution details. 176s 176s R is a collaborative project with many contributors. 176s Type 'contributors()' for more information and 176s 'citation()' on how to cite R or R packages in publications. 176s 176s Type 'demo()' for some demos, 'help()' for on-line help, or 176s 'help.start()' for an HTML browser interface to help. 176s Type 'q()' to quit R. 176s 176s > #' 176s > #' Header for all (concatenated) test files 176s > #' 176s > #' Require spatstat.model 176s > #' Obtain environment variable controlling tests. 176s > #' 176s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 176s > 176s > require(spatstat.model) 176s Loading required package: spatstat.model 176s Loading required package: spatstat.data 177s Loading required package: spatstat.univar 177s spatstat.univar 3.1-2 177s Loading required package: spatstat.geom 177s spatstat.geom 3.3-6 177s Loading required package: spatstat.random 177s spatstat.random 3.3-3 177s Loading required package: spatstat.explore 177s Loading required package: nlme 177s spatstat.explore 3.3-4 177s Loading required package: rpart 177s spatstat.model 3.3-4 177s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 177s > ALWAYS <- TRUE 177s > cat(paste("--------- Executing", 177s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 177s + "test code -----------\n")) 177s --------- Executing **RESTRICTED** subset of test code ----------- 177s > #' tests/aucroc.R 177s > #' 177s > #' AUC and ROC code 177s > #' 177s > #' $Revision: 1.6 $ $Date: 2020/11/02 06:26:45 $ 177s > 177s > local({ 177s + if(FULLTEST) { 177s + fit <- kppm(redwood ~ I(y-x)) 177s + a <- roc(fit) 177s + b <- auc(fit) 177s + fet <- ppm(amacrine~x+y+marks) 177s + d <- roc(fet) 177s + e <- auc(fet) 177s + } 177s + }) 177s > ## tests/cdf.test.R 177s > 177s > 177s > local({ 177s + NSIM <- 9 177s + op <- spatstat.options(ndummy.min=16, npixel=32) 177s + if(FULLTEST) { 177s + ## Monte Carlo test for Gibbs model 177s + fit <- ppm(cells ~ 1, Strauss(0.07)) 177s + cdf.test(fit, "x", nsim=NSIM) 177s + 177s + ## cdf.test.slrm 177s + fut <- slrm(japanesepines ~ x + y) 177s + Z <- distmap(japanesepines) 177s + cdf.test(fut, Z) 177s + } 177s + reset.spatstat.options() 177s + }) 177s > 177s > 177s > #' 177s > #' tests/contrib.R 177s > #' 177s > #' Tests for user-contributed code in spatstat 177s > #' 177s > #' $Revision: 1.4 $ $Date: 2021/04/17 02:32:24 $ 177s > 177s > local({ 177s + #' Jinhom 177s + #' Marie-Colette van Lieshout and Ottmar Cronie 177s + X <- redwood3 177s + if(FULLTEST) { 177s + fit <- ppm(X ~ polynom(x,y,2)) 177s + } else { 177s + X <- X[c(TRUE,FALSE)] 177s + spatstat.options(npixel=32, ndummy.min=16) 177s + fit <- ppm(X ~ x) 177s + } 177s + lam <- predict(fit) 177s + lamX <- fitted(fit, dataonly=TRUE) 177s + lmin <- 0.9 * min(lam) 177s + g1 <- Ginhom(X, lambda=fit, update=TRUE) 177s + if(FULLTEST) { 177s + g2 <- Ginhom(X, lambda=fit, update=FALSE, lmin = lmin) 177s + g3 <- Ginhom(X, lambda=lam, lmin=lmin) 177s + g4 <- Ginhom(X, lambda=lamX, lmin=lmin) 177s + } 177s + if(ALWAYS) { 177s + f2 <- Finhom(X, lambda=fit, update=FALSE) 177s + } 177s + if(FULLTEST) { 177s + f1 <- Finhom(X, lambda=fit, update=TRUE) 177s + f3 <- Finhom(X, lambda=lam, lmin=lmin) 177s + } 177s + if(!FULLTEST) reset.spatstat.options() 177s + }) 178s > 178s BEGIN TEST testsD.R 178s 178s R version 4.4.3 (2025-02-28) -- "Trophy Case" 178s Copyright (C) 2025 The R Foundation for Statistical Computing 178s Platform: arm-unknown-linux-gnueabihf (32-bit) 178s 178s R is free software and comes with ABSOLUTELY NO WARRANTY. 178s You are welcome to redistribute it under certain conditions. 178s Type 'license()' or 'licence()' for distribution details. 178s 178s R is a collaborative project with many contributors. 178s Type 'contributors()' for more information and 178s 'citation()' on how to cite R or R packages in publications. 178s 178s Type 'demo()' for some demos, 'help()' for on-line help, or 178s 'help.start()' for an HTML browser interface to help. 178s Type 'q()' to quit R. 178s 178s > #' 178s > #' Header for all (concatenated) test files 178s > #' 178s > #' Require spatstat.model 178s > #' Obtain environment variable controlling tests. 178s > #' 178s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 178s > 178s > require(spatstat.model) 178s Loading required package: spatstat.model 178s Loading required package: spatstat.data 179s Loading required package: spatstat.univar 179s spatstat.univar 3.1-2 179s Loading required package: spatstat.geom 179s spatstat.geom 3.3-6 179s Loading required package: spatstat.random 179s spatstat.random 3.3-3 179s Loading required package: spatstat.explore 179s Loading required package: nlme 179s spatstat.explore 3.3-4 179s Loading required package: rpart 179s spatstat.model 3.3-4 179s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 179s > ALWAYS <- TRUE 179s > cat(paste("--------- Executing", 179s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 179s + "test code -----------\n")) 179s --------- Executing **RESTRICTED** subset of test code ----------- 179s > #' 179s > #' tests/deltasuffstat.R 179s > #' 179s > #' Explicit tests of 'deltasuffstat' 179s > #' 179s > #' $Revision: 1.4 $ $Date: 2021/01/22 08:08:48 $ 179s > 179s > if(!FULLTEST) 179s + spatstat.options(npixel=32, ndummy.min=16) 179s > 179s > if(ALWAYS) { # depends on C code 179s + local({ 179s + 179s + disagree <- function(x, y, tol=1e-7) { !is.null(x) && !is.null(y) && max(abs(x-y)) > tol } 179s + 179s + flydelta <- function(model, modelname="") { 179s + ## Check execution of different algorithms for 'deltasuffstat' 179s + dSS <- deltasuffstat(model, sparseOK=TRUE) 179s + dBS <- deltasuffstat(model, sparseOK=TRUE, use.special=FALSE, force=TRUE) 179s + dBF <- deltasuffstat(model, sparseOK=FALSE, use.special=FALSE, force=TRUE) 179s + ## Compare results 179s + if(disagree(dBS, dSS)) 179s + stop(paste(modelname, "model: Brute force algorithm disagrees with special algorithm")) 179s + if(disagree(dBF, dBS)) 179s + stop(paste(modelname, "model: Sparse and full versions of brute force algorithm disagree")) 179s + return(invisible(NULL)) 179s + } 179s + 179s + modelS <- ppm(cells ~ x, Strauss(0.13), nd=10) 179s + flydelta(modelS, "Strauss") 179s + 179s + antsub <- ants[c(FALSE,TRUE,FALSE)] 179s + rmat <- matrix(c(130, 90, 90, 60), 2, 2) 179s + 179s + modelM <- ppm(antsub ~ 1, MultiStrauss(rmat), nd=16) 179s + flydelta(modelM, "MultiStrauss") 179s + 179s + modelA <- ppm(antsub ~ 1, HierStrauss(rmat, archy=c(2,1)), nd=16) 179s + flydelta(modelA, "HierStrauss") 179s + }) 179s + 179s + } 183s > 183s > reset.spatstat.options() 183s > #' 183s > #' tests/density.R 183s > #' 183s > #' Test behaviour of density() methods, 183s > #' relrisk(), Smooth() 183s > #' and inhomogeneous summary functions 183s > #' and idw, adaptive.density, intensity 183s > #' and SpatialMedian, SpatialQuantile 183s > #' 183s > #' $Revision: 1.67 $ $Date: 2024/01/29 07:07:16 $ 183s > #' 183s > 183s > if(!FULLTEST) 183s + spatstat.options(npixel=32, ndummy.min=16) 183s > 183s > 183s > local({ 183s + ## likewise 'relrisk.ppm' 183s + fit <- ppm(ants ~ x) 183s + rants <- function(..., model=fit) { 183s + a <- relrisk(model, sigma=100, se=TRUE, ...) 183s + return(TRUE) 183s + } 183s + if(ALWAYS) { 183s + rants() 183s + rants(diggle=TRUE) 183s + rants(edge=FALSE) 183s + rants(at="points") 183s + rants(casecontrol=FALSE) 183s + rants(relative=TRUE) 183s + } 183s + if(FULLTEST) { 183s + rants(diggle=TRUE, at="points") 183s + rants(edge=FALSE, at="points") 183s + rants(casecontrol=FALSE, relative=TRUE) 183s + rants(casecontrol=FALSE,at="points") 183s + rants(relative=TRUE,at="points") 183s + rants(casecontrol=FALSE, relative=TRUE,at="points") 183s + rants(relative=TRUE, control="Cataglyphis", case="Messor") 183s + rants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 183s + } 184s + ## more than 2 types 184s + fut <- ppm(sporophores ~ x) 184s + if(ALWAYS) { 184s + rants(model=fut) 184s + } 184s + if(FULLTEST) { 184s + rants(model=fut, at="points") 184s + rants(model=fut, relative=TRUE, at="points") 184s + } 184s + if(FULLTEST) { 184s + ## cases of 'intensity' etc 184s + a <- intensity(ppm(amacrine ~ 1)) 184s + } 184s + }) 184s > 184s > reset.spatstat.options() 184s > 184s > #' 184s > #' tests/diagnostique.R 184s > #' 184s > #' Diagnostic tools such as diagnose.ppm, qqplot.ppm 184s > #' 184s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 184s > #' 184s > 184s > if(FULLTEST) { 184s + local({ 184s + fit <- ppm(cells ~ x) 184s + diagE <- diagnose.ppm(fit, type="eem") 184s + diagI <- diagnose.ppm(fit, type="inverse") 184s + diagP <- diagnose.ppm(fit, type="Pearson") 184s + plot(diagE, which="all") 184s + plot(diagI, which="smooth") 184s + plot(diagP, which="x") 184s + plot(diagP, which="marks", plot.neg="discrete") 184s + plot(diagP, which="marks", plot.neg="contour") 184s + plot(diagP, which="smooth", srange=c(-5,5)) 184s + plot(diagP, which="smooth", plot.smooth="contour") 184s + plot(diagP, which="smooth", plot.smooth="image") 184s + 184s + fitS <- ppm(cells ~ x, Strauss(0.08)) 184s + diagES <- diagnose.ppm(fitS, type="eem", clip=FALSE) 184s + diagIS <- diagnose.ppm(fitS, type="inverse", clip=FALSE) 184s + diagPS <- diagnose.ppm(fitS, type="Pearson", clip=FALSE) 184s + plot(diagES, which="marks", plot.neg="imagecontour") 184s + plot(diagPS, which="marks", plot.neg="discrete") 184s + plot(diagPS, which="marks", plot.neg="contour") 184s + plot(diagPS, which="smooth", plot.smooth="image") 184s + plot(diagPS, which="smooth", plot.smooth="contour") 184s + plot(diagPS, which="smooth", plot.smooth="persp") 184s + 184s + #' infinite reach, not border-corrected 184s + fut <- ppm(cells ~ x, Softcore(0.5), correction="isotropic") 184s + diagnose.ppm(fut) 184s + 184s + #' 184s + diagPX <- diagnose.ppm(fit, type="Pearson", cumulative=FALSE) 184s + plot(diagPX, which="y") 184s + 184s + #' simulation based 184s + e <- envelope(cells, nsim=4, savepatterns=TRUE, savefuns=TRUE) 184s + Plist <- rpoispp(40, nsim=5) 184s + 184s + qf <- qqplot.ppm(fit, nsim=4, expr=e, plot.it=FALSE) 184s + print(qf) 184s + qp <- qqplot.ppm(fit, nsim=5, expr=Plist, fast=FALSE) 184s + print(qp) 184s + qp <- qqplot.ppm(fit, nsim=5, expr=expression(rpoispp(40)), plot.it=FALSE) 184s + print(qp) 184s + qg <- qqplot.ppm(fit, nsim=5, style="classical", plot.it=FALSE) 184s + print(qg) 184s + 184s + #' lurking.ppm 184s + #' covariate is numeric vector 184s + fitx <- ppm(cells ~ x) 184s + yvals <- coords(as.ppp(quad.ppm(fitx)))[,"y"] 184s + lurking(fitx, yvals) 184s + #' covariate is stored but is not used in model 184s + Z <- as.im(function(x,y){ x+y }, Window(cells)) 184s + fitxx <- ppm(cells ~ x, data=solist(Zed=Z), allcovar=TRUE) 184s + lurking(fitxx, expression(Zed)) 184s + #' envelope is a ppplist; length < nsim; glmdata=NULL 184s + fit <- ppm(cells ~ 1) 184s + stuff <- lurking(fit, expression(x), envelope=Plist, plot.sd=FALSE) 184s + #' plot.lurk 184s + plot(stuff, shade=NULL) 184s + }) 184s + } 184s > 184s > #' 184s > #' tests/deepeepee.R 184s > #' 184s > #' Tests for determinantal point process models 184s > #' 184s > #' $Revision: 1.9 $ $Date: 2022/04/24 09:14:46 $ 184s > 184s > local({ 184s + if(ALWAYS) { 184s + #' simulate.dppm 184s + jpines <- residualspaper$Fig1 184s + fit <- dppm(jpines ~ 1, dppGauss) 184s + set.seed(10981) 184s + simulate(fit, W=square(5)) 184s + } 184s + if(FULLTEST) { 184s + #' simulate.detpointprocfamily - code blocks 184s + model <- dppGauss(lambda=100, alpha=.05, d=2) 184s + simulate(model, seed=1999, correction="border") 184s + u <- is.stationary(model) 184s + #' other methods for dppm 184s + kay <- Kmodel(fit) 184s + gee <- pcfmodel(fit) 184s + lam <- intensity(fit) 184s + arr <- reach(fit) 184s + pah <- parameters(fit) 184s + #' a user bug report - matrix dimension error 184s + set.seed(256) 184s + dat <- simulate( dppGauss(lambda = 8.5, alpha = 0.1, d = 2), nsim = 1) 184s + } 184s + if(FULLTEST) { 184s + ## cover print.summary.dppm 184s + jpines <- japanesepines[c(TRUE,FALSE,FALSE,FALSE)] 184s + print(summary(dppm(jpines ~ 1, dppGauss))) 184s + print(summary(dppm(jpines ~ 1, dppGauss, method="c"))) 184s + print(summary(dppm(jpines ~ 1, dppGauss, method="p"))) 184s + print(summary(dppm(jpines ~ 1, dppGauss, method="a"))) 184s + } 184s + #' dppeigen code blocks 184s + if(ALWAYS) { 184s + mod <- dppMatern(lambda=2, alpha=0.01, nu=1, d=2) 184s + uT <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=TRUE) 184s + } 184s + if(FULLTEST) { 184s + uF <- dppeigen(mod, trunc=1.1, Wscale=c(1,1), stationary=FALSE) 184s + vT <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=TRUE) 184s + vF <- dppeigen(mod, trunc=0.98, Wscale=c(1,1), stationary=FALSE) 184s + } 184s + }) 185s > 185s BEGIN TEST testsEtoF.R 185s 185s R version 4.4.3 (2025-02-28) -- "Trophy Case" 185s Copyright (C) 2025 The R Foundation for Statistical Computing 185s Platform: arm-unknown-linux-gnueabihf (32-bit) 185s 185s R is free software and comes with ABSOLUTELY NO WARRANTY. 185s You are welcome to redistribute it under certain conditions. 185s Type 'license()' or 'licence()' for distribution details. 185s 185s R is a collaborative project with many contributors. 185s Type 'contributors()' for more information and 185s 'citation()' on how to cite R or R packages in publications. 185s 185s Type 'demo()' for some demos, 'help()' for on-line help, or 185s 'help.start()' for an HTML browser interface to help. 185s Type 'q()' to quit R. 185s 185s > #' 185s > #' Header for all (concatenated) test files 185s > #' 185s > #' Require spatstat.model 185s > #' Obtain environment variable controlling tests. 185s > #' 185s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 185s > 185s > require(spatstat.model) 185s Loading required package: spatstat.model 185s Loading required package: spatstat.data 186s Loading required package: spatstat.univar 186s spatstat.univar 3.1-2 186s Loading required package: spatstat.geom 186s spatstat.geom 3.3-6 186s Loading required package: spatstat.random 187s spatstat.random 3.3-3 187s Loading required package: spatstat.explore 187s Loading required package: nlme 187s spatstat.explore 3.3-4 187s Loading required package: rpart 187s spatstat.model 3.3-4 187s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 187s > ALWAYS <- TRUE 187s > cat(paste("--------- Executing", 187s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 187s + "test code -----------\n")) 187s --------- Executing **RESTRICTED** subset of test code ----------- 187s > # 187s > # tests/envelopes.R 187s > # 187s > # Test validity of envelope data 187s > # 187s > # $Revision: 1.29 $ $Date: 2024/01/10 13:45:29 $ 187s > # 187s > 187s > local({ 187s + 187s + 187s + checktheo <- function(fit) { 187s + fitname <- deparse(substitute(fit)) 187s + en <- envelope(fit, nsim=4, verbose=FALSE, nrep=1e3) 187s + nama <- names(en) 187s + expecttheo <- is.poisson(fit) && is.stationary(fit) 187s + context <- paste("Envelope of", fitname) 187s + if(expecttheo) { 187s + if(!("theo" %in% nama)) 187s + stop(paste(context, "did not contain", sQuote("theo"))) 187s + if("mmean" %in% nama) 187s + stop(paste(context, "unexpectedly contained", sQuote("mmean"))) 187s + } else { 187s + if("theo" %in% nama) 187s + stop(paste(context, "unexpectedly contained", sQuote("theo"))) 187s + if(!("mmean" %in% nama)) 187s + stop(paste(context, "did not contain", sQuote("mmean"))) 187s + } 187s + cat(paste(context, "has correct format\n")) 187s + } 187s + 187s + if(ALWAYS) { 187s + checktheo(ppm(cells ~x)) 187s + } 187s + if(FULLTEST) { 187s + checktheo(ppm(cells)) 187s + checktheo(ppm(cells ~1, Strauss(0.1))) 187s + } 187s + 187s + 187s + #' check savefuns/savepatterns with global 187s + fit <- ppm(cells~x) 187s + if(ALWAYS) Ef <- envelope(fit, Kest, nsim=4, savefuns=TRUE, global=TRUE) 187s + if(FULLTEST) Ep <- envelope(fit, Kest, nsim=4, savepatterns=TRUE, global=TRUE) 187s + #' check handling of 'dangerous' cases 187s + if(FULLTEST) { 187s + fut <- ppm(redwood ~ x) 187s + Ek <- envelope(fut, Kinhom, update=FALSE, nsim=4) 187s + kfut <- kppm(redwood3 ~ x) 187s + Ekk <- envelope(kfut, Kinhom, lambda=density(redwood3), nsim=7) 187s + } 187s + 187s + 187s + if(ALWAYS) { # invokes C code 187s + fit <- ppm(japanesepines ~ 1, Strauss(0.04)) 187s + e6 <- envelope(fit, Kest, nsim=4, fix.n=TRUE) 187s + fit2 <- ppm(amacrine ~ 1, Strauss(0.03)) 187s + e7 <- envelope(fit2, Gcross, nsim=4, fix.marks=TRUE) 187s + } 187s + 187s + 187s + if(FULLTEST) { 187s + fit <- ppm(cells ~ 1, Strauss(0.07)) 187s + U <- envelope(fit, nsim=3, simulate=expression(runifpoint(20))) 187s + kfit <- kppm(redwood3 ~ x) 187s + UU <- envelope(kfit, nsim=7, simulate=expression(simulate(kfit, drop=TRUE))) 187s + VV <- envelope(kfit, nsim=7, weights=1:7) 187s + MM <- envelope(kfit, nsim=7, Kinhom, lambda=density(redwood3)) 187s + } 187s + 187s + if(FULLTEST) { 187s + ## from Marcelino de la Cruz - scoping in update.ppm 187s + X <- cells 187s + Z <- density(X) 187s + pfit <- ppm(X ~ Z) 187s + cat("Fitted ppm(X~Z)", fill=TRUE) 187s + penv <- envelope(pfit, Kinhom, lambda=pfit, nsim=3) 187s + RX <- rotate(X, pi/3, centre="centroid") 187s + RZ <- density(RX) 187s + Rpfit <- ppm(RX ~ RZ) 187s + cat("Fitted ppm(RX~RZ)", fill=TRUE) 187s + Rpenv <- envelope(Rpfit, Kinhom, lambda=Rpfit, nsim=3) 187s + } 187s + 187s + if(FULLTEST) { 187s + #' envelope computations in other functions 187s + P <- lurking(cells, expression(x), envelope=TRUE, nsim=9) 187s + print(P) 187s + #' re-using envelope objects in other functions 187s + A <- envelope(cells, nsim=9, savepatterns=TRUE, savefuns=TRUE) 187s + S <- lurking(cells, expression(x), envelope=A, nsim=9) 187s + #' envelope.envelope 187s + B <- envelope(cells, nsim=5, savepatterns=TRUE, savefuns=FALSE) 187s + envelope(B) 187s + } 187s + 187s + 187s + 187s + ## close 'local' 187s + }) 187s Envelope of ppm(cells ~ x) has correct format 187s Generating 8 simulated realisations of fitted Poisson model (4 to estimate the 187s mean and 4 to calculate envelopes) ... 187s 1, 2, 3, 4, 5, 6, 7, 187s 8. 187s 187s Done. 187s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 187s points ... 187s 1, 2, 3, 187s 4. 187s 187s Done. 187s Generating 4 simulated realisations of fitted Gibbs model with fixed number of 187s points of each type ... 188s 1, 2, 3, 188s 4. 188s 188s Done. 188s > #' tests/enveltest.R 188s > #' Envelope tests (dclf.test, mad.test) 188s > #' and two-stage tests (bits.test, dg.test, bits.envelope, dg.envelope) 188s > #' 188s > #' $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 188s > #' 188s > if(FULLTEST) { 188s + local({ 188s + #' handling of NA function values (due to empty point patterns) 188s + set.seed(1234) 188s + X <- rThomas(5, 0.05, 10) 188s + fit <- kppm(X ~ 1, "Thomas") 188s + set.seed(100000) 188s + dclf.test(fit) 188s + set.seed(909) 188s + dg.test(fit, nsim=9) 188s + #' other code blocks 188s + dclf.test(fit, rinterval=c(0, 3), nsim=9) 188s + envelopeTest(X, exponent=3, clamp=TRUE, nsim=9) 188s + }) 188s + } 188s > # 188s > # tests/fastgeyer.R 188s > # 188s > # checks validity of fast C implementation of Geyer interaction 188s > # 188s > # $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 188s > # 188s > if(FULLTEST) { # depends on hardware 188s + local({ 188s + X <- redwood 188s + Q <- quadscheme(X) 188s + U <- union.quad(Q) 188s + EP <- equalpairs.quad(Q) 188s + G <- Geyer(0.11, 2) 188s + # The value r=0.11 is chosen to avoid hardware numerical effects (gcc bug 323). 188s + # It avoids being close any value of pairdist(redwood). 188s + # The nearest such values are 0.1077.. and 0.1131.. 188s + # By contrast if r = 0.1 there are values differing from 0.1 by 3e-17 188s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 188s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 188s + if(!all(a==b)) 188s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match") 188s + # ... 188s + # and again for a non-integer value of 'sat' 188s + # (spotted by Thordis Linda Thorarinsdottir) 188s + G <- Geyer(0.11, 2.5) 188s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 188s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 188s + if(!all(a==b)) 188s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat is not an integer") 188s + # and again for sat < 1 188s + # (spotted by Rolf) 188s + G <- Geyer(0.11, 0.5) 188s + a <- pairsat.family$eval(X,U,EP,G$pot,G$par,"border") 188s + b <- G$fasteval(X,U,EP,G$pot,G$par,"border") 188s + if(!all(a==b)) 188s + stop("Results of Geyer()$fasteval and pairsat.family$eval do not match when sat < 1") 188s + }) 188s + } 188s > 188s > #' tests/formuli.R 188s > #' 188s > #' Test machinery for manipulating formulae 188s > #' 188s > #' $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 188s > 188s > local({ 188s + 188s + ff <- function(A, deletevar, B) { 188s + D <- reduceformula(A, deletevar) 188s + if(!spatstat.utils::identical.formulae(D, B)) { 188s + AD <- as.expression(substitute(reduceformula(A,d), 188s + list(A=A, d=deletevar))) 188s + stop(paste(AD, "\n\tyields ", spatstat.utils::pasteFormula(D), 188s + " instead of ", spatstat.utils::pasteFormula(B)), 188s + call.=FALSE) 188s + } 188s + invisible(NULL) 188s + } 188s + 188s + ff(~ x + z, "x", ~z) 188s + 188s + ff(y ~ x + z, "x", y~z) 188s + 188s + ff(~ I(x^2) + z, "x", ~z) 188s The formula does not involve “g” and is therefore unchanged 188s Don't know how to reduce the term “sin(x - z)” 188s + 188s + ff(y ~ poly(x,2) + poly(z,3), "x", y ~poly(z,3)) 188s + 188s + ff(y ~ x + z, "g", y ~ x + z) 188s + 188s + reduceformula(y ~ x+z, "g", verbose=TRUE) 188s + reduceformula(y ~ sin(x-z), "z", verbose=TRUE) 188s + 188s + illegal.iformula(~str*g, itags="str", dfvarnames=c("marks", "g", "x", "y")) 188s + }) 188s NULL 188s > 188s > 188s > 188s > ## 188s > ## tests/funnymarks.R 188s > ## 188s > ## tests involving strange mark values 188s > ## $Revision: 1.7 $ $Date: 2020/04/28 12:58:26 $ 188s > 188s > if(ALWAYS) { # depends on locale 188s + local({ 188s + ## ppm() where mark levels contain illegal characters 188s + hyphenated <- c("a", "not-a") 188s + spaced <- c("U", "non U") 188s + suffixed <- c("a+", "a*") 188s + charred <- c("+", "*") 188s + 188s + irad <- matrix(0.1, 2,2) 188s + hrad <- matrix(0.005, 2, 2) 188s + 188s + tryit <- function(types, X, irad, hrad) { 188s + levels(marks(X)) <- types 188s + fit <- ppm(X ~marks + polynom(x,y,2), 188s + MultiStraussHard(types=types,iradii=irad,hradii=hrad)) 188s + print(fit) 188s + print(coef(fit)) 188s + val <- fitted(fit) 188s + pred <- predict(fit) 188s + return(invisible(NULL)) 188s + } 188s + 188s + tryit(hyphenated, amacrine, irad, hrad) 188s + tryit(spaced, amacrine, irad, hrad) 188s + tryit(suffixed, amacrine, irad, hrad) 188s + tryit(charred, amacrine, irad, hrad) 188s + 188s + ## marks which are dates 188s + X <- cells 188s + n <- npoints(X) 188s + endoftime <- rep(ISOdate(2001,1,1), n) 188s + eotDate <- rep(as.Date("2001-01-01"), n) 188s + markformat(endoftime) 188s + markformat(eotDate) 188s + marks(X) <- endoftime 188s + print(X) 188s + Y <- X %mark% data.frame(id=1:42, date=endoftime, dd=eotDate) 188s + print(Y) 188s + md <- markformat(endoftime) 188s + 188s + ## mark formats 188s + Z <- Y 188s + marks(Z) <- marks(Z)[1,,drop=FALSE] 188s + ms <- markformat(solist(cells, redwood)) 188s + marks(Z) <- factor(1:npoints(Z)) 188s + marks(Z)[12] <- NA 188s + mz <- is.multitype(Z) 188s + cZ <- coerce.marks.numeric(Z) 188s + marks(Z) <- data.frame(n=1:npoints(Z), 188s + a=factor(sample(letters, npoints(Z), replace=TRUE))) 188s + cZ <- coerce.marks.numeric(Z) 188s + stopifnot(is.multitype(cells %mark% data.frame(a=factor(1:npoints(cells))))) 188s + 188s + a <- numeric.columns(finpines) 188s + b1 <- numeric.columns(amacrine) 188s + b2 <- coerce.marks.numeric(amacrine) 188s + d <- numeric.columns(cells) 188s + f <- numeric.columns(longleaf) 188s + ff <- data.frame(a=factor(letters[1:10]), y=factor(sample(letters, 10))) 188s + numeric.columns(ff) 188s + 188s + ## mark operations 188s + df <- data.frame(x=1:2, y=sample(letters, 2)) 188s + h <- hyperframe(z=1:2, p=solist(cells, cells)) 188s + a <- NULL %mrep% 3 188s + a <- 1:4 %mrep% 3 188s + a <- df %mrep% 3 188s + a <- h %mrep% 3 188s + b <- markcbind(df, h) 188s + b <- markcbind(h, df) 188s + }) 188s + } 188s Nonstationary Multitype Strauss Hardcore process 188s Fitted to point pattern dataset ‘X’ 188s 188s Possible marks: ‘a’ and ‘not-a’ 188s 188s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 188s 188s Fitted trend coefficients: 188s (Intercept) marksnot-a x y I(x^2) I(x * y) 188s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 188s I(y^2) 188s -0.5425654 188s 188s 2 types of points 188s Possible types: 188s [1] a not-a 188s Interaction radii: 188s a not-a 188s a 0.1 0.1 188s not-a 0.1 0.1 188s Hardcore radii: 188s a not-a 188s a 0.005 0.005 188s not-a 0.005 0.005 188s Fitted interaction parameters gamma_ij 188s a not-a 188s a 0.2699920 0.8920719 188s not-a 0.8920719 0.2694374 188s 188s Relevant coefficients: 188s markaxa markaxnot.a marknot.axnot.a 188s -1.3093629 -0.1142086 -1.3114192 188s 188s For standard errors, type coef(summary(x)) 188s (Intercept) marksnot-a x y I(x^2) 188s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 188s I(x * y) I(y^2) markaxa markaxnot.a marknot.axnot.a 188s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 188s Nonstationary Multitype Strauss Hardcore process 188s Fitted to point pattern dataset ‘X’ 188s 188s Possible marks: ‘U’ and ‘non U’ 188s 188s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 188s 188s Fitted trend coefficients: 188s (Intercept) marksnon U x y I(x^2) I(x * y) 188s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 188s I(y^2) 188s -0.5425654 188s 189s 2 types of points 189s Possible types: 189s [1] U non U 189s Interaction radii: 189s U non U 189s U 0.1 0.1 189s non U 0.1 0.1 189s Hardcore radii: 189s U non U 189s U 0.005 0.005 189s non U 0.005 0.005 189s Fitted interaction parameters gamma_ij 189s U non U 189s U 0.2699920 0.8920719 189s non U 0.8920719 0.2694374 189s 189s Relevant coefficients: 189s markUxU markUxnon.U marknon.Uxnon.U 189s -1.3093629 -0.1142086 -1.3114192 189s 189s For standard errors, type coef(summary(x)) 189s (Intercept) marksnon U x y I(x^2) 189s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 189s I(x * y) I(y^2) markUxU markUxnon.U marknon.Uxnon.U 189s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 189s Nonstationary Multitype Strauss Hardcore process 189s Fitted to point pattern dataset ‘X’ 189s 189s Possible marks: ‘a+’ and ‘a*’ 189s 189s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 189s 189s Fitted trend coefficients: 189s (Intercept) marksa* x y I(x^2) I(x * y) 189s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 189s I(y^2) 189s -0.5425654 189s 189s 2 types of points 189s Possible types: 189s [1] a+ a* 189s Interaction radii: 189s a+ a* 189s a+ 0.1 0.1 189s a* 0.1 0.1 189s Hardcore radii: 189s a+ a* 189s a+ 0.005 0.005 189s a* 0.005 0.005 189s Fitted interaction parameters gamma_ij 189s a+ a* 189s a+ 0.2699920 0.8920719 189s a* 0.8920719 0.2694374 189s 189s Relevant coefficients: 189s marka.xa. marka.xa..1 marka..1xa..1 189s -1.3093629 -0.1142086 -1.3114192 189s 189s For standard errors, type coef(summary(x)) 189s (Intercept) marksa* x y I(x^2) 189s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 189s I(x * y) I(y^2) marka.xa. marka.xa..1 marka..1xa..1 189s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 189s Nonstationary Multitype Strauss Hardcore process 189s Fitted to point pattern dataset ‘X’ 189s 189s Possible marks: ‘+’ and ‘*’ 189s 189s Log trend: ~marks + (x + y + I(x^2) + I(x * y) + I(y^2)) 189s 189s Fitted trend coefficients: 189s (Intercept) marks* x y I(x^2) I(x * y) 189s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 0.3384324 189s I(y^2) 189s -0.5425654 189s 189s 2 types of points 189s Possible types: 189s [1] + * 189s Warning messages: 189s 1: In is.multitype.ppp(Z) : some mark values are NA in the point pattern Z 189s 2: Factor-valued marks were converted to integer codes 189s 3: Factor-valued mark variable ‘a’ was converted to integer codes 189s 4: Factor-valued marks were converted to integer codes 189s Interaction radii: 189s + * 189s + 0.1 0.1 189s * 0.1 0.1 189s Hardcore radii: 189s + * 189s + 0.005 0.005 189s * 0.005 0.005 189s Fitted interaction parameters gamma_ij 189s + * 189s + 0.2699920 0.8920719 189s * 0.8920719 0.2694374 189s 189s Relevant coefficients: 189s markX.xX. markX.xX..1 markX..1xX..1 189s -1.3093629 -0.1142086 -1.3114192 189s 189s For standard errors, type coef(summary(x)) 189s (Intercept) marks* x y I(x^2) 189s 7.3741600 0.1223023 1.2302865 0.2403500 -0.7560707 189s I(x * y) I(y^2) markX.xX. markX.xX..1 markX..1xX..1 189s 0.3384324 -0.5425654 -1.3093629 -0.1142086 -1.3114192 189s Marked planar point pattern: 42 points 189s marks are dates, of class ‘POSIXt’ 189s window: rectangle = [0, 1] x [0, 1] units 189s Marked planar point pattern: 42 points 189s Mark variables: id, date, dd 189s window: rectangle = [0, 1] x [0, 1] units 189s > 189s BEGIN TEST testsGtoJ.R 189s 189s R version 4.4.3 (2025-02-28) -- "Trophy Case" 189s Copyright (C) 2025 The R Foundation for Statistical Computing 189s Platform: arm-unknown-linux-gnueabihf (32-bit) 189s 189s R is free software and comes with ABSOLUTELY NO WARRANTY. 189s You are welcome to redistribute it under certain conditions. 189s Type 'license()' or 'licence()' for distribution details. 189s 189s R is a collaborative project with many contributors. 189s Type 'contributors()' for more information and 189s 'citation()' on how to cite R or R packages in publications. 189s 189s Type 'demo()' for some demos, 'help()' for on-line help, or 189s 'help.start()' for an HTML browser interface to help. 189s Type 'q()' to quit R. 189s 189s > #' 189s > #' Header for all (concatenated) test files 189s > #' 189s > #' Require spatstat.model 189s > #' Obtain environment variable controlling tests. 189s > #' 189s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 189s > 189s > require(spatstat.model) 189s Loading required package: spatstat.model 189s Loading required package: spatstat.data 190s Loading required package: spatstat.univar 190s spatstat.univar 3.1-2 190s Loading required package: spatstat.geom 190s spatstat.geom 3.3-6 190s Loading required package: spatstat.random 190s spatstat.random 3.3-3 190s Loading required package: spatstat.explore 190s Loading required package: nlme 190s spatstat.explore 3.3-4 190s Loading required package: rpart 191s spatstat.model 3.3-4 191s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 191s > ALWAYS <- TRUE 191s > cat(paste("--------- Executing", 191s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 191s + "test code -----------\n")) 191s --------- Executing **RESTRICTED** subset of test code ----------- 191s > #' 191s > #' tests/hobjects.R 191s > #' 191s > #' Validity of methods for ppm(... method="ho") 191s > #' 191s > #' $Revision: 1.4 $ $Date: 2022/06/18 10:14:44 $ 191s > 191s > 191s > if(FULLTEST) { 191s + local({ 191s + set.seed(42) 191s + fit <- ppm(cells ~1, Strauss(0.1), improve.type="ho", nsim=10) 191s + fitx <- ppm(cells ~offset(x), Strauss(0.1), improve.type="ho", nsim=10) 191s + 191s + a <- AIC(fit) 191s + ax <- AIC(fitx) 191s + 191s + f <- fitted(fit) 191s + fx <- fitted(fitx) 191s + 191s + p <- predict(fit) 191s + px <- predict(fitx) 191s + }) 191s + } 191s > 191s > 191s > #' tests/hypotests.R 191s > #' Hypothesis tests 191s > #' 191s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 191s > 191s > if(FULLTEST) { 191s + local({ 191s + 191s + #' scan test with baseline 191s + fit <- ppm(cells ~ x) 191s + lam <- predict(fit) 191s + rr <- c(0.05, 1) 191s + scan.test(cells, rr, nsim=5, 191s + method="poisson", baseline=fit, alternative="less") 191s + scan.test(cells, rr, nsim=5, 191s + method="poisson", baseline=lam, alternative="less") 191s + }) 191s + } 191s > #' 191s > #' tests/interact.R 191s > #' 191s > #' Support for interaction objects 191s > #' 191s > #' $Revision: 1.2 $ $Date: 2020/04/28 12:58:26 $ 191s > 191s > if(FULLTEST) { 191s + local({ 191s + #' print.intermaker 191s + Strauss 191s + Geyer 191s + Ord 191s + #' intermaker 191s + BS <- get("BlankStrauss", envir=environment(Strauss)) 191s + BD <- function(r) { instantiate.interact(BS, list(r=r)) } 191s + BlueDanube <- intermaker(BD, BS) 191s + }) 191s + } 191s > 191s > #' tests/ippm.R 191s > #' Tests of 'ippm' class 191s > #' $Revision: 1.6 $ $Date: 2020/04/28 12:58:26 $ 191s > 191s > if(FULLTEST) { 191s + local({ 191s + # .......... set up example from help file ................. 191s + nd <- 10 191s + gamma0 <- 3 191s + delta0 <- 5 191s + POW <- 3 191s + # Terms in intensity 191s + Z <- function(x,y) { -2*y } 191s + f <- function(x,y,gamma,delta) { 1 + exp(gamma - delta * x^POW) } 191s + # True intensity 191s + lamb <- function(x,y,gamma,delta) { 200 * exp(Z(x,y)) * f(x,y,gamma,delta) } 191s + # Simulate realisation 191s + lmax <- max(lamb(0,0,gamma0,delta0), lamb(1,1,gamma0,delta0)) 191s + set.seed(42) 191s + X <- rpoispp(lamb, lmax=lmax, win=owin(), gamma=gamma0, delta=delta0) 191s + # Partial derivatives of log f 191s + DlogfDgamma <- function(x,y, gamma, delta) { 191s + topbit <- exp(gamma - delta * x^POW) 191s + topbit/(1 + topbit) 191s + } 191s + DlogfDdelta <- function(x,y, gamma, delta) { 191s + topbit <- exp(gamma - delta * x^POW) 191s + - (x^POW) * topbit/(1 + topbit) 191s + } 191s + # irregular score 191s + Dlogf <- list(gamma=DlogfDgamma, delta=DlogfDdelta) 191s + # fit model 191s + fit <- ippm(X ~Z + offset(log(f)), 191s + covariates=list(Z=Z, f=f), 191s + iScore=Dlogf, 191s + start=list(gamma=1, delta=1), 191s + nd=nd) 191s + # fit model with logistic likelihood but without iScore 191s + fitlo <- ippm(X ~Z + offset(log(f)), 191s + method="logi", 191s + covariates=list(Z=Z, f=f), 191s + start=list(gamma=1, delta=1), 191s + nd=nd) 191s + 191s + ## ............. test ippm class support ...................... 191s + Ar <- model.matrix(fit) 191s + Ai <- model.matrix(fit, irregular=TRUE) 191s + An <- model.matrix(fit, irregular=TRUE, keepNA=FALSE) 191s + AS <- model.matrix(fit, irregular=TRUE, subset=(abs(Z) < 0.5)) 191s + 191s + Zr <- model.images(fit) 191s + Zi <- model.images(fit, irregular=TRUE) 191s + ## update.ippm 191s + fit2 <- update(fit, . ~ . + I(Z^2)) 191s + fit0 <- update(fit, 191s + . ~ . - Z, 191s + start=list(gamma=2, delta=4)) 191s + oldfit <- ippm(X, 191s + ~Z + offset(log(f)), 191s + covariates=list(Z=Z, f=f), 191s + iScore=Dlogf, 191s + start=list(gamma=1, delta=1), 191s + nd=nd) 191s + oldfit2 <- update(oldfit, . ~ . + I(Z^2)) 191s + oldfit0 <- update(oldfit, 191s + . ~ . - Z, 191s + start=list(gamma=2, delta=4)) 191s + ## again with logistic 191s + fitlo2 <- update(fitlo, . ~ . + I(Z^2)) 191s + fitlo0 <- update(fitlo, 191s + . ~ . - Z, 191s + start=list(gamma=2, delta=4)) 191s + oldfitlo <- ippm(X, 191s + ~Z + offset(log(f)), 191s + method="logi", 191s + covariates=list(Z=Z, f=f), 191s + start=list(gamma=1, delta=1), 191s + nd=nd) 191s + oldfitlo2 <- update(oldfitlo, . ~ . + I(Z^2)) 191s + oldfitlo0 <- update(oldfitlo, 191s + . ~ . - Z, 191s + start=list(gamma=2, delta=4)) 191s + ## anova.ppm including ippm objects 191s + fit0 <- update(fit, . ~ Z) 191s + fit0lo <- update(fitlo, . ~ Z) 191s + A <- anova(fit0, fit) 191s + Alo <- anova(fit0lo, fitlo) 191s + }) 191s + } 191s > 191s BEGIN TEST testsK.R 191s 191s R version 4.4.3 (2025-02-28) -- "Trophy Case" 191s Copyright (C) 2025 The R Foundation for Statistical Computing 191s Platform: arm-unknown-linux-gnueabihf (32-bit) 191s 191s R is free software and comes with ABSOLUTELY NO WARRANTY. 191s You are welcome to redistribute it under certain conditions. 191s Type 'license()' or 'licence()' for distribution details. 191s 191s R is a collaborative project with many contributors. 191s Type 'contributors()' for more information and 191s 'citation()' on how to cite R or R packages in publications. 191s 191s Type 'demo()' for some demos, 'help()' for on-line help, or 191s 'help.start()' for an HTML browser interface to help. 191s Type 'q()' to quit R. 191s 191s > #' 191s > #' Header for all (concatenated) test files 191s > #' 191s > #' Require spatstat.model 191s > #' Obtain environment variable controlling tests. 191s > #' 191s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 191s > 191s > require(spatstat.model) 191s Loading required package: spatstat.model 191s Loading required package: spatstat.data 192s Loading required package: spatstat.univar 192s spatstat.univar 3.1-2 192s Loading required package: spatstat.geom 192s spatstat.geom 3.3-6 192s Loading required package: spatstat.random 192s spatstat.random 3.3-3 192s Loading required package: spatstat.explore 192s Loading required package: nlme 192s spatstat.explore 3.3-4 192s Loading required package: rpart 192s spatstat.model 3.3-4 192s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 192s > ALWAYS <- TRUE 192s > cat(paste("--------- Executing", 192s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 192s + "test code -----------\n")) 192s --------- Executing **RESTRICTED** subset of test code ----------- 192s > # 192s > # tests/kppm.R 192s > # 192s > # $Revision: 1.40 $ $Date: 2024/02/26 05:44:02 $ 192s > # 192s > # Test functionality of kppm that once depended on RandomFields 192s > # Test update.kppm for old style kppm objects 192s > 192s > if(!FULLTEST) 192s + spatstat.options(npixel=32, ndummy.min=16) 192s > 192s > local({ 192s + 192s + fit <- kppm(redwood ~1, "Thomas") # sic 192s + fitx <- kppm(redwood ~x, "Thomas", verbose=TRUE) 192s + if(FULLTEST) { 192s + fitx <- update(fit, ~ . + x) 192s + fitM <- update(fit, clusters="MatClust") 192s + fitC <- update(fit, cells) 192s + fitCx <- update(fit, cells ~ x) 192s + #' 192s + Wsub <- owin(c(0, 0.5), c(-0.5, 0)) 192s + Zsub <- (bdist.pixels(Window(redwood)) > 0.1) 192s + fitWsub <- kppm(redwood ~1, "Thomas", subset=Wsub) 192s + fitZsub <- kppm(redwood ~1, "Thomas", subset=Zsub) 192s + fitWsub 192s + 192s + #' various methods 192s + ff <- as.fv(fitx) 192s + uu <- unitname(fitx) 192s + unitname(fitCx) <- "furlong" 192s + mo <- model.images(fitCx) 192s + p <- psib(fit) 192s + px <- psib(fitx) 192s + } 192s + if(ALWAYS) { 192s + Y <- simulate(fitx, seed=42, saveLambda=TRUE)[[1]] 192s + } 192s + 192s + if(FULLTEST) { 192s + #' vcov.kppm different algorithms 192s + vc <- vcov(fitx) 192s + vc2 <- vcov(fitx, fast=TRUE) 192s + vc3 <- vcov(fitx, fast=TRUE, splitup=TRUE) 192s + vc4 <- vcov(fitx, splitup=TRUE) 192s + 192s + ## other code blocks 192s + a <- varcount(fitx, function(x,y){x+1}) # always positive 192s + a <- varcount(fitx, function(x,y){y-1}) # always negative 192s + a <- varcount(fitx, function(x,y){x+y}) # positive or negative 192s + 192s + #' improve.kppm 192s + fitI <- update(fit, improve.type="quasi") 192s + fitxI <- update(fitx, improve.type="quasi") 192s + fitxIs <- update(fitx, improve.type="quasi", fast=FALSE) 192s + #' vcov.kppm 192s + vcI <- vcov(fitxI) 192s + } 192s + 192s + ## plot.kppm including predict.kppm 192s + if(ALWAYS) { 192s + fitMC <- kppm(redwood ~ x, "Thomas") 192s + plot(fitMC) 192s + } 192s + if(FULLTEST) { 192s + fitCL <- kppm(redwood ~ x, "Thomas", method="c") 192s + fitPA <- kppm(redwood ~ x, "Thomas", method="p") 192s + plot(fitCL) 192s + plot(fitPA) 192s + 192s + ## fit with composite likelihood method [thanks to Abdollah Jalilian] 192s + fut <- kppm(redwood ~ x, "VarGamma", method="clik2", nu.ker=-3/8) 192s + kfut <- as.fv(fut) 192s + } 192s + 192s + if(ALWAYS) { 192s + fit0 <- kppm(redwood ~1, "LGCP") 192s + is.poisson(fit0) 192s + Y0 <- simulate(fit0, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y0)) 192s + p0 <- psib(fit0) # issues a warning 192s + 192s + if(FULLTEST) { 192s + ## fit LGCP using K function: slow 192s + fit1 <- kppm(redwood ~x, "LGCP", 192s + covmodel=list(model="matern", nu=0.3), 192s + control=list(maxit=3)) 192s + Y1 <- simulate(fit1, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y1)) 192s + } 192s + 192s + ## fit LGCP using pcf 192s + fit1p <- kppm(redwood ~x, "LGCP", 192s + covmodel=list(model="matern", nu=0.3), 192s + statistic="pcf") 192s + Y1p <- simulate(fit1p, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y1p)) 192s + 192s + ## .. and using different fitting methods 192s + if(FULLTEST) { 192s + fit1pClik <- update(fit1p, method="clik") 192s + fit1pPalm <- update(fit1p, method="palm") 192s + } 192s + 192s + ## shortcut evaluation of pcf 192s + ## (the code being tested is in spatstat.random::clusterinfo.R) 192s + if(FULLTEST) { 192s + putSpatstatVariable("RFshortcut", TRUE) 192s + fitGshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 192s + fitSshort <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 192s + putSpatstatVariable("RFshortcut", FALSE) 192s + fitGlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="gauss")) 192s + fitSlong <- kppm(redwood ~ 1, "LGCP", covmodel=list(model="stable", alpha=1)) 192s + discrepG <- unlist(parameters(fitGshort)) - unlist(parameters(fitGlong)) 192s + discrepS <- unlist(parameters(fitSshort)) - unlist(parameters(fitSlong)) 192s + print(discrepG) 192s + print(discrepS) 192s + if(max(abs(discrepG) > 0.01)) 192s + stop("Discrepancy in short-cut fitting of Gaussian LGCP") 192s + if(max(abs(discrepS) > 0.01)) 192s + stop("Discrepancy in short-cut fitting of stable LGCP") 192s + } 192s + 192s + ## image covariate (a different code block) 192s + xx <- as.im(function(x,y) x, Window(redwood)) 192s + fit1xx <- update(fit1p, . ~ xx, data=solist(xx=xx)) 192s + Y1xx <- simulate(fit1xx, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y1xx)) 192s + if(FULLTEST) { 192s + fit1xxVG <- update(fit1xx, clusters="VarGamma", nu=-1/4) 192s + Y1xxVG <- simulate(fit1xxVG, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y1xxVG)) 192s + } 192s + fit1xxLG <- update(fit1xx, clusters="LGCP", 192s + covmodel=list(model="matern", nu=0.3), 192s + statistic="pcf") 192s + Y1xxLG <- simulate(fit1xxLG, saveLambda=TRUE, drop=TRUE) 192s + stopifnot(is.ppp(Y1xxLG)) 192s + 192s + # ... and Abdollah's code 192s + if(FULLTEST) { 192s + fit2 <- kppm(redwood ~x, cluster="Cauchy", statistic="K") 192s + Y2 <- simulate(fit2, saveLambda=TRUE)[[1]] 192s + stopifnot(is.ppp(Y2)) 192s + } 192s + } 192s + 192s + }) 192s Fitting cluster model 192s Retrieved cluster model information 192s Algorithm parameters: 192s $rmax 192s NULL 192s 192s $q 192s [1] 0.25 192s 192s $p 192s [1] 2 192s 192s $rmin 192s NULL 192s 192s Using point pattern data 192s Starting parameters: 192s kappa sigma2 192s 62.000000000 0.006173033 192s Calculating summary function...Done. 192s Starting minimum contrast fit 192s Returned from minimum contrast fit 192s Returning from clusterfit 194s Warning messages: 194s 1: Internal error: fvlabels truncated the function name 194s 2: Internal error: fvlabels truncated the function name 194s 3: Internal error: fvlabels truncated the function name 194s 4: In psib.kppm(fit0) : The model is not a cluster process 194s 5: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 194s 6: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 194s 7: The value of the empirical function ‘pcf’ for r= 0 was Inf. Range of r values was reset to [0.00048828125, 0.25] 194s > 194s > if(FULLTEST) { 194s + local({ 194s + #' various code blocks 194s + fut <- kppm(redwood, ~x) 194s + fet <- update(fut, redwood3) 194s + fot <- update(fut, trend=~y) 194s + fit <- kppm(redwoodfull ~ x) 194s + Y <- simulate(fit, window=redwoodfull.extra$regionII, saveLambda=TRUE) 194s + gut <- improve.kppm(fit, type="wclik1") 194s + gut <- improve.kppm(fit, vcov=TRUE, fast.vcov=TRUE, save.internals=TRUE) 194s + hut <- kppm(redwood ~ x, method="clik", weightfun=NULL) 194s + hut <- kppm(redwood ~ x, method="palm", weightfun=NULL) 194s + mut <- kppm(redwood) 194s + nut <- update(mut, Y) 194s + }) 194s + } 194s > 194s > if(FULLTEST) { 194s + local({ 194s + #' minimum contrast code 194s + K <- Kest(redwood) 194s + a <- matclust.estK(K) 194s + a <- thomas.estK(K) 194s + a <- cauchy.estK(K) 194s + a <- vargamma.estK(K) 194s + a <- lgcp.estK(K) 194s + 194s + print(a) 194s + u <- unitname(a) 194s + 194s + g <- pcf(redwood) 194s + a <- matclust.estpcf(g) 194s + a <- thomas.estpcf(g) 194s + a <- cauchy.estpcf(g) 194s + a <- vargamma.estpcf(g) 194s + a <- lgcp.estpcf(g) 194s + 194s + #' auxiliary functions 194s + b <- resolve.vargamma.shape(nu.pcf=1.5) 194s + Z <- clusterfield("Thomas", kappa=1, scale=0.2) 194s + 194s + aa <- NULL 194s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 194s + aa <- accumulateStatus(simpleMessage("Sit"), aa) 194s + aa <- accumulateStatus(simpleMessage("Woof"), aa) 194s + printStatusList(aa) 194s + 194s + RMIN <- 0.01 194s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=RMIN,q=1/2)) 194s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 194s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl' ") 194s + fit <- kppm(redwood ~ 1, ctrl=list(rmin=0,q=1/2), rmin=RMIN) 194s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 194s + stop("kppm did not handle parameter 'rmin' in argument 'ctrl'") 194s + 194s + RMIN <- 2 194s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=RMIN,q=1)) 194s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 194s + stop("dppm did not handle parameter 'rmin' in argument 'ctrl'") 194s + fit <- dppm(swedishpines~1, dppGauss(), ctrl=list(rmin=0,q=1), rmin=RMIN) 194s + if(fit$Fit$mcfit$ctrl$rmin != RMIN) 194s + stop("dppm did not handle argument 'rmin'") 194s + }) 194s + } 194s > 194s > 194s > 194s > if(FULLTEST) { 194s + local({ 194s + #' cover a few code blocks 194s + fut <- kppm(redwood ~ x, method="clik") 194s + print(summary(fut)) 194s + a <- residuals(fut) 194s + fut2 <- kppm(redwood ~ x, "LGCP", method="palm") 194s + print(summary(fut2)) 194s + b <- residuals(fut2) 194s + #' 194s + po <- ppm(redwood ~ 1) 194s + A <- kppmComLik(redwood, Xname="redwood", po=po, clusters="Thomas", 194s + statistic="pcf", statargs=list(), control=list(), 194s + weightfun=NULL, rmax=0.1) 194s + A <- kppmPalmLik(redwood, Xname="redwood", po=po, clusters="Thomas", 194s + statistic="pcf", statargs=list(), control=list(), 194s + weightfun=NULL, rmax=0.1) 194s + }) 194s + } 194s > 194s > reset.spatstat.options() 194s > 194s > #' 194s > #' tests/Kfuns.R 194s > #' 194s > #' Various K and L functions and pcf 194s > #' 194s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 194s > #' 194s > #' Assumes 'EveryStart.R' was run 194s > 194s > if(FULLTEST) { 194s + Cells <- cells 194s + Amacrine <- amacrine 194s + Redwood <- redwood 194s + } else { 194s + ## reduce numbers of data + dummy points 194s + spatstat.options(npixel=32, ndummy.min=16) 194s + Cells <- cells[c(FALSE, TRUE)] 194s + Amacrine <- amacrine[c(FALSE, TRUE)] 194s + Redwood <- redwood[c(FALSE, TRUE)] 194s + } 194s > 194s > 194s > if(FULLTEST) { 194s + local({ 194s + #' code blocks using fitted model to determine intensity 194s + #' Kinhom 194s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 194s + fut <- ppm(X ~ x) 194s + Kio <- Kinhom(X, fut, update=FALSE) 194s + Kiu <- Kinhom(X, fut, update=TRUE, diagonal=FALSE) 194s + fit <- ppm(Amacrine ~ marks) 194s + #' lohboot Linhom 194s + Zred <- predict(ppm(Redwood ~ x+y)) 194s + Lred <- lohboot(Redwood, Linhom, lambda=Zred) 194s + #' Kmulti.inhom 194s + K1 <- Kcross.inhom(Amacrine, lambdaX=fit) 194s + On <- split(Amacrine)$on 194s + Off <- split(Amacrine)$off 194s + K4 <- Kcross.inhom(Amacrine, lambdaI=ppm(On), lambdaJ=ppm(Off)) 194s + #' local K functions 194s + fut <- ppm(swedishpines ~ polynom(x,y,2)) 194s + Z <- predict(fut) 194s + Lam <- fitted(fut, dataonly=TRUE) 194s + a <- localLinhom(swedishpines, lambda=fut) 194s + a <- localLinhom(swedishpines, lambda=Z) 194s + a <- localLinhom(swedishpines, lambda=Lam) 194s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 194s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 194s + #' local cross K functions 194s + fat <- ppm(Amacrine ~ x * marks) 194s + Zed <- predict(fat) 194s + Lum <- fitted(fat, dataonly=TRUE) 194s + moff <- (marks(Amacrine) == "off") 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=fat) 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", 194s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 194s + correction="none") 194s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 194s + correction="translate") 194s + #' cases of resolve.lambdacross 194s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat) 194s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=fat, update=FALSE) 194s + h <- resolve.lambdacross(Amacrine, moff, !moff, 194s + lambdaI=fat, lambdaJ=fat) 194s + h <- resolve.lambdacross(Amacrine, moff, !moff, 194s + lambdaI=fat, lambdaJ=fat, 194s + update=FALSE) 194s + #' lohboot 194s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Zed) 194s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=Lum) 194s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", lambdaX=fat) 194s + b <- lohboot(Amacrine, Lcross.inhom, from="off", to="on", 194s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 194s + #' 194s + #' residual K functions etc 194s + #' 194s + rco <- compareFit(Cells, Kcom, 194s + interaction=anylist(P=Poisson(), S=Strauss(0.08)), 194s + same="trans", different="tcom") 194s + fit <- ppm(Cells ~ x, Strauss(0.07)) 194s + K <- Kcom(Cells, model=fit, restrict=TRUE) 194s + }) 194s + } 194s > 194s > reset.spatstat.options() 194s > 194s BEGIN TEST testsL.R 194s 194s R version 4.4.3 (2025-02-28) -- "Trophy Case" 194s Copyright (C) 2025 The R Foundation for Statistical Computing 194s Platform: arm-unknown-linux-gnueabihf (32-bit) 194s 194s R is free software and comes with ABSOLUTELY NO WARRANTY. 194s You are welcome to redistribute it under certain conditions. 194s Type 'license()' or 'licence()' for distribution details. 194s 194s R is a collaborative project with many contributors. 194s Type 'contributors()' for more information and 194s 'citation()' on how to cite R or R packages in publications. 194s 194s Type 'demo()' for some demos, 'help()' for on-line help, or 194s 'help.start()' for an HTML browser interface to help. 194s Type 'q()' to quit R. 194s 194s > #' 194s > #' Header for all (concatenated) test files 194s > #' 194s > #' Require spatstat.model 194s > #' Obtain environment variable controlling tests. 194s > #' 194s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 194s > 194s > require(spatstat.model) 194s Loading required package: spatstat.model 194s Loading required package: spatstat.data 195s Loading required package: spatstat.univar 195s spatstat.univar 3.1-2 195s Loading required package: spatstat.geom 195s spatstat.geom 3.3-6 195s Loading required package: spatstat.random 195s spatstat.random 3.3-3 195s Loading required package: spatstat.explore 195s Loading required package: nlme 195s spatstat.explore 3.3-4 195s Loading required package: rpart 195s spatstat.model 3.3-4 195s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 195s > ALWAYS <- TRUE 195s > cat(paste("--------- Executing", 195s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 195s + "test code -----------\n")) 195s --------- Executing **RESTRICTED** subset of test code ----------- 195s > ## 195s > ## tests/legacy.R 195s > ## 195s > ## Test that current version of spatstat is compatible with outmoded usage 195s > ## $Revision: 1.3 $ $Date: 2020/04/29 08:55:17 $ 195s > 195s > if(FULLTEST) { 195s + local({ 195s + 195s + ## (1) Old syntax of ppm 195s + ppm(cells, ~x) 195s + 195s + ## (2) Old syntax of MultiStrauss etc. 195s + r <- matrix(3, 2, 2) 195s + a <- MultiStrauss( , r) 195s + a <- MultiStrauss(NULL, r) 195s + a <- MultiHard(, r) 195s + 195s + h <- r/2 195s + a <- MultiStraussHard( , r, h) 195s + 195s + NULL 195s + }) 195s + } 195s > #' 195s > #' tests/leverinf.R 195s > #' 195s > #' leverage and influence for Gibbs models 195s > #' 195s > #' $Revision: 1.35 $ $Date: 2022/06/18 10:15:17 $ 195s > #' 195s > 195s > if(FULLTEST) { 195s + Cells <- cells 195s + Amacrine <- amacrine 195s + Redwood <- redwood 195s + } else { 195s + ## reduce number of data + dummy points 195s + spatstat.options(npixel=32, ndummy.min=16) 195s + Cells <- cells[c(FALSE,TRUE)] 195s + Redwood <- redwood[c(FALSE, TRUE)] 195s + Amacrine <- amacrine[c(FALSE, TRUE)] 195s + } 195s > 195s > local({ 195s + cat("Running non-sparse algorithm...", fill=TRUE) 195s + # original non-sparse algorithm 195s + Leverage <- function(...) leverage(..., sparseOK=FALSE) 195s + Influence <- function(...) influence(..., sparseOK=FALSE) 195s + Dfbetas <- function(...) dfbetas(..., sparseOK=FALSE) 195s + if(ALWAYS) { 195s + ## Strauss()$delta2 195s + fitS <- ppm(Cells ~ x, Strauss(0.12), rbord=0) 195s + levS <- Leverage(fitS) 195s + infS <- Influence(fitS) 195s + dfbS <- Dfbetas(fitS) 195s + ## Geyer()$delta2 195s + fitG <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0) 195s + levG <- Leverage(fitG) 195s + infG <- Influence(fitG) 195s + ## AreaInter()$delta2 195s + fitA <- ppm(Cells ~ 1, AreaInter(0.06), rbord=0, nd=11) 195s + levA <- Leverage(fitA) 195s + infA <- Influence(fitA) 195s + ## pairwise.family$delta2 195s + fitD <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), rbord=0) 195s + levD <- Leverage(fitD) 195s + infD <- Influence(fitD) 195s + ## DiggleGratton() special code 195s + fitDG <- ppm(Cells ~ 1, DiggleGratton(0.05, 0.12), rbord=0) 195s + levDG <- Leverage(fitDG) 195s + infDG <- Influence(fitDG) 195s + ## ppmInfluence; offset is present; coefficient vector has length 0 195s + fitH <- ppm(Cells ~ 1, Hardcore(0.07)) 195s + levH <- Leverage(fitH) 195s + infH <- Influence(fitH) 195s + ## ppmInfluence; hard core 195s + fitSH <- ppm(Cells ~ 1, StraussHard(0.07, 0.01)) 195s + levSH <- Leverage(fitSH) 195s + infSH <- Influence(fitSH) 195s + ## ppmInfluence; offset is present; coefficient vector has length 1 195s + fitHx <- ppm(Cells ~ x, Hardcore(0.07), rbord=0) 195s + levHx <- Leverage(fitHx) 195s + infHx <- Influence(fitHx) 195s + ## multitype 195s + futAm <- ppm(Amacrine ~ x + marks, Strauss(0.07)) 195s + levAm <- leverage(futAm) 195s + } 195s + 195s + if(FULLTEST) { 195s + ## ......... class support ............................. 195s + ## other methods for classes leverage.ppm and influence.ppm 195s + ## not elsewhere tested 195s + cat("Testing class support...", fill=TRUE) 195s + w <- domain(levS) 195s + w <- Window(infS) 195s + vv <- shift(levS, c(1.2, 1.3)) 195s + vv <- shift(infS, c(1.2, 1.3)) 195s + A <- quadrats(Window(Cells), 2) 195s + a <- integral(levS,domain=A) 195s + b <- integral(infS,domain=A) 195s + u <- Smooth(levS, sigma=0.07) 195s + v <- Smooth(infS, sigma=0.1) 195s + ## plot options 195s + plot(levS, what="exact") 195s + plot(levS, what="nearest") 195s + contour(levS, what="nearest") 195s + persp(levS, what="nearest") 195s + ## plotting for multitype models 195s + plot(levAm) 195s + contour(levAm) 195s + persp(levAm) 195s + plot(levAm, multiplot=FALSE) 195s + contour(levAm, multiplot=FALSE) 195s + } 195s + 195s + if(ALWAYS) { 195s + ## .......... compare algorithms ......................... 195s + ## divide and recombine algorithm 195s + cat("Reduce maximum block side to 50,000 ...", fill=TRUE) 195s + op <- spatstat.options(maxmatrix=50000) 195s + ## non-sparse 195s + levSB <- Leverage(fitS) 195s + infSB <- Influence(fitS) 195s + dfbSB <- Dfbetas(fitS) 195s + } 195s + 195s + chk <- function(x, y, what, 195s + from="single-block and multi-block", 195s + thresh=1e-12) { 195s + if(max(abs(x-y)) > thresh) 195s + stop(paste("Different results for", what, "obtained from", 195s + from, "algorithms"), 195s + call.=FALSE) 195s + invisible(NULL) 195s + } 195s + 195s + if(ALWAYS) { 195s + cat("Compare single-block to multi-block...", fill=TRUE) 195s + chk(marks(as.ppp(infS)), marks(as.ppp(infSB)), "influence") 195s + chk(as.im(levS), as.im(levSB), "leverage") 195s + chk(dfbS$val, dfbSB$val, "dfbetas$value") 195s + chk(dfbS$density, dfbSB$density, "dfbetas$density") 195s + } 195s + 195s + if(FULLTEST) { 195s + ## also check case of zero cif 195s + cat("Check zero cif cases...", fill=TRUE) 195s + levHB <- Leverage(fitH) 195s + infHB <- Influence(fitH) 195s + dfbHB <- Dfbetas(fitH) 195s + levHxB <- Leverage(fitHx) 195s + infHxB <- Influence(fitHx) 195s + dfbHxB <- Dfbetas(fitHx) 195s + } 195s + 195s + ## run all code segments 195s + Everything <- function(model, ...) { ppmInfluence(model, ..., what="all") } 195s + 195s + if(FULLTEST) { 195s + cat("Run full code on AreaInteraction model...", fill=TRUE) 195s + pmiA <- Everything(fitA) 195s + 195s + ## sparse algorithm, with blocks 195s + cat("Run sparse algorithm with blocks...", fill=TRUE) 195s + pmiSSB <- Everything(fitS, sparseOK=TRUE) 195s + ## also check case of zero cif 195s + pmiHSB <- Everything(fitH, sparseOK=TRUE) 195s + pmiSHSB <- Everything(fitSH, sparseOK=TRUE) 195s + pmiHxSB <- Everything(fitHx, sparseOK=TRUE) 195s + 195s + cat("Reinstate maxmatrix...", fill=TRUE) 195s + spatstat.options(op) 195s + } 195s + 195s + if(ALWAYS) { 195s + ## sparse algorithm, no blocks 195s + cat("Compare sparse and non-sparse results...", fill=TRUE) 195s + pmi <- Everything(fitS, sparseOK=TRUE) 195s + levSp <- pmi$leverage 195s + infSp <- pmi$influence 195s + dfbSp <- pmi$dfbetas 195s + chks <- function(...) chk(..., from="sparse and non-sparse") 195s + 195s + chks(marks(as.ppp(infS)), marks(as.ppp(infSp)), "influence") 195s + chks(as.im(levS), as.im(levSp), "leverage") 195s + chks(dfbS$val, dfbSp$val, "dfbetas$value") 195s + chks(dfbS$density, dfbSp$density, "dfbetas$density") 195s + } 195s + 195s + if(ALWAYS) { 195s + #' case of zero cif 195s + cat("zero cif...", fill=TRUE) 195s + pmiH <- Everything(fitH, sparseOK=TRUE) 195s + pmiSH <- Everything(fitSH, sparseOK=TRUE) 195s + pmiHx <- Everything(fitHx, sparseOK=TRUE) 195s + } 195s + if(FULLTEST) { 195s + #' other code blocks - check execution only 195s + cat("other code blocks...", fill=TRUE) 195s + a <- Everything(fitS) 195s + a <- Everything(fitS, method="interpreted") 195s + a <- Everything(fitS, method="interpreted", entrywise=FALSE) 195s + a <- Everything(fitS, entrywise=FALSE) 195s + #' zero cif 195s + b <- Everything(fitSH) 195s + b <- Everything(fitSH, method="interpreted") 195s + b <- Everything(fitSH, method="interpreted", entrywise=FALSE) 195s + b <- Everything(fitSH, entrywise=FALSE) 195s + } 195s + #' NOTE: code for irregular parameters is tested below, and in 'make bookcheck' 195s + 195s + ## ........... logistic fits ....................... 195s + cat("Logistic fits...", fill=TRUE) 195s + #' special algorithm for delta2 195s + fitSlogi <- ppm(Cells ~ x, Strauss(0.12), rbord=0, method="logi") 195s + 195s + if(FULLTEST) { 195s + pmiSlogi <- Everything(fitSlogi) 195s + #' special algorithm for delta2 195s + fitGlogi <- ppm(Redwood ~ 1, Geyer(0.1, 2), rbord=0, method="logi") 195s + pmiGlogi <- Everything(fitGlogi) 195s + #' generic algorithm for delta2 195s + fitDlogi <- ppm(Cells ~ 1, DiggleGatesStibbard(0.12), 195s + rbord=0, method="logi") 195s + pmiDlogi <- Everything(fitDlogi) 195s + #' generic algorithm for delta2 : offset; zero-dimensional 195s + fitHlogi <- ppm(Cells ~ 1, Hardcore(0.07), method="logi") 195s + pmiHlogi <- Everything(fitHlogi) 195s + #' generic algorithm for delta2 : offset; 1-dimensional 195s + fitHxlogi <- ppm(Cells ~ x, Hardcore(0.07), rbord=0, method="logi") 195s + pmiHxlogi <- Everything(fitHxlogi) 195s + #' plotting 195s + plot(leverage(fitSlogi)) 195s + plot(influence(fitSlogi)) 195s + plot(dfbetas(fitSlogi)) 195s + } 195s + 195s + if(ALWAYS) { 195s + #' other code blocks - check execution only 195s + cat("Other code blocks...", fill=TRUE) 195s + b <- Everything(fitSlogi) # i.e. full set of results 195s + b <- Everything(fitSlogi, method="interpreted") 195s + b <- Everything(fitSlogi, method="interpreted", entrywise=FALSE) 195s + b <- Everything(fitSlogi, entrywise=FALSE) 195s + } 195s + 195s + #' irregular parameters 195s + cat("Irregular parameters...", fill=TRUE) 195s + ytoa <- function(x,y, alpha=1) { y^alpha } 195s + lam <- function(x,y,alpha=1) { exp(4 + y^alpha) } 195s + set.seed(90210) 195s + X <- rpoispp(lam, alpha=2) 195s + iScor <- list(alpha=function(x,y,alpha) { alpha * y^(alpha-1) } ) 195s + iHess <- list(alpha=function(x,y,alpha) { alpha * (alpha-1) * y^(alpha-2) } ) 195s + gogo <- function(tag, ..., iS=iScor, iH=iHess) { 195s + cat(tag, fill=TRUE) 195s + #' compute all leverage+influence terms 195s + ppmInfluence(..., what="all", iScore=iS, iHessian=iH) 195s + } 195s + gogogo <- function(hdr, fit) { 195s + cat(hdr, fill=TRUE) 195s + force(fit) 195s + #' try all code options 195s + d <- gogo("a", fit) 195s + d <- gogo("b", fit, method="interpreted") 195s + d <- gogo("c", fit, method="interpreted", entrywise=FALSE) 195s + d <- gogo("d", fit, entrywise=FALSE) 195s + invisible(NULL) 195s + } 195s + gogogo("Offset model...", 195s + ippm(X ~ offset(ytoa), start=list(alpha=1), iterlim=40)) 195s + gogogo("Offset model (logistic) ...", 195s + ippm(X ~ offset(ytoa), start=list(alpha=1), 195s + method="logi", iterlim=40)) 195s + gogogo("Offset+x model...", 195s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), iterlim=40)) 195s + gogogo("Offset+x model (logistic) ...", 195s + ippm(X ~ x + offset(ytoa), start=list(alpha=1), 195s + method="logi", iterlim=40)) 195s + gogogo("Offset model Strauss ...", 195s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), iterlim=40)) 195s + gogogo("Offset model Strauss (logistic) ...", 195s + ippm(X ~ offset(ytoa), Strauss(0.07), start=list(alpha=1), 195s + method="logi", iterlim=40)) 195s + if(FULLTEST) { 195s + gogogo("Offset+x model Strauss ...", 195s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 195s + iterlim=40)) 195s + gogogo("Offset+x model Strauss (logistic)...", 195s + ippm(X ~ x + offset(ytoa), Strauss(0.07), start=list(alpha=1), 195s + method="logi", iterlim=40)) 195s + } 195s + #' 195s + if(FULLTEST) { 195s + set.seed(452) 195s + foo <- ppm(Cells ~ 1, Strauss(0.15), improve.type="ho", nsim=5) 195s + aa <- Everything(foo) 195s + 195s + #' Gradient and Hessian obtained by symbolic differentiation 195s + f <- deriv(expression((1+x)^a), 195s + "a", function.arg=c("x", "y", "a"), 195s + hessian=TRUE) 195s + #' check they can be extracted 195s + fit <- ippm(Cells ~offset(f), start=list(a=0.7)) 195s + Everything(fit) 195s + } 195s + }) 195s Running non-sparse algorithm... 203s Reduce maximum block side to 50,000 ... 204s Compare single-block to multi-block... 204s Compare sparse and non-sparse results... 205s zero cif... 207s Logistic fits... 207s Other code blocks... 211s Irregular parameters... 211s Offset model... 211s a 211s b 212s c 212s d 213s Offset model (logistic) ... 213s a 214s b 215s c 215s d 216s Offset+x model... 216s a 217s b 217s c 218s d 219s Offset+x model (logistic) ... 219s a 220s b 220s c 221s d 222s Offset model Strauss ... 222s a 222s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 223s b 223s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 223s c 223s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 224s d 224s Large quadrature scheme split into blocks to avoid memory size limits; 404 dummy points split into 2 blocks, each containing 202 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 225s Offset model Strauss (logistic) ... 226s a 226s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 227s b 227s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 227s c 227s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 228s d 228s Large quadrature scheme split into blocks to avoid memory size limits; 400 dummy points split into 2 blocks, each containing 200 dummy points. Consider increasing the matrix size limit spatstat.options('maxmatrix') if you have sufficient RAM 229s > 229s > reset.spatstat.options() 229s > 229s There were 11 warnings (use warnings() to see them) 229s BEGIN TEST testsM.R 229s 229s R version 4.4.3 (2025-02-28) -- "Trophy Case" 229s Copyright (C) 2025 The R Foundation for Statistical Computing 229s Platform: arm-unknown-linux-gnueabihf (32-bit) 229s 229s R is free software and comes with ABSOLUTELY NO WARRANTY. 229s You are welcome to redistribute it under certain conditions. 229s Type 'license()' or 'licence()' for distribution details. 229s 229s R is a collaborative project with many contributors. 229s Type 'contributors()' for more information and 229s 'citation()' on how to cite R or R packages in publications. 229s 229s Type 'demo()' for some demos, 'help()' for on-line help, or 229s 'help.start()' for an HTML browser interface to help. 229s Type 'q()' to quit R. 229s 229s Loading required package: spatstat.model 229s Loading required package: spatstat.data 229s > #' 229s > #' Header for all (concatenated) test files 229s > #' 229s > #' Require spatstat.model 229s > #' Obtain environment variable controlling tests. 229s > #' 229s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 229s > 229s > require(spatstat.model) 230s Loading required package: spatstat.univar 230s spatstat.univar 3.1-2 230s Loading required package: spatstat.geom 230s spatstat.geom 3.3-6 230s Loading required package: spatstat.random 230s spatstat.random 3.3-3 230s Loading required package: spatstat.explore 230s Loading required package: nlme 230s spatstat.explore 3.3-4 230s Loading required package: rpart 230s spatstat.model 3.3-4 230s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 230s > ALWAYS <- TRUE 230s > cat(paste("--------- Executing", 230s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 230s + "test code -----------\n")) 230s --------- Executing **RESTRICTED** subset of test code ----------- 230s > ## 230s > ## tests/marcelino.R 230s > ## 230s > ## $Revision: 1.4 $ $Date: 2020/04/30 02:18:23 $ 230s > ## 230s > 230s > local({ 230s + if(FULLTEST) { 230s + Y <- split(urkiola) 230s + B <- Y$birch 230s + O <- Y$oak 230s + B.lam <- predict (ppm(B ~polynom(x,y,2)), type="trend") 230s + O.lam <- predict (ppm(O ~polynom(x,y,2)), type="trend") 230s + 230s + Kinhom(B, lambda=B.lam, correction="iso") 230s + Kinhom(B, lambda=B.lam, correction="border") 230s + 230s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam) 230s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "iso") 230s + Kcross.inhom(urkiola, i="birch", j="oak", B.lam, O.lam, correction = "border") 230s + } 230s + }) 230s > 230s > 230s > #' tests/mctests.R 230s > #' Monte Carlo tests 230s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 230s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 230s > 230s > 230s > local({ 230s + if(FULLTEST) { 230s + fitx <- ppm(redwood~x) 230s + ax <- envelopeTest(fitx, exponent=2, nsim=9, savefuns=TRUE) 230s + print(ax) 230s + } 230s + }) 230s > 230s > 230s > # 230s > # tests/mppm.R 230s > # 230s > # Basic tests of mppm 230s > # 230s > # $Revision: 1.23 $ $Date: 2022/07/08 04:55:13 $ 230s > # 230s > 230s > if(!FULLTEST) 230s + spatstat.options(npixel=32, ndummy.min=16) 230s > 230s > local({ 230s + ## test interaction formulae and subfits 230s + fit1 <- mppm(Points ~ group, simba, 230s + hyperframe(po=Poisson(), str=Strauss(0.1)), 230s + iformula=~ifelse(group=="control", po, str)) 230s + fit2 <- mppm(Points ~ group, simba, 230s + hyperframe(po=Poisson(), str=Strauss(0.1)), 230s + iformula=~str/id) 230s + fit2w <- mppm(Points ~ group, simba, 230s + hyperframe(po=Poisson(), str=Strauss(0.1)), 230s + iformula=~str/id, weights=runif(nrow(simba))) 230s + # currently invalid 230s + # fit3 <- mppm(Points ~ group, simba, 230s + # hyperframe(po=Poisson(), pie=PairPiece(c(0.05,0.1))), 230s + # iformula=~I((group=="control") * po) + I((group=="treatment") * pie)) 230s + 230s + fit1 230s + fit2 230s + fit2w 230s + # fit3 230s + 230s + if(FULLTEST) { 230s + ## run summary.mppm which currently sits in spatstat-internal.Rd 230s + summary(fit1) 230s + summary(fit2) 230s + summary(fit2w) 230s + # summary(fit3) 230s + } 230s + 230s + ## test vcov algorithm 230s + vcov(fit1) 230s + vcov(fit2) 230s + # vcov(fit3) 230s + 230s + if(FULLTEST) { 230s + fit4 <- mppm(Points ~ group, simba, hyperframe(str=Strauss(0.1)), iformula=~str/group) 230s + fit4 230s + summary(fit4) 230s + vcov(fit4) 230s + fit0 <- mppm(Points ~ group, simba) 230s + anova(fit0, fit4, test="Chi") 230s + ## [bug from Fernando Milesi] 230s + fit5 <- mppm(Wat ~ id, 230s + data=hyperframe(Wat=waterstriders), 230s + interaction=StraussHard(4.5, 1.5), 230s + iformula=~Interaction:id) 230s + fit5 230s + summary(fit5) 230s + vcov(fit5) 230s + } 230s + 230s + ## test subfits algorithm 230s + if(FULLTEST) { 230s + s1 <- subfits(fit1) 230s + s2 <- subfits(fit2) 230s + # s3 <- subfits(fit3) 230s + s4 <- subfits(fit4) 230s + s5 <- subfits(fit5) 230s + 230s + ## validity of results of subfits() 230s + p1 <- solapply(s1, predict) 230s + p2 <- solapply(s2, predict) 230s + # p3 <- solapply(s3, predict) 230s + p4 <- solapply(s4, predict) 230s + p5 <- solapply(s5, predict) 230s + } 230s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## cases of predict.mppm 233s + W <- solapply(waterstriders, Window) 233s + Fakes <- solapply(W, runifpoint, n=30) 233s + FakeDist <- solapply(Fakes, distfun) 233s + H <- hyperframe(Bugs=waterstriders, 233s + D=FakeDist) 233s + fit <- mppm(Bugs ~ D, data=H) 233s + p1 <- predict(fit) 233s + p2 <- predict(fit, locations=Fakes) 233s + p3 <- predict(fit, locations=solapply(W, erosion, r=4)) 233s + locn <- as.data.frame(do.call(cbind, lapply(Fakes, coords))) 233s + df <- data.frame(id=sample(1:3, nrow(locn), replace=TRUE), 233s + D=runif(nrow(locn))) 233s + p4 <- predict(fit, locations=locn, newdata=df) 233s + 233s + fitG <- mppm(Bugs ~ D, data=H, use.gam=TRUE) 233s + p1G <- predict(fitG) 233s + p2G <- predict(fitG, locations=Fakes) 233s + p3G <- predict(fitG, locations=solapply(W, erosion, r=4)) 233s + p4G <- predict(fitG, locations=locn, newdata=df) 233s + } 233s + }) 233s > 233s > local({ 233s + ## [thanks to Sven Wagner] 233s + ## factor covariate, with some levels unused in some rows 233s + if(FULLTEST) { 233s + set.seed(14921788) 233s + H <- hyperframe(X=replicate(3, runifpoint(20), simplify=FALSE), 233s + Z=solist(as.im(function(x,y){x}, owin()), 233s + as.im(function(x,y){y}, owin()), 233s + as.im(function(x,y){x+y}, owin()))) 233s + H$Z <- solapply(H$Z, cut, breaks=(0:4)/2) 233s + 233s + fit6 <- mppm(X ~ Z, H) 233s + v6 <- vcov(fit6) 233s + s6 <- subfits(fit6) 233s + p6 <- solapply(s6, predict) 233s + 233s + ## random effects 233s + fit7 <- mppm(X ~ Z, H, random=~1|id) 233s + v7 <- vcov(fit7) 233s + s7 <- subfits(fit7) 233s + p7 <- solapply(s7, predict) 233s + 233s + fit7a <- mppm(X ~ Z, H, random=~x|id) 233s + v7a <- vcov(fit7a) 233s + s7a <- subfits(fit7a) 233s + p7a <- solapply(s7a, predict) 233s + 233s + ## multitype: collisions in vcov.ppm, predict.ppm 233s + H$X <- lapply(H$X, rlabel, labels=factor(c("a","b")), permute=FALSE) 233s + M <- MultiStrauss(matrix(0.1, 2, 2), c("a","b")) 233s + fit8 <- mppm(X ~ Z, H, M) 233s + v8 <- vcov(fit8, fine=TRUE) 233s + s8 <- subfits(fit8) 233s + p8 <- lapply(s8, predict) 233s + c8 <- lapply(s8, predict, type="cif") 233s + 233s + fit9 <- mppm(X ~ Z, H, M, iformula=~Interaction * id) 233s + v9 <- vcov(fit9, fine=TRUE) 233s + s9 <- subfits(fit9) 233s + p9 <- lapply(s9, predict) 233s + c9 <- lapply(s9, predict, type="cif") 233s + 233s + ## and a simple error in recognising 'marks' 233s + fit10 <- mppm(X ~ marks, H) 233s + } 233s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## test handling of offsets and zero cif values in mppm 233s + H <- hyperframe(Y = waterstriders) 233s + (fit1 <- mppm(Y ~ 1, data=H, Hardcore(1.5))) 233s + (fit2 <- mppm(Y ~ 1, data=H, StraussHard(7, 1.5))) 233s + (fit3 <- mppm(Y ~ 1, data=H, Hybrid(S=Strauss(7), H=Hardcore(1.5)))) 233s + s1 <- subfits(fit1) 233s + s2 <- subfits(fit2) 233s + s3 <- subfits(fit3) 233s + 233s + ## prediction, in training/testing context 233s + ## (example from Markus Herrmann and Ege Rubak) 233s + X <- waterstriders 233s + dist <- solapply(waterstriders, 233s + function(z) distfun(runifpoint(1, Window(z)))) 233s + i <- 3 233s + train <- hyperframe(pattern = X[-i], dist = dist[-i]) 233s + test <- hyperframe(pattern = X[i], dist = dist[i]) 233s + fit <- mppm(pattern ~ dist, data = train) 233s + pred <- predict(fit, type="cif", newdata=test, verbose=TRUE) 233s + 233s + ## examples from Robert Aue 233s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 233s + res <- mppm(Points ~ 1, interaction = GH, data=demohyper) 233s + print(summary(res)) 233s + sub <- subfits(res, verbose=TRUE) 233s + print(sub) 233s + } 233s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## test handling of interaction coefficients in multitype case 233s + set.seed(42) 233s + XX <- as.solist(replicate(3, rthin(amacrine, 0.8), simplify=FALSE)) 233s + H <- hyperframe(X=XX) 233s + M <- MultiStrauss(matrix(0.1, 2, 2), levels(marks(amacrine))) 233s + fit <- mppm(X ~ 1, H, M) 233s + co <- coef(fit) 233s + subco <- sapply(subfits(fit), coef) 233s + if(max(abs(subco - co)) > 0.001) 233s + stop("Wrong coefficient values in subfits, for multitype interaction") 233s + } 233s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## test lurking.mppm 233s + ## example from 'mppm' 233s + n <- 7 233s + H <- hyperframe(V=1:n, 233s + U=runif(n, min=-1, max=1)) 233s + H$Z <- setcov(square(1)) 233s + H$U <- with(H, as.im(U, as.rectangle(Z))) 233s + H$Y <- with(H, rpoispp(eval.im(exp(2+3*Z)))) 233s + fit <- mppm(Y ~ Z + U + V, data=H) 233s + 233s + lurking(fit, expression(Z), type="P") 233s + lurking(fit, expression(V), type="raw") # design covariate 233s + lurking(fit, expression(U), type="raw") # image, constant in each row 233s + lurking(fit, H$Z, type="P") # list of images 233s + } 233s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## test anova.mppm code blocks and scoping problem 233s + H <- hyperframe(X=waterstriders) 233s + mod0 <- mppm(X~1, data=H, Poisson()) 233s + modxy <- mppm(X~x+y, data=H, Poisson()) 233s + mod0S <- mppm(X~1, data=H, Strauss(2)) 233s + modxyS <- mppm(X~x+y, data=H, Strauss(2)) 233s + anova(mod0, modxy, test="Chi") 233s + anova(mod0S, modxyS, test="Chi") 233s + anova(modxy, test="Chi") 233s + anova(modxyS, test="Chi") 233s + #' models with random effects (example from Marcelino de la Cruz) 233s + mod0r <- mppm(X~1, data=H, Poisson(), random = ~1|id) 233s + modxr <- mppm(X~x, data=H, Poisson(), random = ~1|id) 233s + anova(mod0r, modxr, test="Chi") 233s + } 233s + }) 233s > 233s > local({ 233s + if(FULLTEST) { 233s + ## test multitype stuff 233s + foo <- flu[1:3,] 233s + msh <- MultiStraussHard(iradii=matrix(100, 2, 2), 233s + hradii=matrix(10,2,2), 233s + types=levels(marks(foo$pattern[[1]]))) 233s + msh0 <- MultiStraussHard(iradii=matrix(100, 2, 2), 233s + hradii=matrix(10,2,2)) 233s + fit <- mppm(pattern ~ 1, data=foo, interaction=msh0) 233s + print(fit) 233s + print(summary(fit)) 233s + v <- vcov(fit) 233s + } 233s + }) 233s > 233s > reset.spatstat.options() 233s > #' 233s > #' tests/msr.R 233s > #' 233s > #' $Revision: 1.5 $ $Date: 2020/11/30 07:27:44 $ 233s > #' 233s > #' Tests of code for measures 233s > #' 233s > 233s > if(FULLTEST) { 233s + local({ 233s + 233s + ## cases of 'msr' 233s + Q <- quadscheme(cells) 233s + nQ <- n.quad(Q) 233s + nX <- npoints(cells) 233s + A <- matrix(nX * 3, nX, 3) 233s + B <- matrix(nQ * 3, nQ, 3) 233s + 233s + m <- msr(Q, A, B) 233s + 233s + M <- msr(Q, A, 1) 233s + M <- msr(Q, 1, B) 233s + M <- msr(Q, A, B[,1]) 233s + M <- msr(Q, A[,1], B) 233s + M <- msr(Q, A, B[,1,drop=FALSE]) 233s + M <- msr(Q, A[,1,drop=FALSE], B) 233s + 233s + ## methods 233s + a <- summary(m) 233s + b <- is.marked(m) 233s + w <- as.owin(m) 233s + z <- domain(m) 233s + ss <- scalardilate(m, 2) 233s + tt <- rescale(m, 2) 233s + ee <- rotate(m, pi/4) 233s + aa <- affine(m, mat=diag(c(1,2)), vec=c(0,1)) 233s + ff <- flipxy(m) 233s + 233s + am <- augment.msr(m, sigma=0.08) 233s + ua <- update(am) 233s + 233s + rr <- residuals(ppm(cells ~ x)) 233s + mm <- residuals(ppm(amacrine ~ x)) 233s + ss <- residuals(ppm(amacrine ~ x), type="score") 233s + gg <- rescale(ss, 1/662, c("micron", "microns")) 233s + 233s + plot(mm) 233s + plot(mm, multiplot=FALSE) 233s + plot(mm, equal.markscale=TRUE, equal.ribbon=TRUE) 233s + plot(ss) 233s + plot(ss, multiplot=FALSE) 233s + }) 233s + } 233s > 233s BEGIN TEST testsNtoO.R 233s 233s R version 4.4.3 (2025-02-28) -- "Trophy Case" 233s Copyright (C) 2025 The R Foundation for Statistical Computing 233s Platform: arm-unknown-linux-gnueabihf (32-bit) 233s 233s R is free software and comes with ABSOLUTELY NO WARRANTY. 233s You are welcome to redistribute it under certain conditions. 233s Type 'license()' or 'licence()' for distribution details. 233s 233s R is a collaborative project with many contributors. 233s Type 'contributors()' for more information and 233s 'citation()' on how to cite R or R packages in publications. 233s 233s Type 'demo()' for some demos, 'help()' for on-line help, or 233s 'help.start()' for an HTML browser interface to help. 233s Type 'q()' to quit R. 233s 233s Loading required package: spatstat.model 233s > #' 233s > #' Header for all (concatenated) test files 233s > #' 233s > #' Require spatstat.model 233s > #' Obtain environment variable controlling tests. 233s > #' 233s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 233s > 233s > require(spatstat.model) 233s Loading required package: spatstat.data 234s Loading required package: spatstat.univar 234s spatstat.univar 3.1-2 234s Loading required package: spatstat.geom 234s spatstat.geom 3.3-6 234s Loading required package: spatstat.random 234s spatstat.random 3.3-3 234s Loading required package: spatstat.explore 234s Loading required package: nlme 234s spatstat.explore 3.3-4 234s Loading required package: rpart 234s spatstat.model 3.3-4 234s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 234s > ALWAYS <- TRUE 234s > cat(paste("--------- Executing", 234s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 234s + "test code -----------\n")) 234s --------- Executing **RESTRICTED** subset of test code ----------- 234s > # 234s > # tests/NAinCov.R 234s > # 234s > # Testing the response to the presence of NA's in covariates 234s > # 234s > # $Revision: 1.10 $ $Date: 2024/09/30 23:13:54 $ 234s > 234s > if(FULLTEST) { 234s + local({ 234s + X <- runifpoint(42) 234s + Y <- as.im(function(x,y) { x+y }, owin()) 234s + Y[owin(c(0.2,0.4),c(0.2,0.4))] <- NA 234s + ## ..... ppm ...................................... 234s + ## fit model: should produce a warning but no failure 234s + misfit <- ppm(X ~ Y) 234s + ## prediction 234s + Z <- predict(misfit, type="trend", se=TRUE) 234s + ## canonical covariates 234s + M <- model.images(misfit) 234s + ## covariance matrix: all should be silent 234s + v <- vcov(misfit) 234s + ss <- vcov(misfit, what="internals") 234s + ## ..... kppm ...................................... 234s + ## should produce warnings but no failures 234s + misfit <- kppm(X ~Y) 234s + V <- predict(misfit, type="trend", se=TRUE) 234s + M <- model.images(misfit) 234s + refit <- improve.kppm(misfit, dimyx=20) 234s + }) 234s + } 234s > 234s BEGIN TEST testsP1.R 234s 234s R version 4.4.3 (2025-02-28) -- "Trophy Case" 234s Copyright (C) 2025 The R Foundation for Statistical Computing 234s Platform: arm-unknown-linux-gnueabihf (32-bit) 234s 234s R is free software and comes with ABSOLUTELY NO WARRANTY. 234s You are welcome to redistribute it under certain conditions. 234s Type 'license()' or 'licence()' for distribution details. 234s 234s R is a collaborative project with many contributors. 234s Type 'contributors()' for more information and 234s 'citation()' on how to cite R or R packages in publications. 234s 234s Type 'demo()' for some demos, 'help()' for on-line help, or 234s 'help.start()' for an HTML browser interface to help. 234s Type 'q()' to quit R. 234s 234s Loading required package: spatstat.model 234s > #' 234s > #' Header for all (concatenated) test files 234s > #' 234s > #' Require spatstat.model 234s > #' Obtain environment variable controlling tests. 234s > #' 234s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 234s > 234s > require(spatstat.model) 234s Loading required package: spatstat.data 235s Loading required package: spatstat.univar 235s spatstat.univar 3.1-2 235s Loading required package: spatstat.geom 235s spatstat.geom 3.3-6 235s Loading required package: spatstat.random 235s spatstat.random 3.3-3 235s Loading required package: spatstat.explore 235s Loading required package: nlme 235s spatstat.explore 3.3-4 235s Loading required package: rpart 236s spatstat.model 3.3-4 236s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 236s > ALWAYS <- TRUE 236s > cat(paste("--------- Executing", 236s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 236s + "test code -----------\n")) 236s --------- Executing **RESTRICTED** subset of test code ----------- 236s > ## 236s > ## tests/percy.R 236s > ## 236s > ## Tests of Percus-Yevick approximations 236s > ## 236s > ## $Revision: 1.3 $ $Date: 2020/04/30 05:23:52 $ 236s > 236s > if(FULLTEST) { 236s + local({ 236s + fit <- ppm(swedishpines ~1, DiggleGatesStibbard(6)) 236s + K <- Kmodel(fit) 236s + }) 236s + } 236s > 236s > ## 236s > ## tests/pixelgripes.R 236s > ## Problems related to pixellation of windows 236s > ## 236s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 236s > 236s > if(FULLTEST) { 236s + local({ 236s + 236s + ## From Philipp Hunziker: bug in rNeymanScott (etc) 236s + ## Create an irregular window 236s + PM <- matrix(c(1,0,0.5,1,0,0), 3, 2, byrow=TRUE) 236s + P <- owin(poly=PM) 236s + ## Generate Matern points 236s + X <- rMatClust(50, 0.05, 5, win=P) 236s + ## Some distance function as a covariate 236s + distorigin <- function(x, y) { sqrt(x^2 + y^2) } 236s + ## No covariates: works fine 236s + fit0 <- kppm(X ~ 1, clusters="MatClust") 236s + Y0 <- simulate(fit0, retry=0) 236s + ## Covariates: Simulation fails 236s + fit1 <- kppm(X ~ distorigin, clusters="MatClust") 236s + Y1 <- simulate(fit1, retry=0) 236s + 236s + }) 236s + } 236s > 236s BEGIN TEST testsP2.R 236s 236s R version 4.4.3 (2025-02-28) -- "Trophy Case" 236s Copyright (C) 2025 The R Foundation for Statistical Computing 236s Platform: arm-unknown-linux-gnueabihf (32-bit) 236s 236s R is free software and comes with ABSOLUTELY NO WARRANTY. 236s You are welcome to redistribute it under certain conditions. 236s Type 'license()' or 'licence()' for distribution details. 236s 236s R is a collaborative project with many contributors. 236s Type 'contributors()' for more information and 236s 'citation()' on how to cite R or R packages in publications. 236s 236s Type 'demo()' for some demos, 'help()' for on-line help, or 236s 'help.start()' for an HTML browser interface to help. 236s Type 'q()' to quit R. 236s 236s > #' 236s > #' Header for all (concatenated) test files 236s > #' 236s > #' Require spatstat.model 236s > #' Obtain environment variable controlling tests. 236s > #' 236s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 236s > 236s > require(spatstat.model) 236s Loading required package: spatstat.model 236s Loading required package: spatstat.data 237s Loading required package: spatstat.univar 237s spatstat.univar 3.1-2 237s Loading required package: spatstat.geom 237s spatstat.geom 3.3-6 237s Loading required package: spatstat.random 237s spatstat.random 3.3-3 237s Loading required package: spatstat.explore 237s Loading required package: nlme 237s spatstat.explore 3.3-4 237s Loading required package: rpart 237s spatstat.model 3.3-4 237s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 237s > ALWAYS <- TRUE 237s > cat(paste("--------- Executing", 237s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 237s + "test code -----------\n")) 237s --------- Executing **RESTRICTED** subset of test code ----------- 237s > # 237s > # tests/ppmBadData.R 237s > # 237s > # $Revision: 1.6 $ $Date: 2020/04/30 05:23:52 $ 237s > 237s > # Testing robustness of ppm and support functions 237s > # when data are rubbish 237s > 237s > local({ 237s + if(ALWAYS) { 237s + ## from Rolf: very large proportion of data is NA 237s + SEED <- 42 237s + K <- 101 237s + A <- 500 237s + X <- seq(0, A, length=K) 237s + G <- expand.grid(x=X, y=X) 237s + FOO <- function(x,y) { sin(x)^2 + cos(y)^2 } 237s + M1 <- im(matrix(FOO(G$x, G$y), K, K), xcol=X, yrow=X) 237s + M <- im(matrix(FOO(G$x, G$y), K, K)) 237s + BAR <- function(x) { exp(-6.618913 + 5.855337 * x - 8.432483 * x^2) } 237s + V <- im(BAR(M$v), xcol=X, yrow=X) 237s + # V <- eval.im(exp(-6.618913 + 5.855337 * M - 8.432483 * M^2)) 237s + set.seed(SEED) 237s + Y <- rpoispp(V) 237s + fY <- ppm(Y ~cv + I(cv^2), data=list(cv=M), correction="translate") 237s + diagnose.ppm(fY) 237s + lurking(fY, covariate=as.im(function(x,y){x}, square(A)), type="raw") 237s + } 237s + 237s + if(ALWAYS) { 237s + ## from Andrew Bevan: numerical overflow, ill-conditioned Fisher information 237s + SEED <- 42 237s + nongranite<- owin(poly = list(x = c(0, 8500, 7000, 6400, 6400, 6700, 7000, 7200, 7300, 8000, 8100, 8800, 9500, 10000, 10000, 0), y = c(0, 0, 2000, 3800, 4000, 5000, 6500, 7400, 7500, 8000, 8100, 9000, 9500, 9600, 10000, 10000))) 237s + ## Trend on raster grid 237s + rain <- as.im(X=function(x,y) { x^2 + y^2 }, W=nongranite, dimyx=100) 237s + ## Generate a point pattern via a Lennard-Jones process 237s + set.seed(SEED) 237s + mod4<- rmhmodel(cif="lennard", 237s + par=list(beta=1, sigma=250, epsilon=2.2), 237s + trend=rain, w=nongranite) 237s + ljtr<- rmh(mod4, start=list(n.start=80), control=list(p=1, nrep=1e5)) 237s + 237s + ## Fit a point process model to the pattern with rain as a covariate 237s + ## NOTE INCORRECT TREND FORMULA 237s + ljtrmod <- ppm(ljtr, trend= ~ Z, interaction=NULL, data=list(Z=rain)) 237s + ss <- summary(ljtrmod) 237s + } 237s + 237s + if(FULLTEST) { 237s + ## From Ege 237s + ## Degenerate but non-null argument 'covariates' 237s + xx <- list() 237s + names(xx) <- character(0) 237s + fit <- ppm(cells ~x, covariates = xx) 237s + st <- summary(fit) 237s + } 237s + 237s + }) 237s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 237s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 238s > 238s > 238s > 238s > #' tests/ppmclass.R 238s > #' 238s > #' Class support for ppm 238s > #' 238s > #' $Revision: 1.9 $ $Date: 2022/03/07 03:26:09 $ 238s > 238s > if(FULLTEST) { 238s + local({ 238s + #' (1) print.ppm, summary.ppm, print.summary.ppm 238s + Z <- as.im(function(x,y){x}, Window(cells)) 238s + fitZ <- ppm(cells ~ Z) 238s + print(fitZ) 238s + print(summary(fitZ)) 238s + #' logistic 238s + fitl <- ppm(swedishpines ~ x+y, method="logi") 238s + print(fitl) 238s + print(summary(fitl)) 238s + #' Model with covariate arguments 238s + f <- function(x,y,b) { x+b } 238s + fitf <- ppm(cells ~ f, covfunargs=list(b=1)) 238s + print(fitf) 238s + print(summary(fitf)) 238s + #' Invalid model 238s + fitN <- ppm(redwood ~ 1, Strauss(0.1)) 238s Error in solve.default(M) : 238s system is computationally singular: reciprocal condition number = 5.72218e-18 238s In addition: Warning messages: 238s 1: Values of the covariate ‘cv’ were NA or undefined at 96% (1774 out of 1845) of the quadrature points. Occurred while executing: ppm.ppp(Q = Y, trend = ~cv + I(cv^2), data = list(list(c(1, 1.91953576453823, 238s 2: Some infinite, NA or NaN increments were removed 238s 3: Numerical underflow detected: sigma is probably too small 238s 4: Some infinite, NA or NaN increments were removed 238s Error in solve.default(M) : 238s system is computationally singular: reciprocal condition number = 5.72218e-18 238s In addition: Warning message: 238s Cannot compute variance: Fisher information matrix is singular 238s Warning message: 238s Cannot compute variance: Fisher information matrix is singular 238s + print(fitN) 238s + print(summary(fitN)) 238s + #' standard errors in output 238s + fat <- ppm(cells ~ x, Strauss(0.12)) 238s + op <- spatstat.options(print.ppm.SE='always') 238s + print(fat) 238s + spatstat.options(print.ppm.SE='never') 238s + print(fat) 238s + print(fitZ) 238s + spatstat.options(op) 238s + 238s + ## (2) plot.ppm 238s + plot(fitZ) 238s + plot(fat, trend=FALSE, cif=FALSE, se=FALSE) 238s + 238s + ## (3) emend.ppm 238s + fitZe <- emend(fitZ, trace=TRUE) 238s + ZZ <- Z 238s + fitZZ <- ppm(cells ~ Z + ZZ) 238s + fitZZe <- emend(fitZZ, trace=TRUE) 238s + fitOK <- ppm(redwood ~1, Strauss(0.1), emend=TRUE) 238s + print(fitOK) 238s + fitNot <- ppm(redwood ~1, Strauss(0.1)) 238s + fitSlow <- emend(fitNot, trace=TRUE) 238s + print(fitSlow) 238s + op <- spatstat.options(project.fast=TRUE) 238s + fitFast <- emend(fitNot, trace=TRUE) 238s + print(fitFast) 238s + fitZZe <- emend(fitZZ, trace=TRUE) 238s + spatstat.options(op) 238s + 238s + #' (4) methods for other generics 238s + logLik(fitZ, absolute=TRUE) 238s + unitname(fitZ) 238s + unitname(fat) <- c("metre", "metres") 238s + is.expandable(fitf) 238s + fit0 <- update(fitZ, . ~ 1) 238s + anova(fit0, fitZ, override=TRUE) 238s + interactionfamilyname(fat) 238s + interactionorder(fat) 238s + hardcoredist(fat) 238s + 238s + #' (5) miscellaneous 238s + 238s + ## example from Robert Aue - handling offsets 238s + X <- demohyper$Points[[1]] 238s + GH <- Hybrid(G=Geyer(r=0.1, sat=3), H=Hardcore(0.01)) 238s + fit <- ppm(X ~ 1, GH) 238s + valid.ppm(fit) 238s + 238s + #' hard core distance of hybrid 238s + hardcoredist(fit) 238s + #' interaction order of hybrid 238s + interactionorder(fit) 238s + 238s + #' case of boundingbox 238s + boundingbox(cells, ppm(cells ~ 1)) 238s + }) 238s + 238s + reset.spatstat.options() 238s + } 238s > # 238s > # tests/ppmgam.R 238s > # 238s > # Test ppm with use.gam=TRUE 238s > # 238s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 238s > # 238s > 238s > if(FULLTEST) { 238s + local({ 238s + fit <- ppm(nztrees ~s(x,y), use.gam=TRUE) 238s + mm <- model.matrix(fit) 238s + mf <- model.frame(fit) 238s + v <- vcov(fit) 238s + prd <- predict(fit) 238s + }) 238s + } 238s > #' 238s > #' tests/ppmlogi.R 238s > #' 238s > #' Tests of ppm(method='logi') 238s > #' and related code (predict, leverage etc) 238s > #' 238s > #' $Revision: 1.15 $ $Date: 2020/04/30 05:23:52 $ 238s > #' 238s > 238s > local({ 238s + if(FULLTEST) { 238s + fit <- ppm(cells ~x, method="logi") 238s + f <- fitted(fit) 238s + p <- predict(fit) 238s + u <- summary(fit) 238s + fitS <- ppm(cells ~x, Strauss(0.12), method="logi") 238s + fS <- fitted(fitS) 238s + pS <- predict(fitS) 238s + uS <- summary(fitS) 238s + print(uS) 238s + 238s + plot(leverage(fit)) 238s + plot(influence(fit)) 238s + plot(dfbetas(fit)) 238s + plot(leverage(fitS)) 238s + plot(influence(fitS)) 238s + plot(dfbetas(fitS)) 238s + } 238s + 238s + if(FULLTEST) { 238s + #' same with hard core - A1 is singular 238s + fitH <- ppm(cells ~x, Strauss(0.08), method="logi") 238s + print(fitH) 238s + fH <- fitted(fitH) 238s + pH <- predict(fitH) 238s + uH <- summary(fitH) 238s + print(uH) 238s + plot(leverage(fitH)) 238s + plot(influence(fitH)) 238s + plot(dfbetas(fitH)) 238s + } 238s + 238s + if(FULLTEST) { 238s + #' logistic fit to data frame of covariates 238s + z <- c(rep(TRUE, 5), rep(FALSE, 5)) 238s + df <- data.frame(A=z + 2* runif(10), 238s + B=runif(10)) 238s + Y <- quadscheme.logi(runifpoint(5), runifpoint(5)) 238s + fut <- ppm(Y ~ A+B, data=df, method="logi") 238s + sf <- summary(fut) 238s + print(sf) 238s + } 238s + 238s + if(FULLTEST) { 238s + #' vblogit code, just to check that it runs. 238s + fee <- ppm(cells ~ x, method="VBlogi", nd=21) 238s + print(fee) 238s + summary(fee) 238s + logLik(fee) 238s + AIC(fee) 238s + extractAIC(fee) 238s + Z <- predict(fee) 238s + summary(Z) 238s + print(fee$internal$glmfit) # print.vblogit 238s + } 238s + }) 238s > 238s > # 238s > # tests/ppmmarkorder.R 238s > # 238s > # $Revision: 1.4 $ $Date: 2020/04/30 05:23:52 $ 238s > # 238s > # Test that predict.ppm, plot.ppm and plot.fitin 238s > # tolerate marks with levels that are not in alpha order 238s > # 238s > if(ALWAYS) { # locale-dependent? 238s + local({ 238s + X <- amacrine 238s + levels(marks(X)) <- c("ZZZ", "AAA") 238s + fit <- ppm(X ~marks, MultiStrauss(c("ZZZ","AAA"), matrix(0.06, 2, 2))) 238s + aa <- predict(fit, type="trend") 238s + bb <- predict(fit, type="cif") 238s + plot(fit) 238s + plot(fitin(fit)) 238s + }) 238s + } 240s > 240s > 240s > # 240s > # tests/ppmscope.R 240s > # 240s > # Test things that might corrupt the internal format of ppm objects 240s > # 240s > # $Revision: 1.7 $ $Date: 2022/01/19 09:18:20 $ 240s > # 240s > 240s > if(ALWAYS) { # dependent on R version? 240s + local({ 240s + 240s + ## (1) Scoping problem that can arise when ppm splits the data 240s + fit <- ppm(bei ~elev, data=bei.extra) 240s + mm <- model.matrix(fit) 240s + 240s + ## (2) Fast update mechanism 240s + fit1 <- ppm(cells ~x+y, Strauss(0.07)) 240s + fit2 <- update(fit1, ~y) 240s + fit3 <- update(fit2, ~x) 240s + 240s + ## (3) New formula-based syntax 240s + attach(bei.extra) 240s + slfit <- ppm(bei ~ grad) 240s + sl2fit <- update(slfit, ~grad + I(grad^2)) 240s + slfitup <- update(slfit, use.internal=TRUE) 240s + sl2fitup <- update(sl2fit, use.internal=TRUE) 240s + 240s + ## (4) anova.ppm 240s + fut1 <- ppm(cells ~ 1, Strauss(0.1)) 240s + futx <- ppm(cells ~ x, Strauss(0.1)) 240s + anova(fut1, test="Chi") 240s + anova(futx, test="Chi") 240s + fut1a <- ppm(cells ~ 1, Strauss(0.1), rbord=0) 240s + anova(fut1a, futx, test="Chi") 240s + fut1d <- ppm(cells ~ 1, Strauss(0.1), nd=23) 240s + anova(fut1d, futx, test="Chi") 240s + ## This now works! 240s + futxyg <- ppm(cells ~ x + s(y), Strauss(0.1), use.gam=TRUE) 240s + anova(futx, futxyg) 240s + ## marked 240s + fatP <- ppm(amacrine ~ marks) 240s + fatM <- ppm(amacrine ~ marks, MultiStrauss(matrix(0.07, 2, 2))) 240s + anova(fatP, fatM, test="Chi") 240s + 240s + ## (5) expansion of "." in update.ppm 240s + fitb <- ppm(bei ~ . , data=bei.extra) 240s + step(fitb) 240s + }) 240s + } 242s Start: AIC=42295.11 242s ~elev + grad 242s 242s Df AIC 242s 42295 242s - elev 1 42383 242s - grad 1 42760 242s Warning messages: 242s 1: anova.ppm now computes the *adjusted* deviances when the models are not Poisson processes. 242s 2: Models were re-fitted using a common value of 'rbord' 242s 3: Models were re-fitted using a common quadrature scheme 242s 4: Models were re-fitted with use.gam=TRUE 242s 5: Deviance adjustment is not available for gam fits; unadjusted composite deviance calculated. 242s 6: Models were re-fitted using a common value of 'rbord' 242s Nonstationary Poisson process 242s Fitted to point pattern dataset ‘bei’ 242s 242s Log intensity: ~elev + grad 242s 242s Fitted trend coefficients: 242s (Intercept) elev grad 242s -8.56355220 0.02143995 5.84646680 242s 242s Estimate S.E. CI95.lo CI95.hi Ztest Zval 242s (Intercept) -8.56355220 0.341113849 -9.23212306 -7.89498134 *** -25.104675 242s elev 0.02143995 0.002287866 0.01695581 0.02592408 *** 9.371155 242s grad 5.84646680 0.255781018 5.34514522 6.34778838 *** 22.857313 242s > grep# 242s function (pattern, x, ignore.case = FALSE, perl = FALSE, value = FALSE, 242s fixed = FALSE, useBytes = FALSE, invert = FALSE) 242s { 242s pattern <- as.character(pattern) 242s if (is.factor(x) && length(levx <- levels(x)) < length(x) && 242s !is.na(pattern[1L])) { 242s value <- is.character(idxna <- suppressWarnings(grep(pattern, 242s NA_character_, ignore.case, perl, value, fixed, useBytes, 242s invert))) 242s idx <- logical(length(levx)) 242s idx[grep(pattern, levx, ignore.case, perl, FALSE, fixed, 242s useBytes, invert)] <- TRUE 242s idx <- idx[x] 242s if (length(idxna)) 242s idx[is.na(x)] <- TRUE 242s idx <- which(idx) 242s if (value) { 242s idx <- x[idx] 242s structure(as.character(idx), names = names(idx)) 242s } 242s else idx 242s } 242s else { 242s if (!is.character(x)) 242s x <- structure(as.character(x), names = names(x)) 242s .Internal(grep(pattern, x, ignore.case, value, perl, 242s fixed, useBytes, invert)) 242s } 242s } 242s 242s 242s > # tests/ppmtricks.R 242s > # 242s > # Test backdoor exits, hidden options, internals and tricks in ppm 242s > # 242s > # $Revision: 1.19 $ $Date: 2020/04/30 05:23:52 $ 242s > # 242s > local({ 242s + 242s + ## (1) skip.border 242s + if(ALWAYS) { # needed below 242s + fit <- ppm(cells, ~1, Strauss(0.1), skip.border=TRUE) 242s + } 242s + 242s + ## (2) subset arguments of different kinds 242s + if(FULLTEST) { 242s + fut <- ppm(cells ~ x, subset=(x > 0.5)) 242s + fot <- ppm(cells ~ x, subset=(x > 0.5), method="logi") 242s + W <- owin(c(0.4, 0.8), c(0.2, 0.7)) 242s + fut <- ppm(cells ~ x, subset=W) 242s + fot <- ppm(cells ~ x, subset=W, method="logi") 242s + V <- as.im(inside.owin, Window(cells), w=W) 242s + fet <- ppm(cells ~ x, subset=V) 242s + fet <- ppm(cells ~ x, subset=V, method="logi") 242s + } 242s + 242s + ## (3) profilepl -> ppm 242s + ## uses 'skip.border' and 'precomputed' 242s + ## also tests scoping for covariates 242s + if(FULLTEST) { 242s + splants <- split(ants) 242s + mess <- splants[["Messor"]] 242s + cats <- splants[["Cataglyphis"]] 242s + ss <- data.frame(r=seq(60,120,by=20),hc=29/6) 242s + dM <- distmap(mess,dimyx=256) 242s + mungf <- profilepl(ss, StraussHard, cats ~ dM) 242s + mungp <- profilepl(ss, StraussHard, trend=~dM, Q=cats) 242s + } 242s + 242s + ## (4) splitting large quadschemes into blocks 242s + if(FULLTEST) { 242s + mop <- spatstat.options(maxmatrix=5000) 242s + qr <- quadBlockSizes(quadscheme(cells)) 242s + pr <- predict(ppm(cells ~ x, AreaInter(0.05))) 242s + spatstat.options(mop) 242s + qr <- quadBlockSizes(quadscheme(cells)) 242s + } 242s + 242s + ## (5) shortcuts in summary.ppm 242s + ## and corresponding behaviour of print.summary.ppm 242s + if(FULLTEST) { 242s + print(summary(fit, quick=TRUE)) 242s + print(summary(fit, quick="entries")) 242s + print(summary(fit, quick="no prediction")) 242s + print(summary(fit, quick="no variances")) 242s + } 242s + 242s + ## (6) suffstat.R 242s + if(ALWAYS) { 242s + fitP <- update(fit, Poisson()) 242s + suffstat.poisson(fitP, cells) 242s + fit0 <- killinteraction(fit) 242s + suffstat.poisson(fit0, cells) 242s + } 242s + 242s + ## (7) various support for class ppm 242s + if(FULLTEST) { 242s + fut <- kppm(redwood ~ x) 242s + A <- quad.ppm(fut) 242s + Z <- as.im(function(x,y){x}, Window(cells)) 242s + fitZ <- ppm(cells ~ Z) 242s + U <- getppmOriginalCovariates(fitZ) 242s + } 242s + 242s + ## (8) support for class profilepl 242s + if(FULLTEST) { 242s + rr <- data.frame(r=seq(0.05, 0.15, by=0.02)) 242s + ps <- profilepl(rr, Strauss, cells) 242s + ## plot(ps) ## covered in plot.profilepl.Rd 242s + simulate(ps, nrep=1e4) 242s + parameters(ps) 242s + fitin(ps) 242s + predict(ps, type="cif") 242s + } 242s + 242s + ## (9) class 'plotppm' 242s + if(FULLTEST) { 242s + fut <- ppm(amacrine ~ marks + polynom(x,y,2), Strauss(0.07)) 242s + p <- plot(fut, plot.it=FALSE) 242s + print(p) 242s + plot(p, how="contour") 242s + plot(p, how="persp") 242s + } 242s + 242s + ## (10) ppm -> mpl.engine -> mpl.prepare 242s + if(ALWAYS) { # includes C code 242s + fit <- ppm(cells, NULL) 242s + fit <- ppm(cells ~ x, clipwin=square(0.7)) 242s + fit <- ppm(cells ~ x, subset=square(0.7)) 242s + DG <- as.im(function(x,y){x+y < 1}, square(1)) 242s + fit <- ppm(cells ~ x, subset=DG) 242s + fit <- ppm(cells ~ x, GLM=glm) 242s + fit <- ppm(cells ~ x, famille=quasi(link='log', variance='mu')) 242s + fit <- ppm(cells ~ x, Hardcore(0.07), skip.border=TRUE, splitInf=TRUE) 242s + } 242s + 242s + ## (11) unidentifiable model (triggers an error in ppm) 242s + if(FULLTEST) { 242s + Q <- quadscheme(cells) 242s + M <- mpl.prepare(Q, cells, as.ppp(Q), trend=~1, covariates=NULL, 242s + interaction=Hardcore(0.3), correction="none") 242s + } 242s + }) 242s > 242s > reset.spatstat.options() 242s > # 242s > # tests/prediction.R 242s > # 242s > # Things that might go wrong with predict() 242s > # 242s > # $Revision: 1.23 $ $Date: 2024/04/13 03:37:42 $ 242s > # 242s > 242s > local({ 242s + if(ALWAYS) { 242s + ## test of 'covfunargs' - platform dependent? 242s + f <- function(x,y,a){ y - a } 242s + fit <- ppm(cells ~x + f, covariates=list(f=f), covfunargs=list(a=1/2)) 242s + p <- predict(fit) 242s + 242s + ## prediction involving 0 * NA 242s + qc <- quadscheme(cells, nd=10) 242s + r <- minnndist(as.ppp(qc))/10 242s + fit <- ppm(qc ~ 1, Strauss(r)) # model has NA for interaction coefficient 242s + p1 <- predict(fit) 242s + p2 <- predict(fit, type="cif", ngrid=10) 242s + stopifnot(all(is.finite(as.matrix(p1)))) 242s + stopifnot(all(is.finite(as.matrix(p2)))) 242s + } 242s + 242s + if(FULLTEST) { 242s + ## test of 'new.coef' mechanism 242s + fut <- ppm(cells ~ x, Strauss(0.15), rbord=0) 242s + p0 <- predict(fut, type="cif") 242s + pe <- predict(fut, type="cif", new.coef=coef(fut)) 242s + pn <- predict(fut, type="cif", new.coef=unname(coef(fut))) 242s + if(max(abs(pe-p0)) > 0.01) 242s + stop("new.coef mechanism is broken!") 242s + if(max(abs(pn-p0)) > 0.01) 242s + stop("new.coef mechanism gives wrong answer, for unnamed vectors") 242s + #' adaptcoef 242s + a <- c(A=1,B=2,Z=42) 242s + b <- c(B=41,A=0) 242s + ab <- adaptcoef(a, b, drop=TRUE) 242s + #' check that grid parameters 'dimyx' and 'eps' are respected 242s + pyx <- predict(fut, type="cif", dimyx=7) 242s + if(all(dim(pyx) == dim(p0))) 242s + stop("predict.ppm ignores argument dimyx") 242s + peps <- predict(fut, type="cif", eps=0.14) 242s + if(all(dim(peps) == dim(p0))) 242s + stop("predict.ppm ignores argument eps") 242s + } 242s + 242s + if(FULLTEST) { 242s + ## tests of relrisk.ppm 242s + fut <- ppm(amacrine ~ x * marks) 242s + a <- relrisk(fut, control=2, relative=TRUE) 242s + a <- relrisk(fut, se=TRUE) 242s + a <- relrisk(fut, relative=TRUE, se=TRUE) 242s + fut <- ppm(sporophores ~ marks + x) 242s + a <- relrisk(fut, control=2, relative=TRUE) 242s + a <- relrisk(fut, se=TRUE) 242s + a <- relrisk(fut, relative=TRUE, se=TRUE) 242s + 242s + ## untested cases of predict.ppm 242s + fit0 <- ppm(cells) 242s + a <- predict(fit0, interval="confidence") 242s + a <- predict(fit0, interval="confidence", type="count") 242s + fit <- ppm(cells ~ x) 242s + b <- predict(fit, se=TRUE, locations=cells) 242s + b <- predict(fit, se=TRUE, interval="confidence") 242s + b <- predict(fit, type="count", se=TRUE) 242s + b <- predict(fit, type="count", window=square(0.5), se=TRUE) 242s + b <- predict(fit, type="count", window=quadrats(cells, 3), se=TRUE) 242s + d <- predict(fit, type="count", interval="prediction", se=TRUE) 242s + d <- predict(fit, type="count", interval="confidence", se=TRUE) 242s + d <- predict(fit, interval="confidence", se=TRUE) 242s + foot <- ppm(cells ~ x, StraussHard(0.12)) 242s + d <- predict(foot, ignore.hardcore=TRUE) 242s + dX <- predict(foot, ignore.hardcore=TRUE, locations=cells) 242s + 242s + ## superseded usages 242s + b <- predict(fit, type="se", getoutofjail=TRUE) 242s + b <- predict(fit, type="se", locations=cells) # warning 242s + b <- predict(fit, total=TRUE) 242s + b <- predict(fit, total=square(0.5)) 242s + b <- predict(fit, total=quadrats(cells, 3)) 242s + 242s + ## supporting code 242s + u <- model.se.image(fit, square(0.5)) 242s + u <- model.se.image(fit, square(0.5), what="cv") 242s + u <- model.se.image(fit, square(0.5), what="ce") 242s + co <- c(Intercept=5, slope=3, kink=2) 242s + re <- c("Intercept", "slope") 242s + a <- fill.coefs(co, re) # warning 242s + b <- fill.coefs(co, rev(names(co))) 242s + d <- fill.coefs(co, letters[1:3]) 242s + ## model matrix etc 242s + v <- model.frame(ppm(cells)) 242s + fut <- ppm(cells ~ x, Strauss(0.1)) 242s + v <- model.matrix(fut, subset=(x<0.5), keepNA=FALSE) 242s + df <- data.frame(x=runif(10), y=runif(10), 242s + Interaction=sample(0:1, 10, TRUE)) 242s + m10 <- PPMmodelmatrix(fut, data=df) 242s + mmm <- PPMmodelmatrix(fut, Q=quad.ppm(fut)) 242s + #' effectfun for Gibbs 242s + effectfun(fut, "x") 242s + effectfun(fut, "x", se.fit=TRUE) 242s + #' implicit covariate when there is only one 242s + effectfun(fut) 242s + effectfun(fut, se.fit=TRUE) 242s + #' given covariate 242s + dlin <- distfun(copper$SouthLines) 242s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 242s + effectfun(copfit, "dlin") 242s + effectfun(copfit) 242s + #' covariate that is not used in model 242s + effectfun(fut, "y", x=0) 242s + futS <- ppm(cells ~ 1, Strauss(0.1)) 242s + effectfun(futS, "x") 242s + effectfun(futS, "y") 242s + #' factor covariate 242s + fot <- ppm(amacrine~x+marks) 242s + effectfun(fot, "marks", x=0.5, se.fit=TRUE) 242s + #' covariate retained but not used 242s + W <- Window(swedishpines) 242s + a <- solist(A=funxy(function(x,y){x < 20}, W), 242s + B=funxy(function(x,y){factor(x < 20)}, W)) 242s + fvt <- ppm(swedishpines ~ A, data=a, allcovar=TRUE) 242s + effectfun(fvt, "A", se.fit=TRUE) 242s + effectfun(fvt, "B", A=TRUE, se.fit=TRUE) 242s + 242s + ## ppm with covariate values in data frame 242s + X <- rpoispp(42) 242s + Q <- quadscheme(X) 242s + weirdfunction <- function(x,y){ 10 * x^2 + 5 * sin(10 * y) } 242s + Zvalues <- weirdfunction(x.quad(Q), y.quad(Q)) 242s + fot <- ppm(Q ~ y + Z, data=data.frame(Z=Zvalues)) 242s + effectfun(fot, "y", Z=0) 242s + effectfun(fot, "Z", y=0) 242s + 242s + #' multitype 242s + modX <- ppm(amacrine ~ polynom(x,2)) 242s + effectfun(modX) 242s + effectfun(modX, "x") 242s + modXM <- ppm(amacrine ~ marks*polynom(x,2)) 242s + effectfun(modXM, "x", marks="on") 242s + modXYM <- ppm(amacrine ~ marks*polynom(x,y,2)) 242s + effectfun(modXYM, "x", y=0, marks="on") 242s + 242s + df <- as.data.frame(simulate(modXM, drop=TRUE)) 242s + df$marks <- as.character(df$marks) 242s + dfpr <- predict(modXM, locations=df) 242s + } 242s + }) 242s > 242s > # 242s > # tests/project.ppm.R 242s > # 242s > # $Revision: 1.7 $ $Date: 2020/04/30 05:41:59 $ 242s > # 242s > # Tests of projection mechanism 242s > # 242s > 242s > local({ 242s + chk <- function(m) { 242s + if(!valid.ppm(m)) stop("Projected model was still not valid") 242s + return(invisible(NULL)) 242s + } 242s + 242s + if(FULLTEST) { 242s + ## a very unidentifiable model 242s + fit <- ppm(cells ~Z, Strauss(1e-06), covariates=list(Z=0)) 242s + chk(emend(fit)) 242s + ## multitype 242s + r <- matrix(1e-06, 2, 2) 242s + fit2 <- ppm(amacrine ~1, MultiStrauss(types=c("off", "on"), radii=r)) 242s + chk(emend(fit2)) 242s + ## complicated multitype 242s + fit3 <- ppm(amacrine ~1, MultiStraussHard(types=c("off", "on"), 242s + iradii=r, hradii=r/5)) 242s + chk(emend(fit3)) 242s + 242s + #' code coverage 242s + op <- spatstat.options(project.fast=TRUE) 242s + fut <- emend(fit, trace=TRUE) 242s + chk(fut) 242s + spatstat.options(op) 242s + 242s + #' hierarchical 242s + ra <- r 242s + r[2,1] <- NA 242s + fit4 <- ppm(amacrine ~1, HierStrauss(types=c("off", "on"), radii=r)) 242s + chk(emend(fit4)) 242s + #' complicated hierarchical 242s + fit5 <- ppm(amacrine ~1, HierStraussHard(types=c("off", "on"), 242s + iradii=r, hradii=r/5)) 242s + chk(emend(fit5)) 242s + 242s + ## hybrids 242s + r0 <- min(nndist(redwood)) 242s + ra <- 1.25 * r0 242s + rb <- 0.8 * r0 242s + f1 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Geyer(0.1, 2)), project=TRUE) 242s + chk(f1) 242s + f2 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Geyer(0.1, 2)), project=TRUE) 242s + chk(f2) 242s + f3 <- ppm(redwood ~1, Hybrid(A=Strauss(ra), B=Strauss(0.1)), project=TRUE) 242s + chk(f3) 242s + f4 <- ppm(redwood ~1, Hybrid(A=Strauss(rb), B=Strauss(0.1)), project=TRUE) 242s + chk(f4) 242s + f5 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Strauss(0.1)), project=TRUE) 242s + chk(f5) 242s + f6 <- ppm(redwood ~1, Hybrid(A=Hardcore(rb), B=Geyer(0.1, 2)), project=TRUE) 242s + chk(f6) 242s + f7 <- ppm(redwood ~1, Hybrid(A=Geyer(rb, 1), B=Strauss(0.1)), project=TRUE) 242s + chk(f7) 242s + } 242s + }) 242s > 242s > reset.spatstat.options() 242s > 242s BEGIN TEST testsQ.R 242s 242s R version 4.4.3 (2025-02-28) -- "Trophy Case" 242s Copyright (C) 2025 The R Foundation for Statistical Computing 242s Platform: arm-unknown-linux-gnueabihf (32-bit) 242s 242s R is free software and comes with ABSOLUTELY NO WARRANTY. 242s You are welcome to redistribute it under certain conditions. 242s Type 'license()' or 'licence()' for distribution details. 242s 242s R is a collaborative project with many contributors. 242s Type 'contributors()' for more information and 242s 'citation()' on how to cite R or R packages in publications. 242s 242s Type 'demo()' for some demos, 'help()' for on-line help, or 242s 'help.start()' for an HTML browser interface to help. 242s Type 'q()' to quit R. 242s 243s > #' 243s > #' Header for all (concatenated) test files 243s > #' 243s > #' Require spatstat.model 243s > #' Obtain environment variable controlling tests. 243s > #' 243s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 243s > 243s > require(spatstat.model) 243s Loading required package: spatstat.model 243s Loading required package: spatstat.data 243s Loading required package: spatstat.univar 244s spatstat.univar 3.1-2 244s Loading required package: spatstat.geom 244s spatstat.geom 3.3-6 244s Loading required package: spatstat.random 244s spatstat.random 3.3-3 244s Loading required package: spatstat.explore 244s Loading required package: nlme 244s spatstat.explore 3.3-4 244s Loading required package: rpart 244s spatstat.model 3.3-4 244s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 244s > ALWAYS <- TRUE 244s > cat(paste("--------- Executing", 244s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 244s + "test code -----------\n")) 244s --------- Executing **RESTRICTED** subset of test code ----------- 244s > 244s BEGIN TEST testsR1.R 244s 244s R version 4.4.3 (2025-02-28) -- "Trophy Case" 244s Copyright (C) 2025 The R Foundation for Statistical Computing 244s Platform: arm-unknown-linux-gnueabihf (32-bit) 244s 244s R is free software and comes with ABSOLUTELY NO WARRANTY. 244s You are welcome to redistribute it under certain conditions. 244s Type 'license()' or 'licence()' for distribution details. 244s 244s R is a collaborative project with many contributors. 244s Type 'contributors()' for more information and 244s 'citation()' on how to cite R or R packages in publications. 244s 244s Type 'demo()' for some demos, 'help()' for on-line help, or 244s 'help.start()' for an HTML browser interface to help. 244s Type 'q()' to quit R. 244s 244s > #' 244s > #' Header for all (concatenated) test files 244s > #' 244s > #' Require spatstat.model 244s > #' Obtain environment variable controlling tests. 244s > #' 244s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 244s > 244s > require(spatstat.model) 244s Loading required package: spatstat.model 244s Loading required package: spatstat.data 245s Loading required package: spatstat.univar 245s spatstat.univar 3.1-2 245s Loading required package: spatstat.geom 245s spatstat.geom 3.3-6 245s Loading required package: spatstat.random 245s spatstat.random 3.3-3 245s Loading required package: spatstat.explore 245s Loading required package: nlme 245s spatstat.explore 3.3-4 245s Loading required package: rpart 245s spatstat.model 3.3-4 245s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 245s > ALWAYS <- TRUE 245s > cat(paste("--------- Executing", 245s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 245s + "test code -----------\n")) 245s --------- Executing **RESTRICTED** subset of test code ----------- 245s > #' tests/resid.R 245s > #' 245s > #' Stuff related to residuals and residual diagnostics 245s > #' including residual summary functions 245s > #' 245s > #' $Revision: 1.7 $ $Date: 2022/05/22 08:43:31 $ 245s > #' 245s > 245s > local({ 245s + fit <- ppm(cells ~x, Strauss(r=0.15)) 245s + rr <- residuals(fit, quad=quadscheme(cells, nd=128)) 245s + diagnose.ppm(fit, cumulative=FALSE, type="pearson") 245s + 245s + if(FULLTEST) { 245s + diagnose.ppm(fit, cumulative=FALSE) 245s + 245s + fitoff <- ppm(cells ~ sin(x) + offset(y)) 245s + plot(a <- parres(fitoff, "x")) 245s + plot(b <- parres(fitoff, "y")) 245s + print(a) 245s + print(b) 245s + 245s + d <- diagnose.ppm(fit, which="marks") 245s + plot(d, plot.neg="discrete") 245s + plot(d, plot.neg="imagecontour") 245s + 245s + d <- diagnose.ppm(fit, type="pearson", which="smooth") 245s + plot(d, plot.smooth="image") 245s + plot(d, plot.smooth="contour") 245s + plot(d, plot.smooth="imagecontour") 245s + 245s + d <- diagnose.ppm(fit, type="pearson", which="x") 245s + plot(d) 245s + d <- diagnose.ppm(fit, type="pearson", which="y") 245s + plot(d) 245s + 245s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 245s + diagnose.ppm(fit, type="pearson", which="x", cumulative=FALSE) 245s + diagnose.ppm(fit, type="raw", plot.neg="discrete", plot.smooth="image") 245s + diagnose.ppm(fit, type="pearson", plot.neg="contour", plot.smooth="contour") 245s + 245s + diagnose.ppm(fitoff, type="raw", which="smooth", plot.smooth="persp") 245s + diagnose.ppm(fitoff, type="pearson", plot.neg="imagecontour") 245s + 245s + plot(Frame(letterR), main="") 245s + ploterodewin(letterR, erosion(letterR, 0.05), main="jeans") 245s + W <- as.mask(letterR) 245s + plot(Frame(W), main="") 245s + ploterodewin(W, erosion(W, 0.05), main="JeAnS") 245s + 245s + #' entangled terms in model 245s + U <- as.im(1, owin()) 245s + Z <- as.im(function(x,y) x, owin()) 245s + X <- runifpoint(40) 245s + fut <- ppm(X ~ Z:U) 245s + a <- parres(fut, "Z") 245s + futoff <- ppm(X ~ offset(Z*U)) 245s + a <- parres(futoff, "Z") 245s + 245s + #' residual summary functions 245s + pt <- psst(cells, interaction=Strauss(0.1), fun=nndcumfun) 245s + } 245s + }) 246s > 246s > 246s > 246s > ## 246s > ## tests/rhohat.R 246s > ## 246s > ## Test all combinations of options for rhohatCalc 246s > ## 246s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 246s > 246s > local({ 246s + if(FULLTEST) { 246s + X <- rpoispp(function(x,y){exp(3+3*x)}) 246s + Z <- as.im(function(x,y) { x }, Window(X)) 246s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 246s + 246s + 246s + ## rhohat.ppm 246s + fit <- ppm(X ~x) 246s + rhofitA <- rhohat(fit, "x") 246s + rhofitB <- rhohat(fit, "x", method="reweight") 246s + rhofitC <- rhohat(fit, "x", method="transform") 246s + rhofitD <- rhohat(fit, Z) 246s + rhofitD <- rhohat(fit, Z, positiveCI=TRUE) 246s + lam <- predict(fit) 246s + 246s + 246s + ## Horvitz-Thompson 246s + rhofitAH <- rhohat(fit, "x", horvitz=TRUE) 246s + rhofitBH <- rhohat(fit, "x", method="reweight", horvitz=TRUE) 246s + rhofitCH <- rhohat(fit, "x", method="transform", horvitz=TRUE) 246s + 246s + r2myx <- rho2hat(fit, "y", "x") 246s + r2myxw <- rho2hat(fit, "y", "x", method="reweight") 246s + plot(r2myx) 246s + plot(r2myxw) 246s + print(r2myxw) 246s + predict(r2myxw) 246s + predict(r2myxw, relative=TRUE) 246s + } 246s + }) 246s > 246s BEGIN TEST testsR2.R 246s 246s R version 4.4.3 (2025-02-28) -- "Trophy Case" 246s Copyright (C) 2025 The R Foundation for Statistical Computing 246s Platform: arm-unknown-linux-gnueabihf (32-bit) 246s 246s R is free software and comes with ABSOLUTELY NO WARRANTY. 246s You are welcome to redistribute it under certain conditions. 246s Type 'license()' or 'licence()' for distribution details. 246s 246s R is a collaborative project with many contributors. 246s Type 'contributors()' for more information and 246s 'citation()' on how to cite R or R packages in publications. 246s 246s Type 'demo()' for some demos, 'help()' for on-line help, or 246s 'help.start()' for an HTML browser interface to help. 246s Type 'q()' to quit R. 246s 246s > #' 246s > #' Header for all (concatenated) test files 246s > #' 246s > #' Require spatstat.model 246s > #' Obtain environment variable controlling tests. 246s > #' 246s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 246s > 246s > require(spatstat.model) 246s Loading required package: spatstat.model 246s Loading required package: spatstat.data 247s Loading required package: spatstat.univar 247s spatstat.univar 3.1-2 247s Loading required package: spatstat.geom 247s spatstat.geom 3.3-6 247s Loading required package: spatstat.random 247s spatstat.random 3.3-3 247s Loading required package: spatstat.explore 247s Loading required package: nlme 247s spatstat.explore 3.3-4 247s Loading required package: rpart 247s spatstat.model 3.3-4 247s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 247s > ALWAYS <- TRUE 247s > cat(paste("--------- Executing", 247s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 247s + "test code -----------\n")) 247s --------- Executing **RESTRICTED** subset of test code ----------- 247s > # 247s > # tests/rmhExpand.R 247s > # 247s > # test decisions about expansion of simulation window 247s > # 247s > # $Revision: 1.9 $ $Date: 2022/10/23 01:17:33 $ 247s > # 247s > 247s > local({ 247s + if(FULLTEST) { 247s + ## check expansion in rmhmodel.ppm 247s + fit <- ppm(cells ~x) 247s + mod <- rmhmodel(fit) 247s + is.expandable(mod) 247s + wsim <- as.rectangle(mod$trend) 247s + ## work around changes in 'unitname' 247s + wcel <- as.owin(cells) 247s + unitname(wcel) <- unitname(cells) 247s + ## test 247s + if(!identical(wsim, wcel)) 247s + stop("Expansion occurred improperly in rmhmodel.ppm") 247s + } 247s + }) 247s > 247s > 247s > 247s > # 247s > # tests/rmhTrend.R 247s > # 247s > # Problems with trend images (rmhmodel.ppm or rmhEngine) 247s > # 247s > 247s > if(ALWAYS) { 247s + local({ 247s + set.seed(42) 247s + 247s + # Bug folder 37 of 8 feb 2011 247s + # rmhmodel.ppm -> predict.ppm 247s + # + rmhResolveTypes -> is.subset.owin 247s + 247s + Z <- rescale(demopat, 7000) 247s + X <- unmark(Z) 247s + X1 <- split(Z)[[1]] 247s + Int <- density(X,dimyx=200) 247s + Lint <- eval.im(log(npoints(X1)*Int/npoints(X))) 247s + M <- as.owin(Int) 247s + MR <- intersect.owin(M,scalardilate(M,0.5,origin="midpoint")) 247s + X1 <- X1[MR] 247s + Fut <- ppm(X1~offset(Lint),covariates=list(Lint=Lint), 247s + inter=BadGey(r=c(0.03,0.05),sat=3)) 247s + Y <- rmh(Fut,control=list(expand=M,nrep=1e3), verbose=FALSE) 247s + 248s + }) 248s + } 248s > # 248s > # tests/rmhmodel.ppm.R 248s > # 248s > # $Revision: 1.10 $ $Date: 2020/05/01 05:29:42 $ 248s > # 248s > # Case-by-case tests of rmhmodel.ppm 248s > # 248s > 248s > if(FULLTEST) { 248s + local({ 248s + f <- ppm(cells) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~x) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, Strauss(0.1)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, StraussHard(r=0.1,hc=0.05)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + f <- ppm(cells ~1, Hardcore(0.07)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, DiggleGratton(0.05,0.1)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, Softcore(0.5), correction="isotropic") 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, Geyer(0.07,2)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, BadGey(c(0.07,0.1,0.13),2)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, PairPiece(r = c(0.05, 0.1, 0.2))) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~1, AreaInter(r=0.06)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + # multitype 248s + 248s + r <- matrix(0.07, 2, 2) 248s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + h <- matrix(min(nndist(amacrine))/2, 2, 2) 248s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 248s + m <- rmhmodel(f) 248s + 248s + diag(r) <- NA 248s + diag(h) <- NA 248s + f <- ppm(amacrine ~1, MultiStrauss(c("off","on"),r)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(amacrine ~1, MultiStraussHard(c("off","on"),r, h)) 248s + m <- rmhmodel(f) 248s + 248s + # multitype data, interaction not dependent on type 248s + 248s + f <- ppm(amacrine ~marks, Strauss(0.05)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + # trends 248s + 248s + f <- ppm(cells ~x, Strauss(0.1)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~y, StraussHard(r=0.1,hc=0.05)) 248s + m <- rmhmodel(f) 248s + 248s + f <- ppm(cells ~x+y, Hardcore(0.07)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + f <- ppm(cells ~polynom(x,y,2), Softcore(0.5), correction="isotropic") 248s + m <- rmhmodel(f) 248s + 248s + # covariates 248s + 248s + Z <- as.im(function(x,y){ x^2+y^2 }, as.owin(cells)) 248s + f <- ppm(cells ~z, covariates=list(z=Z)) 248s + m <- rmhmodel(f) 248s + m <- rmhmodel(f, control=list(p=1)) 248s + print(m) 248s + 248s + Zim <- as.im(Z, as.owin(cells)) 248s + f <- ppm(cells ~z, covariates=list(z=Zim)) 248s + m <- rmhmodel(f) 248s + 248s + Z <- as.im(function(x,y){ x^2+y }, as.owin(amacrine)) 248s + f <- ppm(amacrine ~z + marks, covariates=list(z=Z)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + m <- rmhmodel(f, control=list(p=1)) 248s + m <- rmhmodel(f, control=list(p=1,fixall=TRUE)) 248s + print(m) 248s + 248s + Zim <- as.im(Z, as.owin(amacrine)) 248s + f <- ppm(amacrine ~z + marks, covariates=list(z=Zim)) 248s + m <- rmhmodel(f) 248s + print(m) 248s + 248s + }) 248s + } 248s > # 248s > # tests/rmhmodelHybrids.R 248s > # 248s > # Test that rmhmodel.ppm and rmhmodel.default 248s > # work on Hybrid interaction models 248s > # 248s > # $Revision: 1.6 $ $Date: 2022/10/23 01:17:56 $ 248s > # 248s > 248s > if(ALWAYS) { # involves C code 248s + local({ 248s + 248s + ## ......... rmhmodel.ppm ....................... 248s + fit1 <- ppm(redwood ~1, 248s + Hybrid(A=Strauss(0.02), B=Geyer(0.1, 2), C=Geyer(0.15, 1))) 248s + m1 <- rmhmodel(fit1) 248s + m1 248s + reach(m1) 248s + 248s + ## Test of handling 'IsOffset' 248s + fit2 <- ppm(cells ~1, Hybrid(H=Hardcore(0.05), G=Geyer(0.15, 2))) 248s + m2 <- rmhmodel(fit2) 248s + ## also test C code for hybrid interaction with hard core 248s + fakecells <- rmh(fit2, nrep=1e4) 248s + 248s + ## Test of handling Poisson components 248s + fit3 <- ppm(cells ~1, Hybrid(P=Poisson(), S=Strauss(0.05))) 248s + X3 <- rmh(fit3, control=list(nrep=1e3,expand=1), verbose=FALSE) 248s + 248s + 248s + }) 248s + } 248s Extracting model information...Evaluating trend...done. 248s Extracting model information...Evaluating trend...done. 248s Extracting model information...Evaluating trend...done. 248s Checking arguments..determining simulation windows...Starting simulation. 248s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 248s > 248s > # 248s > # tests/rmh.ppm.R 248s > # 248s > # $Revision: 1.5 $ $Date: 2020/05/01 05:29:42 $ 248s > # 248s > # Examples removed from rmh.ppm.Rd 248s > # stripped down to minimal tests of validity 248s > # 248s > 248s > local({ 248s + op <- spatstat.options() 248s + spatstat.options(rmh.nrep=10, npixel=10, ndummy.min=10) 248s + spatstat.options(project.fast=TRUE) 248s + Nrep <- 10 248s + 248s + X <- swedishpines 248s + if(FULLTEST) { 248s + ## Poisson process 248s + fit <- ppm(X ~1, Poisson()) 248s + Xsim <- rmh(fit) 248s + } 248s + if(ALWAYS) { # Gibbs model => C code 248s + ## Strauss process 248s + fit <- ppm(X ~1, Strauss(r=7)) 248s + Xsim <- rmh(fit) 248s + 248s + ## Strauss process simulated on a larger window 248s + ## then clipped to original window 248s + Xsim <- rmh(fit, control=list(nrep=Nrep, expand=1.1, periodic=TRUE)) 248s + 248s + ## Extension of model to another window (thanks to Tuomas Rajala) 248s + Xsim <- rmh(fit, w=square(2)) 248s + Xsim <- simulate(fit, w=square(2)) 248s + 248s + ## Strauss - hard core process 248s + ## fit <- ppm(X ~1, StraussHard(r=7,hc=2)) 248s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 248s + 248s + ## Geyer saturation process 248s + ## fit <- ppm(X ~1, Geyer(r=7,sat=2)) 248s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 248s + 248s + ## Area-interaction process 248s + fit <- ppm(X ~1, AreaInter(r=7)) 248s + Xsim <- rmh(fit, start=list(n.start=X$n)) 248s + 248s + ## Penttinen process 248s + fit <- ppm(X ~1, Penttinen(r=7)) 248s + Xsim <- rmh(fit, start=list(n.start=X$n)) 248s + 248s + ## soft core interaction process 248s + ## X <- quadscheme(X, nd=50) 248s + ## fit <- ppm(X ~1, Softcore(kappa=0.1), correction="isotropic") 248s + ## Xsim <- rmh(fit, start=list(n.start=X$n)) 248s + 248s + ## Diggle-Gratton pairwise interaction model 248s + ## fit <- ppm(cells ~1, DiggleGratton(0.05, 0.1)) 248s + ## Xsim <- rmh(fit, start=list(n.start=cells$n)) 248s + ## plot(Xsim, main="simulation from fitted Diggle-Gratton model") 248s + 248s + 248s + ## piecewise-constant pairwise interaction function 248s + X <- rSSI(0.05, 100) 248s + fit <- ppm(X ~1, PairPiece(seq(0.02, 0.1, by=0.01))) 248s + Xsim <- rmh(fit) 248s + } 248s + 248s + ## marked point pattern 248s + Y <- amacrine 248s + 248s + if(FULLTEST) { 248s + #' marked Poisson models 248s + fit <- ppm(Y) 248s + Ysim <- rmh(fit) 248s + 248s + fit <- ppm(Y~marks) 248s + Ysim <- rmh(fit) 248s + 248s + fit <- ppm(Y~x) 248s + Ysim <- rmh(fit) 248s + 248s + fit <- ppm(Y~marks+x) 248s + Ysim <- rmh(fit) 248s + } 248s + 248s + if(ALWAYS) { 248s + #' multitype Strauss 248s + typ <- levels(Y$marks) 248s + MS <- MultiStrauss(types = typ, 248s + radii=matrix(0.07, ncol=2, nrow=2)) 248s + 248s + fit <- ppm(Y~marks*x, MS) 248s + Ysim <- rmh(fit) 248s + 248s + #' multitype Hardcore 248s + h0 <- minnndist(unmark(Y)) * 0.95 248s + MH <- MultiHard(types = typ, 248s + hradii=matrix(h0, ncol=2, nrow=2)) 248s + fit <- ppm(Y ~ marks+x, MH) 248s + Ysim <- rmh(fit) 248s + #' other code blocks 248s + Ysim <- rmh(fit, control=list(periodic=TRUE, expand=1)) 248s + Ysim <- rmh(fit, control=list(periodic=FALSE, expand=1)) 248s + #' multihard core with invalid initial state 248s + Ydouble <- superimpose(Y, rjitter(Y, h0/10)) 248s + Ysim <- rmh(fit, start=list(x.start=Ydouble)) 248s + 248s + #' Lennard-Jones 248s + fut <- ppm(unmark(longleaf) ~ 1, LennardJones(), rbord=1) 248s + Ysim <- rmh(fut) 248s + Ysim <- rmh(fut, control=list(periodic=TRUE, expand=1)) 248s + } 248s + 248s + spatstat.options(op) 248s + }) 248s Extracting model information...Evaluating trend...done. 248s Checking arguments..determining simulation windows...Starting simulation. 248s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 248s Extracting model information...Evaluating trend...done. 248s Checking arguments..determining simulation windows...Starting simulation. 248s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 248s Extracting model information...Evaluating trend...done. 248s Checking arguments..determining simulation windows...Starting simulation. 248s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 251s Extracting model information...Evaluating trend...done. 251s Checking arguments..determining simulation windows...Starting simulation. 251s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 251s Extracting model information...Evaluating trend...done. 251s Checking arguments..determining simulation windows...Starting simulation. 251s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 251s Model is invalid - projecting it 251s Extracting model information...Evaluating trend...done. 251s Checking arguments..determining simulation windows...Starting simulation. 251s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 252s Extracting model information...Evaluating trend...done. 252s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 252s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 252s Extracting model information...Evaluating trend...done. 252s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 252s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 252s Extracting model information...Evaluating trend...done. 252s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 252s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 252s Extracting model information...Evaluating trend...done. 252s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 252s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 252s Extracting model information...Evaluating trend...done. 252s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 252s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 253s Extracting model information...Evaluating trend...done. 253s Checking arguments..determining simulation windows...Starting simulation. 253s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 253s Extracting model information...Evaluating trend...done. 253s Checking arguments..determining simulation windows...Starting simulation. 253s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 253s > 253s > 253s > reset.spatstat.options() 253s > #' 253s > #' tests/rmhsnoopy.R 253s > #' 253s > #' Test the rmh interactive debugger 253s > #' 253s > #' $Revision: 1.11 $ $Date: 2022/10/23 01:19:00 $ 253s > 253s > if(ALWAYS) { # may depend on platform 253s + local({ 253s + R <- 0.1 253s + ## fit a model and prepare to simulate 253s + model <- ppm(amacrine ~ marks + x, Strauss(R)) 253s + siminfo <- rmh(model, preponly=TRUE) 253s + Wsim <- siminfo$control$internal$w.sim 253s + Wclip <- siminfo$control$internal$w.clip 253s + if(is.null(Wclip)) Wclip <- Window(cells) 253s + 253s + ## determine debugger interface panel geometry 253s + Xinit <- runifpoint(ex=amacrine)[1:40] 253s + P <- rmhsnoop(Wsim=Wsim, Wclip=Wclip, R=R, 253s + xcoords=Xinit$x, 253s + ycoords=Xinit$y, 253s + mlevels=levels(marks(Xinit)), 253s + mcodes=as.integer(marks(Xinit)) - 1L, 253s + irep=3L, itype=1L, 253s + proptype=1, proplocn=c(0.5, 0.5), propmark=0, propindx=0, 253s + numerator=42, denominator=24, 253s + panel.only=TRUE) 253s + boxes <- P$boxes 253s + clicknames <- names(P$clicks) 253s + boxcentres <- do.call(concatxy, lapply(boxes, centroid.owin)) 253s + 253s + ## design a sequence of clicks 253s + actionsequence <- c("Up", "Down", "Left", "Right", 253s + "At Proposal", "Zoom Out", "Zoom In", "Reset", 253s + "Accept", "Reject", "Print Info", 253s + "Next Iteration", "Next Shift", "Next Death", 253s + "Skip 10", "Skip 100", "Skip 1000", "Skip 10,000", 253s + "Skip 100,000", "Exit Debugger") 253s + actionsequence <- match(actionsequence, clicknames) 253s + actionsequence <- actionsequence[!is.na(actionsequence)] 253s + xy <- lapply(boxcentres, "[", actionsequence) 253s + 253s + ## queue the click sequence 253s + spatstat.utils::queueSpatstatLocator(xy$x,xy$y) 253s + 253s + ## go 253s + rmh(model, snoop=TRUE) 253s + }) 253s + } 253s Extracting model information...Evaluating trend...done. 253s Checking arguments..determining simulation windows...Evaluating trend integral...Extracting model information...Evaluating trend...done. 253s Checking arguments..determining simulation windows...Evaluating trend integral...Starting simulation. 253s Initial state... 253s Creating debugger environment..Done. 253s Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 254s 254s 254s ------------------- 254s Iteration 0 254s Simulation window: 254s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 254s Clipping window: 254s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 254s Current state: 254s Marked planar point pattern: 72 points 254s Multitype, with levels = off, on 254s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 254s Proposal type: Shift 254s Shift data point 18 from current location (0.290108, 0.0160037, “off”) to 254s new location (0.620599, 0.378428, “off”) 254s Hastings ratio = 6831.92992943033 / 14545.6615344203 = 0.469688498750194 254s Fate of proposal: Rejected 256s Marked planar point pattern: 350 points 256s Multitype, with levels = off, on 256s window: rectangle = [0, 1.6012085] x [0, 1] units (one unit = 662 microns) 256s Pattern was generated by Metropolis-Hastings simulation. 256s > 256s BEGIN TEST testsS.R 256s 256s R version 4.4.3 (2025-02-28) -- "Trophy Case" 256s Copyright (C) 2025 The R Foundation for Statistical Computing 256s Platform: arm-unknown-linux-gnueabihf (32-bit) 256s 256s R is free software and comes with ABSOLUTELY NO WARRANTY. 256s You are welcome to redistribute it under certain conditions. 256s Type 'license()' or 'licence()' for distribution details. 256s 256s R is a collaborative project with many contributors. 256s Type 'contributors()' for more information and 256s 'citation()' on how to cite R or R packages in publications. 256s 256s Type 'demo()' for some demos, 'help()' for on-line help, or 256s 'help.start()' for an HTML browser interface to help. 256s Type 'q()' to quit R. 256s 256s > #' 256s > #' Header for all (concatenated) test files 256s > #' 256s > #' Require spatstat.model 256s > #' Obtain environment variable controlling tests. 256s > #' 256s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 256s > 256s > require(spatstat.model) 256s Loading required package: spatstat.model 256s Loading required package: spatstat.data 257s Loading required package: spatstat.univar 257s spatstat.univar 3.1-2 257s Loading required package: spatstat.geom 257s spatstat.geom 3.3-6 257s Loading required package: spatstat.random 257s spatstat.random 3.3-3 257s Loading required package: spatstat.explore 257s Loading required package: nlme 257s spatstat.explore 3.3-4 257s Loading required package: rpart 257s spatstat.model 3.3-4 257s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 257s > ALWAYS <- TRUE 257s > cat(paste("--------- Executing", 257s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 257s + "test code -----------\n")) 257s --------- Executing **RESTRICTED** subset of test code ----------- 257s > # 257s > # tests/slrm.R 257s > # 257s > # $Revision: 1.3 $ $Date: 2020/05/01 09:59:59 $ 257s > # 257s > # Test slrm fitting and prediction when there are NA's 257s > # 257s > 257s > if(ALWAYS) { 257s + local({ 257s + X <- copper$SouthPoints 257s + W <- owin(poly=list(x=c(0,35,35,1),y=c(1,1,150,150))) 257s + Y <- X[W] 257s + fit <- slrm(Y ~ x+y) 257s + pred <- predict(fit) 257s + extractAIC(fit) 257s + fitx <- update(fit, . ~ x) 257s + simulate(fitx, seed=42) 257s + if(FULLTEST) { 257s + unitname(fitx) 257s + unitname(fitx) <- "km" 257s + 257s + mur <- solapply(murchison,rescale, 1000, "km") 257s + mur$dfault <- distfun(mur$faults) 257s + fut <- slrm(gold ~ dfault, data=mur, splitby="greenstone") 257s + A <- model.images(fut) 257s + } 257s + }) 257s + } 257s > 257s > 257s > # 257s > # tests/step.R 257s > # 257s > # $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 257s > # 257s > # test for step() operation 257s > # 257s > if(FULLTEST) { 257s + local({ 257s + Z <- as.im(function(x,y){ x^3 - y^2 }, nztrees$window) 257s + fitP <- ppm(nztrees ~x+y+Z, covariates=list(Z=Z)) 257s + step(fitP) 257s + fitS <- update(fitP, Strauss(7)) 257s + step(fitS) 257s + fitM <- ppm(amacrine ~ marks*(x+y), 257s + MultiStrauss(types=levels(marks(amacrine)), radii=matrix(0.04, 2, 2))) 257s + step(fitM) 257s + }) 257s + } 257s > 257s > 257s > 257s > 257s BEGIN TEST testsT.R 257s 257s R version 4.4.3 (2025-02-28) -- "Trophy Case" 257s Copyright (C) 2025 The R Foundation for Statistical Computing 257s Platform: arm-unknown-linux-gnueabihf (32-bit) 257s 257s R is free software and comes with ABSOLUTELY NO WARRANTY. 257s You are welcome to redistribute it under certain conditions. 257s Type 'license()' or 'licence()' for distribution details. 257s 257s R is a collaborative project with many contributors. 257s Type 'contributors()' for more information and 257s 'citation()' on how to cite R or R packages in publications. 257s 257s Type 'demo()' for some demos, 'help()' for on-line help, or 257s 'help.start()' for an HTML browser interface to help. 257s Type 'q()' to quit R. 257s 257s > #' 257s > #' Header for all (concatenated) test files 257s > #' 257s > #' Require spatstat.model 257s > #' Obtain environment variable controlling tests. 257s > #' 257s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 257s > 257s > require(spatstat.model) 257s Loading required package: spatstat.model 257s Loading required package: spatstat.data 258s Loading required package: spatstat.univar 258s spatstat.univar 3.1-2 258s Loading required package: spatstat.geom 258s spatstat.geom 3.3-6 258s Loading required package: spatstat.random 258s spatstat.random 3.3-3 258s Loading required package: spatstat.explore 258s Loading required package: nlme 259s spatstat.explore 3.3-4 259s Loading required package: rpart 259s spatstat.model 3.3-4 259s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 259s > ALWAYS <- TRUE 259s > cat(paste("--------- Executing", 259s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 259s + "test code -----------\n")) 259s --------- Executing **RESTRICTED** subset of test code ----------- 259s > # 259s > # tests/testaddvar.R 259s > # 259s > # test addvar options 259s > # 259s > # $Revision: 1.3 $ $Date: 2020/05/02 01:32:58 $ 259s > 259s > if(FULLTEST) { 259s + local({ 259s + X <- rpoispp(function(x,y){exp(3+3*x)}) 259s + model <- ppm(X ~y) 259s + addvar(model, "x", crosscheck=TRUE) 259s + addvar(model, "x", bw.input="quad") 259s + w <- square(0.5) 259s + addvar(model, "x", subregion=w) 259s + addvar(model, "x", subregion=w, bw.input="points") 259s + Z <- as.im(function(x,y) { x }, Window(X)) 259s + addvar(model, Z) 259s + }) 259s + } 259s > # 259s > # tests/testparres.R 259s > # 259s > # additional test of parres 259s > # 259s > # $Revision: 1.8 $ $Date: 2022/05/20 06:59:59 $ 259s > # 259s > 259s > if(FULLTEST) { 259s + local({ 259s + X <- rpoispp(function(x,y){exp(3+x+2*x^2)}) 259s + model <- ppm(X ~x+y) 259s + 259s + # options in parres (and code blocks in print.parres) 259s + parres(model, "x") 259s + parres(model, "x", smooth.effect=TRUE) 259s + parres(model, "x", bw.input="quad") 259s + w <- square(0.5) 259s + parres(model, "x", subregion=w) 259s + parres(model, "x", subregion=w, bw.input="quad") 259s + f <- function(x,y) { x + y } 259s + parres(model, f) 259s + 259s + # check whether 'update.ppm' has messed up internals 259s + mod2 <- update(model, ~x) 259s + parres(mod2, "x") 259s + 259s + #' other kinds of covariates 259s + mod3 <- ppm(X ~ x + offset(y)) 259s + parres(mod3, "offset(y)") 259s + Z <- distmap(runifpoint(3)) 259s + parres(mod3, Z) 259s + mod4 <- ppm(X ~ sin(x), data=solist(B=Z)) 259s + parres(mod4, "sin(x)") 259s + parres(mod4, "B") 259s + 259s + #' models with interaction 259s + mod5 <- ppm(cells ~ x, AreaInter(0.06)) 259s + parres(mod5, "x") 259s + dlin <- distfun(copper$SouthLines) 259s + copfit <- ppm(copper$SouthPoints ~ dlin, Geyer(1,1)) 259s + parres(copfit, "dlin") 259s + 259s + #' covariate need not be specified if there is only one. 259s + parres(mod5) 259s + parres(copfit) 259s + 259s + #' infrastructure 259s + ltuae <- evaluateCovariate(42, cells) 259s + LTUAE <- evaluateCovariate(ltuae, cells) 259s + 259s + fit <- ppm(amacrine ~ x * marks, nd=16) 259s + dmat <- model.depends(fit) 259s + check.separable(dmat, "x", c(x=FALSE, marks=FALSE), FALSE) 259s + check.separable(dmat, "x", c(FALSE, FALSE), FALSE) 259s + check.separable(dmat, "x", c(x=FALSE, marks=TRUE), FALSE) 259s + }) 259s + } 259s > #' 259s > #' tests/threedee.R 259s > #' 259s > #' Tests of 3D code 259s > #' 259s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 259s > #' 259s > 259s > local({ 259s + X <- runifpoint3(30) 259s + Y <- runifpoint3(20) 259s + if(FULLTEST) { 259s + A <- runifpoint3(10, nsim=2) 259s + Z <- ppsubset(X, 2:4) 259s + } 259s + ## 259s + if(ALWAYS) { # includes C code 259s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 259s + d <- crossdist(X, Y, squared=TRUE) 259s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 259s + #' 259s + h <- has.close(X, 0.2) 259s + h <- has.close(X, 0.2, periodic=TRUE) 259s + h <- has.close(X, 0.2, Y=Y) 259s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 259s + #' code blocks not otherwise reached 259s + rmax <- 0.6 * max(nndist(X)) 259s + g <- G3est(X, rmax=rmax, correction="rs") 259s + g <- G3est(X, rmax=rmax, correction="km") 259s + g <- G3est(X, rmax=rmax, correction="Hanisch") 259s + g <- G3est(X, rmax=rmax, sphere="ideal") 259s + g <- G3est(X, rmax=rmax, sphere="digital") 259s + v <- sphere.volume() 259s + v <- digital.volume() 259s + #' older code 259s + co <- coords(X) 259s + xx <- co$x 259s + yy <- co$y 259s + zz <- co$z 259s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 259s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 259s + ff1 <- f3engine(xx, yy, zz, correction="no") 259s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 259s + } 259s + ## 259s + if(ALWAYS) { 259s + #'class support 259s + X <- runifpoint3(10) 259s + print(X) 259s + print(X %mark% runif(10)) 259s + print(X %mark% factor(letters[c(1:5,5:1)])) 259s + print(X %mark% data.frame(a=1:10, b=runif(10))) 259s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 259s + print(X %mark% da) 259s + print(X %mark% data.frame(a=1:10, b=da)) 259s + } 259s + }) 259s Three-dimensional point pattern: 10 points 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s Marked three-dimensional point pattern: 10 points 259s marks are numeric, of storage type ‘double’ 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s Marked three-dimensional point pattern: 10 points 259s Multitype, with levels = a, b, c, d, e 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s Marked three-dimensional point pattern: 10 points 259s Mark variables: a, b 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s Marked three-dimensional point pattern: 10 points 259s marks are dates, of class ‘Date’ 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s Warning messages: 259s 1: In G3est: unrecognised argument ‘sphere’ was ignored 259s 2: In G3est: unrecognised argument ‘sphere’ was ignored 259s Marked three-dimensional point pattern: 10 points 259s Mark variables: a, b 259s Box: [0, 1] x [0, 1] x [0, 1] units 259s > # 259s > # tests/triplets.R 259s > # 259s > # test code for triplet interaction 259s > # 259s > # $Revision: 1.9 $ $Date: 2022/05/22 08:45:38 $ 259s > # 259s > if(ALWAYS) { # C code, platform dependence 259s + local({ 259s + #' valid model 259s + fit <- ppm(cells ~1, Triplets(0.1)) 259s + fit 259s + suffstat(fit) 259s + #' invalid model 259s + fitR <- ppm(redwood ~1, Triplets(0.1)) 259s + fitR 259s + suffstat(fitR) 259s + #' hard core (zero triangles, coefficient is NA) 259s + fit0 <- ppm(cells ~1, Triplets(0.05)) 259s + fit0 259s + suffstat(fit0) 259s + #' bug case (1 triangle in data) 259s + fit1 <- ppm(cells ~1, Triplets(0.15)) 259s + fit1 259s + suffstat(fit1) 259s + #' simulation 259s + X <- simulate(fit) 259s + mod <- list(cif="triplets",par=list(beta=50,gamma=0.2,r=0.07), w=square(1)) 259s + Xm <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 259s + #' hard core 259s + mod$par$gamma <- 0 259s + XmHard <- rmh(model=mod,start=list(n.start=5), control=list(nrep=1e5)) 259s + }) 259s + } 260s Checking arguments..determining simulation windows...Starting simulation. 260s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 260s Checking arguments..determining simulation windows...Starting simulation. 260s Initial state...Ready to simulate. Generating proposal points...Running Metropolis-Hastings. 260s > 260s BEGIN TEST testsUtoZ.R 260s 260s R version 4.4.3 (2025-02-28) -- "Trophy Case" 260s Copyright (C) 2025 The R Foundation for Statistical Computing 260s Platform: arm-unknown-linux-gnueabihf (32-bit) 260s 260s R is free software and comes with ABSOLUTELY NO WARRANTY. 260s You are welcome to redistribute it under certain conditions. 260s Type 'license()' or 'licence()' for distribution details. 260s 260s R is a collaborative project with many contributors. 260s Type 'contributors()' for more information and 260s 'citation()' on how to cite R or R packages in publications. 260s 260s Type 'demo()' for some demos, 'help()' for on-line help, or 260s 'help.start()' for an HTML browser interface to help. 260s Type 'q()' to quit R. 260s 261s Loading required package: spatstat.model 261s > #' 261s > #' Header for all (concatenated) test files 261s > #' 261s > #' Require spatstat.model 261s > #' Obtain environment variable controlling tests. 261s > #' 261s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 261s > 261s > require(spatstat.model) 261s Loading required package: spatstat.data 262s Loading required package: spatstat.univar 262s spatstat.univar 3.1-2 262s Loading required package: spatstat.geom 262s spatstat.geom 3.3-6 262s Loading required package: spatstat.random 262s spatstat.random 3.3-3 262s Loading required package: spatstat.explore 262s Loading required package: nlme 262s spatstat.explore 3.3-4 262s Loading required package: rpart 262s spatstat.model 3.3-4 262s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 262s > ALWAYS <- TRUE 262s > cat(paste("--------- Executing", 262s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 262s + "test code -----------\n")) 262s --------- Executing **RESTRICTED** subset of test code ----------- 262s > # 262s > # tests/undoc.R 262s > # 262s > # $Revision: 1.16 $ $Date: 2020/11/02 07:06:49 $ 262s > # 262s > # Test undocumented hacks, experimental code, etc 262s > 262s > 262s > local({ 262s + if(FULLTEST) { 262s + ## cases of 'pickoption' 262s + aliases <- c(Lenin="Ulyanov", Stalin="Djugashvili", Trotsky="Bronstein") 262s + surname <- "Trot" 262s + pickoption("leader", surname, aliases) 262s + pickoption("leader", surname, aliases, exact=TRUE, die=FALSE) 262s + } 262s + if(ALWAYS) { 262s + ## pixellate.ppp accepts a data frame of weights 262s + pixellate(cells, weights=data.frame(a=1:42, b=42:1)) 262s + ## test parts of 'rmhsnoop' that don't require interaction with user 262s + rmhSnoopEnv(cells, Window(cells), 0.1) 262s + } 262s + if(FULLTEST) { 262s + ## Berman-Turner frame 262s + A <- bt.frame(quadscheme(cells), ~x, Strauss(0.07), rbord=0.07) 262s + print(A) 262s + ## digestCovariates 262s + D <- distfun(cells) 262s + Z <- distmap(cells) 262s + U <- dirichlet(cells) 262s + stopifnot(is.scov(D)) 262s + stopifnot(is.scov(Z)) 262s + stopifnot(is.scov(U)) 262s + stopifnot(is.scov("x")) 262s + dg <- digestCovariates(D=D,Z=Z,U=U,"x",list(A="x", B=D)) 262s + ## 262s + a <- getfields(dg, c("A", "D", "niets"), fatal=FALSE) 262s + ## util.R 262s + gg <- pointgrid(owin(), 7) 262s + checkbigmatrix(1000000L, 1000000L, FALSE, TRUE) 262s + spatstatDiagnostic("whatever") 262s + M <- list(list(a=2, b=FALSE), 262s + list(a=2, b=TRUE)) 262s + stopifnot(!allElementsIdentical(M)) 262s + stopifnot(allElementsIdentical(M, "a")) 262s + ## 262s + A <- Strauss(0.1) 262s + A <- reincarnate.interact(A) 262s + ## 262s + ## special lists 262s + B <- solist(a=cells, b=redwood, c=japanesepines) 262s + BB <- as.ppplist(B) 262s + BL <- as.layered(B) 262s + DB <- as.imlist(lapply(B, density)) 262s + is.solist(B) 262s + is.ppplist(B) 262s + is.imlist(DB) 262s + ## case of density.ppplist 262s + DEB <- density(BB, se=TRUE) 262s + } 262s + 262s + if(ALWAYS) { 262s + ## fft 262s + z <- matrix(1:16, 4, 4) 262s + a <- fft2D(z, west=FALSE) 262s + if(fftwAvailable()) 262s + b <- fft2D(z, west=TRUE) 262s + } 262s + 262s + if(ALWAYS) { 262s + ## experimental interactions 262s + pot <- function(d, par) { d <= 0.1 } 262s + A <- Saturated(pot) 262s + print(A) 262s + A <- update(A, name="something") 262s + ppm(amacrine ~ x, A, rbord=0.1) 262s + } 262s + 262s + if(ALWAYS) { # platform dependent 262s + #' version-checking 262s + now <- Sys.Date() 262s + versioncurrency.spatstat(now + 80, FALSE) 262s + versioncurrency.spatstat(now + 140, FALSE) 262s + versioncurrency.spatstat(now + 400, FALSE) 262s + versioncurrency.spatstat(now + 1000) 262s + } 262s + 262s + if(FULLTEST) { 262s + #' general Ord interaction 262s + gradual <- function(d, pars) { 262s + y <- pmax(0, 0.005 - d)/0.005 262s + if(is.matrix(d)) y <- matrix(y, nrow(d), ncol(d)) 262s + return(y) 262s + } 262s + B <- Ord(gradual, "gradual Ord process") 262s + } 262s + }) 262s Saturated pairwise interaction family 262s Interaction:Saturated process with user-defined potential 262s Potential function: 262s function (d, par) 262s { 262s d <= 0.1 262s } 262s 262s > 262s > 262s > ## 262s > ## tests/updateppm.R 262s > ## 262s > ## Check validity of update.ppm 262s > ## 262s > ## $Revision: 1.8 $ $Date: 2022/10/23 01:19:19 $ 262s > 262s > local({ 262s + if(ALWAYS) { 262s + require(spatstat.utils) 262s + h <- function(m1, m2) { 262s + mc <- short.deparse(sys.call()) 262s + cat(paste(mc, "\t... ")) 262s + m1name <- short.deparse(substitute(m1)) 262s + m2name <- short.deparse(substitute(m2)) 262s + if(!identical(names(coef(m1)), names(coef(m2)))) 262s + stop(paste("Differing results for", m1name, "and", m2name, 262s + "in updateppm.R"), 262s + call.=FALSE) 262s + cat("OK\n") 262s + } 262s + 262s + X <- redwood[c(TRUE,FALSE)] 262s + Y <- redwood[c(FALSE,TRUE)] 262s + fit0f <- ppm(X ~ 1, nd=8) 262s + fit0p <- ppm(X, ~1, nd=8) 262s + fitxf <- ppm(X ~ x, nd=8) 262s + fitxp <- ppm(X, ~x, nd=8) 262s + 262s + cat("Basic consistency ...\n") 262s + h(fit0f, fit0p) 262s + h(fitxf, fitxp) 262s + 262s + cat("\nTest correct handling of model formulas ...\n") 262s + h(update(fitxf, Y), fitxf) 262s + h(update(fitxf, Q=Y), fitxf) 262s + h(update(fitxf, Y~x), fitxf) 262s + h(update(fitxf, Q=Y~x), fitxf) 262s + h(update(fitxf, ~x), fitxf) 262s + } 262s + 262s + if(FULLTEST) { 262s + h(update(fitxf, Y~1), fit0f) 262s + h(update(fitxf, ~1), fit0f) 262s Loading required package: spatstat.utils 262s + h(update(fit0f, Y~x), fitxf) 262s + h(update(fit0f, ~x), fitxf) 262s + 262s + h(update(fitxp, Y), fitxp) 262s + h(update(fitxp, Q=Y), fitxp) 262s + h(update(fitxp, Y~x), fitxp) 262s + h(update(fitxp, Q=Y~x), fitxp) 262s + h(update(fitxp, ~x), fitxp) 262s + 262s + h(update(fitxp, Y~1), fit0p) 262s + h(update(fitxp, ~1), fit0p) 262s + h(update(fit0p, Y~x), fitxp) 262s + h(update(fit0p, ~x), fitxp) 262s + } 262s + 262s + if(ALWAYS) { 262s + cat("\nTest scope handling for left hand side ...\n") 262s + X <- Y 262s + h(update(fitxf), fitxf) 262s + } 262s + 262s + if(ALWAYS) { 262s + cat("\nTest scope handling for right hand side ...\n") 262s + Z <- distmap(X) 262s + fitZf <- ppm(X ~ Z) 262s + fitZp <- ppm(X, ~ Z) 262s + h(update(fitxf, X ~ Z), fitZf) 262s + } 262s + if(FULLTEST) { 262s + h(update(fitxp, X ~ Z), fitZp) 262s + h(update(fitxf, . ~ Z), fitZf) 262s + h(update(fitZf, . ~ x), fitxf) 262s + h(update(fitZf, . ~ . - Z), fit0f) 262s + h(update(fitxp, . ~ Z), fitZp) 262s + h(update(fitZp, . ~ . - Z), fit0p) 262s + h(update(fit0p, . ~ . + Z), fitZp) 262s + h(update(fitZf, . ~ . ), fitZf) 262s + h(update(fitZp, . ~ . ), fitZp) 262s + } 262s + if(ALWAYS) { 262s + cat("\nTest use of internal data ...\n") 262s + h(update(fitZf, ~ x, use.internal=TRUE), fitxf) 262s + fitsin <- update(fitZf, X~sin(Z)) 262s + h(update(fitZf, ~ sin(Z), use.internal=TRUE), fitsin) 262s + } 262s + if(FULLTEST) { 262s + cat("\nTest step() ... ") 262s + fut <- ppm(X ~ Z + x + y, nd=8) 262s + fut0 <- step(fut, trace=0) 262s + cat("OK\n") 262s + } 262s + 262s + }) 262s Basic consistency ... 262s h(fit0f, fit0p) ... OK 262s h(fitxf, fitxp) ... OK 262s 262s Test correct handling of model formulas ... 262s h(update(fitxf, Y), fitxf) ... OK 262s h(update(fitxf, Q = Y), fitxf) ... OK 262s h(update(fitxf, Y ~ x), fitxf) ... OK 262s h(update(fitxf, Q = Y ~ x), fitxf) ... OK 262s h(update(fitxf, ~x), fitxf) ... OK 262s 262s Test scope handling for left hand side ... 262s h(update(fitxf), fitxf) ... OK 262s 262s Test scope handling for right hand side ... 262s h(update(fitxf, X ~ Z), fitZf) ... OK 262s 262s Test use of internal data ... 262s h(update(fitZf, ~x, use.internal = TRUE), fitxf) ... OK 262s h(update(fitZf, ~sin(Z), use.internal = TRUE), fitsin) ... OK 262s > # 262s > # tests/vcovppm.R 262s > # 262s > # Check validity of vcov.ppm algorithms 262s > # 262s > # Thanks to Ege Rubak 262s > # 262s > # $Revision: 1.12 $ $Date: 2020/05/02 01:32:58 $ 262s > # 262s > 262s > local({ 262s + 262s + set.seed(42) 262s + X <- rStrauss(200, .5, .05) 262s + model <- ppm(X, inter = Strauss(.05)) 262s + 262s + if(ALWAYS) { 262s + b <- vcov(model, generic = TRUE, algorithm = "basic") 262s + v <- vcov(model, generic = TRUE, algorithm = "vector") 262s + vc <- vcov(model, generic = TRUE, algorithm = "vectorclip") 262s + vn <- vcov(model, generic = FALSE) 262s + 262s + disagree <- function(x, y, tol=1e-7) { max(abs(x-y)) > tol } 262s + asymmetric <- function(x) { disagree(x, t(x)) } 262s + 262s + if(asymmetric(b)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm") 262s + if(asymmetric(v)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm") 262s + if(asymmetric(vc)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm") 262s + if(asymmetric(vn)) 262s + stop("Non-symmetric matrix produced by vcov.ppm Strauss algorithm") 262s + 262s + if(disagree(v, b)) 262s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' ") 262s + if(disagree(v, vc)) 262s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' ") 262s + if(disagree(vn, vc)) 262s + stop("Disagreement between vcov.ppm generic and Strauss algorithms") 262s + } 262s + 262s + if(ALWAYS) { # C code 262s + ## Geyer code 262s + xx <- c(0.7375956, 0.6851697, 0.6399788, 0.6188382) 262s + yy <- c(0.5816040, 0.6456319, 0.5150633, 0.6191592) 262s + Y <- ppp(xx, yy, window=square(1)) 262s + modelY <- ppm(Y ~1, Geyer(0.1, 1)) 262s + 262s + b <- vcov(modelY, generic = TRUE, algorithm = "basic") 262s + v <- vcov(modelY, generic = TRUE, algorithm = "vector") 262s + vc <- vcov(modelY, generic = TRUE, algorithm = "vectorclip") 262s + 262s + if(asymmetric(b)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'basic' algorithm for Geyer model") 262s + if(asymmetric(v)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'vector' algorithm for Geyer model") 262s + if(asymmetric(vc)) 262s + stop("Non-symmetric matrix produced by vcov.ppm 'vectorclip' algorithm for Geyer model") 262s + 262s + if(disagree(v, b)) 262s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'basic' for Geyer model") 262s + if(disagree(v, vc)) 262s + stop("Disagreement between vcov.ppm algorithms 'vector' and 'vectorclip' for Geyer model") 262s + } 262s + 262s + if(ALWAYS) { # C code 262s + ## tests of 'deltasuffstat' code 262s + ## Handling of offset terms 262s + modelH <- ppm(cells ~x, Hardcore(0.05)) 262s + a <- vcov(modelH, generic=TRUE) ## may fall over 262s + b <- vcov(modelH, generic=FALSE) 262s + if(disagree(a, b)) 262s + stop("Disagreement between vcov.ppm algorithms for Hardcore model") 262s + 262s + ## Correctness of pairwise.family$delta2 262s + modelZ <- ppm(amacrine ~1, MultiStrauss(radii=matrix(0.1, 2, 2))) 262s + b <- vcov(modelZ, generic=FALSE) 262s + g <- vcov(modelZ, generic=TRUE) 262s + if(disagree(b, g)) 262s + stop("Disagreement between vcov.ppm algorithms for MultiStrauss model") 262s + 262s + ## Test that 'deltasuffstat' works for Hybrids 262s + modelHyb <- ppm(japanesepines ~ 1, Hybrid(Strauss(0.05), Strauss(0.1))) 262s + vHyb <- vcov(modelHyb) 262s + } 262s + 262s + if(FULLTEST) { 262s + ## Code blocks for other choices of 'what' 262s + model <- ppm(X ~ 1, Strauss(.05)) 262s + cG <- vcov(model, what="corr") 262s + cP <- vcov(update(model, Poisson()), what="corr") 262s + ## outdated usage 262s + cX <- vcov(model, A1dummy=TRUE) 262s + 262s + ## Model with zero-length coefficient vector 262s + lam <- intensity(X) 262s + f <- function(x,y) { rep(lam, length(x)) } 262s + model0 <- ppm(X ~ offset(log(f)) - 1) 262s + dd <- vcov(model0) 262s + cc <- vcov(model0, what="corr") 262s + 262s + ## Model with NA coefficients 262s + fit <- ppm(X ~ log(f)) 262s + vcov(fit) 262s + fitE <- emend(fit, trace=TRUE) 262s + 262s + ## Other weird stuff 262s + su <- suffloc(ppm(X ~ x)) 262s + } 262s + }) 264s > 265s autopkgtest [02:35:49]: test run-unit-test: -----------------------] 268s run-unit-test PASS 268s autopkgtest [02:35:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 273s autopkgtest [02:35:57]: test pkg-r-autopkgtest: preparing testbed 296s autopkgtest [02:36:20]: testbed dpkg architecture: armhf 297s autopkgtest [02:36:21]: testbed apt version: 3.0.0 301s autopkgtest [02:36:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 303s autopkgtest [02:36:27]: testbed release detected to be: questing 310s autopkgtest [02:36:34]: updating testbed package index (apt update) 312s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 312s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 313s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 313s Get:4 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(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 ... 63953 files and directories currently installed.) 333s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 333s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 333s Setting up dpkg (1.22.18ubuntu3) ... 333s (Reading database ... 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(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 ... 63953 files and directories currently installed.) 334s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 334s Unpacking distro-info-data (0.64) over (0.63) ... 334s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 334s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 334s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 334s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 334s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 334s Unpacking ed (1.21.1-1) over (1.21-1) ... 334s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 334s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 334s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 334s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 334s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 334s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 334s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 334s Unpacking nano (8.4-1) over (8.3-1) ... 334s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 334s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 334s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 334s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 334s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 334s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 334s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 334s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 335s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 335s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 335s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 335s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 335s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 335s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 335s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 335s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 335s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 335s Setting up motd-news-config (13.7ubuntu1) ... 335s Setting up liburcu8t64:armhf (0.15.2-2) ... 335s Setting up distro-info-data (0.64) ... 335s Setting up htop (3.4.1-4) ... 335s Setting up libsensors-config (1:3.6.2-2) ... 335s Installing new version of config file /etc/sensors3.conf ... 335s Setting up libfwupd3:armhf (2.0.8-3) ... 335s Setting up libftdi1-2:armhf (1.5-10) ... 335s Setting up libnvme1t64 (1.13-2) ... 335s Setting up ed (1.21.1-1) ... 335s Setting up usb.ids (2025.04.01-1) ... 335s Setting up libsensors5:armhf (1:3.6.2-2) ... 335s Setting up libdpkg-perl (1.22.18ubuntu3) ... 335s Setting up nano (8.4-1) ... 335s Installing new version of config file /etc/nanorc ... 335s Setting up ubuntu-pro-client (35.1ubuntu0) ... 335s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 335s 335s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 335s 335s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 335s 337s Setting up fwupd (2.0.8-3) ... 337s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 337s fwupd.service is a disabled or a static unit not running, not starting it. 337s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 337s Setting up dpkg-dev (1.22.18ubuntu3) ... 337s Processing triggers for dbus (1.16.2-2ubuntu1) ... 337s Processing triggers for install-info (7.1.1-1) ... 337s Processing triggers for libc-bin (2.41-6ubuntu1) ... 338s Processing triggers for man-db (2.13.0-1) ... 339s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 339s Processing triggers for initramfs-tools (0.147ubuntu1) ... 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 342s Starting pkgProblemResolver with broken count: 0 342s Starting 2 pkgProblemResolver with broken count: 0 342s Done 342s Solving dependencies... 343s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 345s autopkgtest [02:37:09]: rebooting testbed after setup commands that affected boot 408s Reading package lists... 408s Building dependency tree... 408s Reading state information... 409s Starting pkgProblemResolver with broken count: 0 409s Starting 2 pkgProblemResolver with broken count: 0 409s Done 410s The following NEW packages will be installed: 410s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 410s cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config 410s fonts-dejavu-core fonts-dejavu-mono fonts-mathjax g++ g++-14 410s g++-14-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc gcc-14 410s gcc-14-arm-linux-gnueabihf gcc-arm-linux-gnueabihf gfortran gfortran-14 410s gfortran-14-arm-linux-gnueabihf gfortran-arm-linux-gnueabihf icu-devtools 410s libasan8 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcairo2 410s libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 410s libfreetype6 libgcc-14-dev libgfortran-14-dev libgfortran5 libgomp1 410s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libice6 libicu-dev 410s libisl23 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 410s libjpeg8-dev libjs-mathjax liblapack-dev liblapack3 liblerc4 liblzma-dev 410s libmpc3 libncurses-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 410s libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev 410s libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev 410s libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 libthai-data libthai0 410s libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 410s libxft2 libxrender1 libxss1 libxt6t64 linux-libc-dev littler 410s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev r-cran-abind 410s r-cran-codetools r-cran-deldir r-cran-foreach r-cran-glmnet r-cran-goftest 410s r-cran-gsl r-cran-iterators r-cran-lattice r-cran-littler r-cran-matrix 410s r-cran-mgcv r-cran-nleqslv r-cran-nlme r-cran-pkgkitten r-cran-polyclip 410s r-cran-rcpp r-cran-rcppeigen r-cran-rpart r-cran-shape r-cran-sm 410s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 410s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 410s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.univar 410s r-cran-spatstat.utils r-cran-survival r-cran-tensor rpcsvc-proto unzip 410s x11-common xdg-utils zip zlib1g-dev 410s 0 upgraded, 139 newly installed, 0 to remove and 0 not upgraded. 410s Need to get 175 MB of archives. 410s After this operation, 441 MB of additional disk space will be used. 410s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libc-dev-bin armhf 2.41-6ubuntu1 [21.7 kB] 410s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf linux-libc-dev armhf 6.14.0-15.15 [1687 kB] 410s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 411s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 411s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libc6-dev armhf 2.41-6ubuntu1 [1396 kB] 411s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libisl23 armhf 0.27-1 [546 kB] 411s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 411s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9221 kB] 411s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14 armhf 14.2.0-19ubuntu2 [1032 B] 411s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 411s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 411s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libcc1-0 armhf 15-20250404-0ubuntu1 [43.3 kB] 411s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 411s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libasan8 armhf 15-20250404-0ubuntu1 [2951 kB] 411s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libubsan1 armhf 15-20250404-0ubuntu1 [1188 kB] 411s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libgcc-14-dev armhf 14.2.0-19ubuntu2 [897 kB] 411s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [18.0 MB] 412s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14 armhf 14.2.0-19ubuntu2 [510 kB] 412s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 412s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 412s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libstdc++-14-dev armhf 14.2.0-19ubuntu2 [2576 kB] 412s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [10.5 MB] 412s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf g++-14 armhf 14.2.0-19ubuntu2 [23.0 kB] 412s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 412s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 412s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf build-essential armhf 12.12ubuntu1 [5088 B] 412s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 412s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 412s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 412s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 412s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 412s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 412s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig armhf 2.15.0-2.2ubuntu1 [190 kB] 412s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 412s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 412s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran-14-dev armhf 14.2.0-19ubuntu2 [370 kB] 412s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9763 kB] 412s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14 armhf 14.2.0-19ubuntu2 [14.2 kB] 412s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 412s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 412s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 412s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 412s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 412s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 412s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 412s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 412s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 412s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 412s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 412s Get:50 http://ftpmaster.internal/ubuntu questing/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 412s Get:51 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 412s Get:52 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 412s Get:53 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 412s Get:54 http://ftpmaster.internal/ubuntu questing/universe armhf libgslcblas0 armhf 2.8+dfsg-5ubuntu1 [84.4 kB] 412s Get:55 http://ftpmaster.internal/ubuntu questing/universe armhf libgsl28 armhf 2.8+dfsg-5ubuntu1 [876 kB] 412s Get:56 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 413s Get:57 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 413s Get:58 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 413s Get:59 http://ftpmaster.internal/ubuntu questing/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 413s Get:60 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 413s Get:61 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 413s Get:62 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 413s Get:63 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 413s Get:64 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 413s Get:65 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 413s Get:66 http://ftpmaster.internal/ubuntu questing/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 413s Get:67 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 413s Get:68 http://ftpmaster.internal/ubuntu questing/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 413s Get:69 http://ftpmaster.internal/ubuntu questing/main armhf libthai-data all 0.1.29-2build1 [158 kB] 413s Get:70 http://ftpmaster.internal/ubuntu questing/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 413s Get:71 http://ftpmaster.internal/ubuntu questing/main armhf libpango-1.0-0 armhf 1.56.3-1 [216 kB] 414s Get:72 http://ftpmaster.internal/ubuntu questing/main armhf libpangoft2-1.0-0 armhf 1.56.3-1 [44.1 kB] 414s Get:73 http://ftpmaster.internal/ubuntu questing/main armhf libpangocairo-1.0-0 armhf 1.56.3-1 [25.0 kB] 414s Get:74 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 414s Get:75 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 414s Get:76 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 414s Get:77 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 414s Get:78 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 414s Get:79 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 414s Get:80 http://ftpmaster.internal/ubuntu questing/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 414s Get:81 http://ftpmaster.internal/ubuntu questing/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 414s Get:82 http://ftpmaster.internal/ubuntu questing/main armhf libpng-dev armhf 1.6.47-1.1 [251 kB] 414s Get:83 http://ftpmaster.internal/ubuntu questing/main armhf libreadline-dev armhf 8.2-6 [153 kB] 414s Get:84 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 414s Get:85 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 414s Get:86 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 414s Get:87 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 414s Get:88 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 414s Get:89 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 414s Get:90 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 414s Get:91 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 414s Get:92 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 414s Get:93 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 414s Get:94 http://ftpmaster.internal/ubuntu questing/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 414s Get:95 http://ftpmaster.internal/ubuntu questing/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 414s Get:96 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 414s Get:97 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 415s Get:98 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-littler armhf 0.3.20-2 [90.9 kB] 415s Get:99 http://ftpmaster.internal/ubuntu questing/universe armhf littler all 0.3.20-2 [2554 B] 415s Get:100 http://ftpmaster.internal/ubuntu questing/main armhf liblzma-dev armhf 5.6.4-1ubuntu1 [166 kB] 415s Get:101 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 415s Get:102 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 415s Get:103 http://ftpmaster.internal/ubuntu questing/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 415s Get:104 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-dev all 4.4.3-1 [4176 B] 415s Get:105 http://ftpmaster.internal/ubuntu questing/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 415s Get:106 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 415s Get:107 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-codetools all 0.2-20-1 [90.5 kB] 415s Get:108 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-deldir armhf 2.0-4-1build1 [268 kB] 415s Get:109 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-iterators all 1.0.14-1 [336 kB] 415s Get:110 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-foreach all 1.5.2-1 [124 kB] 415s Get:111 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 415s Get:112 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 416s Get:113 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-shape all 1.4.6.1-1 [749 kB] 416s Get:114 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 416s Get:115 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 416s Get:116 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rcpp armhf 1.0.14-1 [1976 kB] 416s Get:117 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rcppeigen armhf 0.3.4.0.2-1 [1402 kB] 416s Get:118 http://ftpmaster.internal/ubuntu questing/main armhf libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 416s Get:119 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-glmnet armhf 4.1-8-1 [1881 kB] 416s Get:120 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-goftest armhf 1.2-3-1 [58.6 kB] 416s Get:121 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-gsl armhf 2.1-8-1build1 [481 kB] 416s Get:122 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 416s Get:123 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 416s Get:124 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-nleqslv armhf 3.3.5-1 [97.2 kB] 416s Get:125 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-polyclip armhf 1.10-7-1 [109 kB] 416s Get:126 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 416s Get:127 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-sm armhf 2.2-6.0-1 [787 kB] 416s Get:128 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatial armhf 7.3-18-1 [131 kB] 416s Get:129 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.utils armhf 3.1-3-1 [384 kB] 416s Get:130 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.data all 3.1-6-1 [4153 kB] 416s Get:131 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.univar armhf 3.1-2-1 [310 kB] 416s Get:132 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.geom armhf 3.3-6-1 [3923 kB] 417s Get:133 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.random armhf 3.3-3-1 [1155 kB] 417s Get:134 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-tensor all 1.5-4 [15.7 kB] 417s Get:135 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.sparse armhf 3.1-0-1 [216 kB] 417s Get:136 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.explore armhf 3.3-4-1 [3271 kB] 417s Get:137 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.model armhf 3.3-4-1 [3397 kB] 417s Get:138 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.linnet armhf 3.2-5-1 [1505 kB] 417s Get:139 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat armhf 3.3-1-1 [4121 kB] 418s Preconfiguring packages ... 418s Fetched 175 MB in 7s (24.8 MB/s) 418s Selecting previously unselected package libc-dev-bin. 418s (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 ... 63951 files and directories currently installed.) 418s Preparing to unpack .../000-libc-dev-bin_2.41-6ubuntu1_armhf.deb ... 418s Unpacking libc-dev-bin (2.41-6ubuntu1) ... 418s Selecting previously unselected package linux-libc-dev:armhf. 418s Preparing to unpack .../001-linux-libc-dev_6.14.0-15.15_armhf.deb ... 418s Unpacking linux-libc-dev:armhf (6.14.0-15.15) ... 418s Selecting previously unselected package libcrypt-dev:armhf. 418s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 418s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 418s Selecting previously unselected package rpcsvc-proto. 418s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 418s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 418s Selecting previously unselected package libc6-dev:armhf. 418s Preparing to unpack .../004-libc6-dev_2.41-6ubuntu1_armhf.deb ... 418s Unpacking libc6-dev:armhf (2.41-6ubuntu1) ... 418s Selecting previously unselected package libisl23:armhf. 418s Preparing to unpack .../005-libisl23_0.27-1_armhf.deb ... 418s Unpacking libisl23:armhf (0.27-1) ... 418s Selecting previously unselected package libmpc3:armhf. 418s Preparing to unpack .../006-libmpc3_1.3.1-1build2_armhf.deb ... 418s Unpacking libmpc3:armhf (1.3.1-1build2) ... 418s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 418s Preparing to unpack .../007-cpp-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 418s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 418s Selecting previously unselected package cpp-14. 418s Preparing to unpack .../008-cpp-14_14.2.0-19ubuntu2_armhf.deb ... 418s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 418s Selecting previously unselected package cpp-arm-linux-gnueabihf. 418s Preparing to unpack .../009-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 418s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 418s Selecting previously unselected package cpp. 418s Preparing to unpack .../010-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 419s Unpacking cpp (4:14.2.0-1ubuntu1) ... 419s Selecting previously unselected package libcc1-0:armhf. 419s Preparing to unpack .../011-libcc1-0_15-20250404-0ubuntu1_armhf.deb ... 419s Unpacking libcc1-0:armhf (15-20250404-0ubuntu1) ... 419s Selecting previously unselected package libgomp1:armhf. 419s Preparing to unpack .../012-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 419s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 419s Selecting previously unselected package libasan8:armhf. 419s Preparing to unpack .../013-libasan8_15-20250404-0ubuntu1_armhf.deb ... 419s Unpacking libasan8:armhf (15-20250404-0ubuntu1) ... 419s Selecting previously unselected package libubsan1:armhf. 419s Preparing to unpack .../014-libubsan1_15-20250404-0ubuntu1_armhf.deb ... 419s Unpacking libubsan1:armhf (15-20250404-0ubuntu1) ... 419s Selecting previously unselected package libgcc-14-dev:armhf. 419s Preparing to unpack .../015-libgcc-14-dev_14.2.0-19ubuntu2_armhf.deb ... 419s Unpacking libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 419s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 419s Preparing to unpack .../016-gcc-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 419s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 419s Selecting previously unselected package gcc-14. 419s Preparing to unpack .../017-gcc-14_14.2.0-19ubuntu2_armhf.deb ... 419s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 419s Selecting previously unselected package gcc-arm-linux-gnueabihf. 419s Preparing to unpack .../018-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 419s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 419s Selecting previously unselected package gcc. 419s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 419s Unpacking gcc (4:14.2.0-1ubuntu1) ... 419s Selecting previously unselected package libstdc++-14-dev:armhf. 419s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-19ubuntu2_armhf.deb ... 419s Unpacking libstdc++-14-dev:armhf (14.2.0-19ubuntu2) ... 420s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 420s Preparing to unpack .../021-g++-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 420s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 420s Selecting previously unselected package g++-14. 420s Preparing to unpack .../022-g++-14_14.2.0-19ubuntu2_armhf.deb ... 420s Unpacking g++-14 (14.2.0-19ubuntu2) ... 420s Selecting previously unselected package g++-arm-linux-gnueabihf. 420s Preparing to unpack .../023-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 420s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 420s Selecting previously unselected package g++. 420s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 420s Unpacking g++ (4:14.2.0-1ubuntu1) ... 420s Selecting previously unselected package build-essential. 420s Preparing to unpack .../025-build-essential_12.12ubuntu1_armhf.deb ... 420s Unpacking build-essential (12.12ubuntu1) ... 420s Selecting previously unselected package dctrl-tools. 420s Preparing to unpack .../026-dctrl-tools_2.24-3build3_armhf.deb ... 420s Unpacking dctrl-tools (2.24-3build3) ... 420s Selecting previously unselected package libfreetype6:armhf. 420s Preparing to unpack .../027-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 420s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 420s Selecting previously unselected package fonts-dejavu-mono. 420s Preparing to unpack .../028-fonts-dejavu-mono_2.37-8_all.deb ... 420s Unpacking fonts-dejavu-mono (2.37-8) ... 420s Selecting previously unselected package fonts-dejavu-core. 420s Preparing to unpack .../029-fonts-dejavu-core_2.37-8_all.deb ... 420s Unpacking fonts-dejavu-core (2.37-8) ... 420s Selecting previously unselected package fontconfig-config. 420s Preparing to unpack .../030-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 420s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 420s Selecting previously unselected package libfontconfig1:armhf. 421s Preparing to unpack .../031-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 421s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 421s Selecting previously unselected package fontconfig. 421s Preparing to unpack .../032-fontconfig_2.15.0-2.2ubuntu1_armhf.deb ... 421s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 421s Selecting previously unselected package fonts-mathjax. 421s Preparing to unpack .../033-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 421s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 421s Selecting previously unselected package libgfortran5:armhf. 421s Preparing to unpack .../034-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 421s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 421s Selecting previously unselected package libgfortran-14-dev:armhf. 421s Preparing to unpack .../035-libgfortran-14-dev_14.2.0-19ubuntu2_armhf.deb ... 421s Unpacking libgfortran-14-dev:armhf (14.2.0-19ubuntu2) ... 421s Selecting previously unselected package gfortran-14-arm-linux-gnueabihf. 421s Preparing to unpack .../036-gfortran-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 421s Unpacking gfortran-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 421s Selecting previously unselected package gfortran-14. 421s Preparing to unpack .../037-gfortran-14_14.2.0-19ubuntu2_armhf.deb ... 421s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 421s Selecting previously unselected package gfortran-arm-linux-gnueabihf. 421s Preparing to unpack .../038-gfortran-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 421s Unpacking gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 421s Selecting previously unselected package gfortran. 421s Preparing to unpack .../039-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 421s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 421s Selecting previously unselected package icu-devtools. 421s Preparing to unpack .../040-icu-devtools_76.1-1ubuntu2_armhf.deb ... 421s Unpacking icu-devtools (76.1-1ubuntu2) ... 421s Selecting previously unselected package libblas3:armhf. 421s Preparing to unpack .../041-libblas3_3.12.1-2_armhf.deb ... 421s Unpacking libblas3:armhf (3.12.1-2) ... 421s Selecting previously unselected package libblas-dev:armhf. 421s Preparing to unpack .../042-libblas-dev_3.12.1-2_armhf.deb ... 421s Unpacking libblas-dev:armhf (3.12.1-2) ... 421s Selecting previously unselected package libbz2-dev:armhf. 421s Preparing to unpack .../043-libbz2-dev_1.0.8-6_armhf.deb ... 421s Unpacking libbz2-dev:armhf (1.0.8-6) ... 421s Selecting previously unselected package libpixman-1-0:armhf. 421s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_armhf.deb ... 421s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 421s Selecting previously unselected package libxcb-render0:armhf. 421s Preparing to unpack .../045-libxcb-render0_1.17.0-2_armhf.deb ... 421s Unpacking libxcb-render0:armhf (1.17.0-2) ... 421s Selecting previously unselected package libxcb-shm0:armhf. 421s Preparing to unpack .../046-libxcb-shm0_1.17.0-2_armhf.deb ... 421s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 421s Selecting previously unselected package libxrender1:armhf. 421s Preparing to unpack .../047-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 421s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 421s Selecting previously unselected package libcairo2:armhf. 421s Preparing to unpack .../048-libcairo2_1.18.4-1_armhf.deb ... 421s Unpacking libcairo2:armhf (1.18.4-1) ... 421s Selecting previously unselected package libdatrie1:armhf. 422s Preparing to unpack .../049-libdatrie1_0.2.13-3build1_armhf.deb ... 422s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 422s Selecting previously unselected package libdeflate0:armhf. 422s Preparing to unpack .../050-libdeflate0_1.23-1_armhf.deb ... 422s Unpacking libdeflate0:armhf (1.23-1) ... 422s Selecting previously unselected package libdeflate-dev:armhf. 422s Preparing to unpack .../051-libdeflate-dev_1.23-1_armhf.deb ... 422s Unpacking libdeflate-dev:armhf (1.23-1) ... 422s Selecting previously unselected package libgraphite2-3:armhf. 422s Preparing to unpack .../052-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 422s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 422s Selecting previously unselected package libgslcblas0:armhf. 422s Preparing to unpack .../053-libgslcblas0_2.8+dfsg-5ubuntu1_armhf.deb ... 422s Unpacking libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 422s Selecting previously unselected package libgsl28:armhf. 422s Preparing to unpack .../054-libgsl28_2.8+dfsg-5ubuntu1_armhf.deb ... 422s Unpacking libgsl28:armhf (2.8+dfsg-5ubuntu1) ... 422s Selecting previously unselected package libharfbuzz0b:armhf. 422s Preparing to unpack .../055-libharfbuzz0b_10.2.0-1_armhf.deb ... 422s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 422s Selecting previously unselected package x11-common. 422s Preparing to unpack .../056-x11-common_1%3a7.7+23ubuntu4_all.deb ... 422s Unpacking x11-common (1:7.7+23ubuntu4) ... 422s Selecting previously unselected package libice6:armhf. 422s Preparing to unpack .../057-libice6_2%3a1.1.1-1_armhf.deb ... 422s Unpacking libice6:armhf (2:1.1.1-1) ... 422s Selecting previously unselected package libicu-dev:armhf. 422s Preparing to unpack .../058-libicu-dev_76.1-1ubuntu2_armhf.deb ... 422s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 422s Selecting previously unselected package libjpeg-turbo8:armhf. 422s Preparing to unpack .../059-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 422s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 422s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 422s Preparing to unpack .../060-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 422s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 422s Selecting previously unselected package libjpeg8:armhf. 422s Preparing to unpack .../061-libjpeg8_8c-2ubuntu11_armhf.deb ... 422s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 422s Selecting previously unselected package libjpeg8-dev:armhf. 422s Preparing to unpack .../062-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 422s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 422s Selecting previously unselected package libjpeg-dev:armhf. 422s Preparing to unpack .../063-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 422s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 422s Selecting previously unselected package liblapack3:armhf. 422s Preparing to unpack .../064-liblapack3_3.12.1-2_armhf.deb ... 422s Unpacking liblapack3:armhf (3.12.1-2) ... 422s Selecting previously unselected package liblapack-dev:armhf. 423s Preparing to unpack .../065-liblapack-dev_3.12.1-2_armhf.deb ... 423s Unpacking liblapack-dev:armhf (3.12.1-2) ... 423s Selecting previously unselected package liblerc4:armhf. 423s Preparing to unpack .../066-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 423s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 423s Selecting previously unselected package libncurses-dev:armhf. 423s Preparing to unpack .../067-libncurses-dev_6.5+20250216-2_armhf.deb ... 423s Unpacking libncurses-dev:armhf (6.5+20250216-2) ... 423s Selecting previously unselected package libthai-data. 423s Preparing to unpack .../068-libthai-data_0.1.29-2build1_all.deb ... 423s Unpacking libthai-data (0.1.29-2build1) ... 423s Selecting previously unselected package libthai0:armhf. 423s Preparing to unpack .../069-libthai0_0.1.29-2build1_armhf.deb ... 423s Unpacking libthai0:armhf (0.1.29-2build1) ... 423s Selecting previously unselected package libpango-1.0-0:armhf. 423s Preparing to unpack .../070-libpango-1.0-0_1.56.3-1_armhf.deb ... 423s Unpacking libpango-1.0-0:armhf (1.56.3-1) ... 423s Selecting previously unselected package libpangoft2-1.0-0:armhf. 423s Preparing to unpack .../071-libpangoft2-1.0-0_1.56.3-1_armhf.deb ... 423s Unpacking libpangoft2-1.0-0:armhf (1.56.3-1) ... 423s Selecting previously unselected package libpangocairo-1.0-0:armhf. 423s Preparing to unpack .../072-libpangocairo-1.0-0_1.56.3-1_armhf.deb ... 423s Unpacking libpangocairo-1.0-0:armhf (1.56.3-1) ... 423s Selecting previously unselected package libpaper2:armhf. 423s Preparing to unpack .../073-libpaper2_2.2.5-0.3_armhf.deb ... 423s Unpacking libpaper2:armhf (2.2.5-0.3) ... 423s Selecting previously unselected package libpaper-utils. 423s Preparing to unpack .../074-libpaper-utils_2.2.5-0.3_armhf.deb ... 423s Unpacking libpaper-utils (2.2.5-0.3) ... 423s Selecting previously unselected package libpcre2-16-0:armhf. 423s Preparing to unpack .../075-libpcre2-16-0_10.45-1_armhf.deb ... 423s Unpacking libpcre2-16-0:armhf (10.45-1) ... 423s Selecting previously unselected package libpcre2-32-0:armhf. 423s Preparing to unpack .../076-libpcre2-32-0_10.45-1_armhf.deb ... 423s Unpacking libpcre2-32-0:armhf (10.45-1) ... 423s Selecting previously unselected package libpcre2-posix3:armhf. 423s Preparing to unpack .../077-libpcre2-posix3_10.45-1_armhf.deb ... 423s Unpacking libpcre2-posix3:armhf (10.45-1) ... 423s Selecting previously unselected package libpcre2-dev:armhf. 423s Preparing to unpack .../078-libpcre2-dev_10.45-1_armhf.deb ... 423s Unpacking libpcre2-dev:armhf (10.45-1) ... 423s Selecting previously unselected package libpkgconf3:armhf. 423s Preparing to unpack .../079-libpkgconf3_1.8.1-4_armhf.deb ... 423s Unpacking libpkgconf3:armhf (1.8.1-4) ... 423s Selecting previously unselected package zlib1g-dev:armhf. 423s Preparing to unpack .../080-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 423s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 423s Selecting previously unselected package libpng-dev:armhf. 423s Preparing to unpack .../081-libpng-dev_1.6.47-1.1_armhf.deb ... 423s Unpacking libpng-dev:armhf (1.6.47-1.1) ... 423s Selecting previously unselected package libreadline-dev:armhf. 423s Preparing to unpack .../082-libreadline-dev_8.2-6_armhf.deb ... 423s Unpacking libreadline-dev:armhf (8.2-6) ... 423s Selecting previously unselected package libsharpyuv0:armhf. 423s Preparing to unpack .../083-libsharpyuv0_1.5.0-0.1_armhf.deb ... 423s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 423s Selecting previously unselected package libsm6:armhf. 423s Preparing to unpack .../084-libsm6_2%3a1.2.4-1_armhf.deb ... 423s Unpacking libsm6:armhf (2:1.2.4-1) ... 423s Selecting previously unselected package libtcl8.6:armhf. 423s Preparing to unpack .../085-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 423s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 423s Selecting previously unselected package libjbig0:armhf. 423s Preparing to unpack .../086-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 423s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 423s Selecting previously unselected package libwebp7:armhf. 423s Preparing to unpack .../087-libwebp7_1.5.0-0.1_armhf.deb ... 423s Unpacking libwebp7:armhf (1.5.0-0.1) ... 423s Selecting previously unselected package libtiff6:armhf. 424s Preparing to unpack .../088-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 424s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 424s Selecting previously unselected package libxft2:armhf. 424s Preparing to unpack .../089-libxft2_2.3.6-1build1_armhf.deb ... 424s Unpacking libxft2:armhf (2.3.6-1build1) ... 424s Selecting previously unselected package libxss1:armhf. 424s Preparing to unpack .../090-libxss1_1%3a1.2.3-1build3_armhf.deb ... 424s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 424s Selecting previously unselected package libtk8.6:armhf. 424s Preparing to unpack .../091-libtk8.6_8.6.16-1_armhf.deb ... 424s Unpacking libtk8.6:armhf (8.6.16-1) ... 424s Selecting previously unselected package libxt6t64:armhf. 424s Preparing to unpack .../092-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 424s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 424s Selecting previously unselected package zip. 424s Preparing to unpack .../093-zip_3.0-14ubuntu2_armhf.deb ... 424s Unpacking zip (3.0-14ubuntu2) ... 424s Selecting previously unselected package unzip. 424s Preparing to unpack .../094-unzip_6.0-28ubuntu6_armhf.deb ... 424s Unpacking unzip (6.0-28ubuntu6) ... 424s Selecting previously unselected package xdg-utils. 424s Preparing to unpack .../095-xdg-utils_1.2.1-2ubuntu1_all.deb ... 424s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 424s Selecting previously unselected package r-base-core. 424s Preparing to unpack .../096-r-base-core_4.4.3-1_armhf.deb ... 424s Unpacking r-base-core (4.4.3-1) ... 424s Selecting previously unselected package r-cran-littler. 424s Preparing to unpack .../097-r-cran-littler_0.3.20-2_armhf.deb ... 424s Unpacking r-cran-littler (0.3.20-2) ... 424s Selecting previously unselected package littler. 424s Preparing to unpack .../098-littler_0.3.20-2_all.deb ... 424s Unpacking littler (0.3.20-2) ... 424s Selecting previously unselected package liblzma-dev:armhf. 424s Preparing to unpack .../099-liblzma-dev_5.6.4-1ubuntu1_armhf.deb ... 424s Unpacking liblzma-dev:armhf (5.6.4-1ubuntu1) ... 424s Selecting previously unselected package pkgconf-bin. 424s Preparing to unpack .../100-pkgconf-bin_1.8.1-4_armhf.deb ... 424s Unpacking pkgconf-bin (1.8.1-4) ... 424s Selecting previously unselected package pkgconf:armhf. 424s Preparing to unpack .../101-pkgconf_1.8.1-4_armhf.deb ... 424s Unpacking pkgconf:armhf (1.8.1-4) ... 424s Selecting previously unselected package libtirpc-dev:armhf. 424s Preparing to unpack .../102-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 424s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 424s Selecting previously unselected package r-base-dev. 424s Preparing to unpack .../103-r-base-dev_4.4.3-1_all.deb ... 425s Unpacking r-base-dev (4.4.3-1) ... 425s Selecting previously unselected package pkg-r-autopkgtest. 425s Preparing to unpack .../104-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 425s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 425s Selecting previously unselected package r-cran-abind. 425s Preparing to unpack .../105-r-cran-abind_1.4-8-1_all.deb ... 425s Unpacking r-cran-abind (1.4-8-1) ... 425s Selecting previously unselected package r-cran-codetools. 425s Preparing to unpack .../106-r-cran-codetools_0.2-20-1_all.deb ... 425s Unpacking r-cran-codetools (0.2-20-1) ... 425s Selecting previously unselected package r-cran-deldir. 425s Preparing to unpack .../107-r-cran-deldir_2.0-4-1build1_armhf.deb ... 425s Unpacking r-cran-deldir (2.0-4-1build1) ... 425s Selecting previously unselected package r-cran-iterators. 425s Preparing to unpack .../108-r-cran-iterators_1.0.14-1_all.deb ... 425s Unpacking r-cran-iterators (1.0.14-1) ... 425s Selecting previously unselected package r-cran-foreach. 425s Preparing to unpack .../109-r-cran-foreach_1.5.2-1_all.deb ... 425s Unpacking r-cran-foreach (1.5.2-1) ... 425s Selecting previously unselected package r-cran-lattice. 425s Preparing to unpack .../110-r-cran-lattice_0.22-6-1_armhf.deb ... 425s Unpacking r-cran-lattice (0.22-6-1) ... 425s Selecting previously unselected package r-cran-matrix. 425s Preparing to unpack .../111-r-cran-matrix_1.7-3-1_armhf.deb ... 425s Unpacking r-cran-matrix (1.7-3-1) ... 425s Selecting previously unselected package r-cran-shape. 425s Preparing to unpack .../112-r-cran-shape_1.4.6.1-1_all.deb ... 425s Unpacking r-cran-shape (1.4.6.1-1) ... 425s Selecting previously unselected package r-cran-survival. 425s Preparing to unpack .../113-r-cran-survival_3.8-3-1_armhf.deb ... 425s Unpacking r-cran-survival (3.8-3-1) ... 425s Selecting previously unselected package r-cran-pkgkitten. 425s Preparing to unpack .../114-r-cran-pkgkitten_0.2.4-1_all.deb ... 425s Unpacking r-cran-pkgkitten (0.2.4-1) ... 425s Selecting previously unselected package r-cran-rcpp. 425s Preparing to unpack .../115-r-cran-rcpp_1.0.14-1_armhf.deb ... 425s Unpacking r-cran-rcpp (1.0.14-1) ... 426s Selecting previously unselected package r-cran-rcppeigen. 426s Preparing to unpack .../116-r-cran-rcppeigen_0.3.4.0.2-1_armhf.deb ... 426s Unpacking r-cran-rcppeigen (0.3.4.0.2-1) ... 426s Selecting previously unselected package libjs-mathjax. 426s Preparing to unpack .../117-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 426s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 426s Selecting previously unselected package r-cran-glmnet. 426s Preparing to unpack .../118-r-cran-glmnet_4.1-8-1_armhf.deb ... 426s Unpacking r-cran-glmnet (4.1-8-1) ... 426s Selecting previously unselected package r-cran-goftest. 426s Preparing to unpack .../119-r-cran-goftest_1.2-3-1_armhf.deb ... 426s Unpacking r-cran-goftest (1.2-3-1) ... 426s Selecting previously unselected package r-cran-gsl. 426s Preparing to unpack .../120-r-cran-gsl_2.1-8-1build1_armhf.deb ... 426s Unpacking r-cran-gsl (2.1-8-1build1) ... 426s Selecting previously unselected package r-cran-nlme. 426s Preparing to unpack .../121-r-cran-nlme_3.1.168-1_armhf.deb ... 426s Unpacking r-cran-nlme (3.1.168-1) ... 427s Selecting previously unselected package r-cran-mgcv. 427s Preparing to unpack .../122-r-cran-mgcv_1.9-1-1_armhf.deb ... 427s Unpacking r-cran-mgcv (1.9-1-1) ... 427s Selecting previously unselected package r-cran-nleqslv. 427s Preparing to unpack .../123-r-cran-nleqslv_3.3.5-1_armhf.deb ... 427s Unpacking r-cran-nleqslv (3.3.5-1) ... 427s Selecting previously unselected package r-cran-polyclip. 427s Preparing to unpack .../124-r-cran-polyclip_1.10-7-1_armhf.deb ... 427s Unpacking r-cran-polyclip (1.10-7-1) ... 427s Selecting previously unselected package r-cran-rpart. 427s Preparing to unpack .../125-r-cran-rpart_4.1.24-1_armhf.deb ... 427s Unpacking r-cran-rpart (4.1.24-1) ... 427s Selecting previously unselected package r-cran-sm. 427s Preparing to unpack .../126-r-cran-sm_2.2-6.0-1_armhf.deb ... 427s Unpacking r-cran-sm (2.2-6.0-1) ... 427s Selecting previously unselected package r-cran-spatial. 427s Preparing to unpack .../127-r-cran-spatial_7.3-18-1_armhf.deb ... 427s Unpacking r-cran-spatial (7.3-18-1) ... 427s Selecting previously unselected package r-cran-spatstat.utils. 427s Preparing to unpack .../128-r-cran-spatstat.utils_3.1-3-1_armhf.deb ... 427s Unpacking r-cran-spatstat.utils (3.1-3-1) ... 427s Selecting previously unselected package r-cran-spatstat.data. 427s Preparing to unpack .../129-r-cran-spatstat.data_3.1-6-1_all.deb ... 427s Unpacking r-cran-spatstat.data (3.1-6-1) ... 427s Selecting previously unselected package r-cran-spatstat.univar. 427s Preparing to unpack .../130-r-cran-spatstat.univar_3.1-2-1_armhf.deb ... 427s Unpacking r-cran-spatstat.univar (3.1-2-1) ... 427s Selecting previously unselected package r-cran-spatstat.geom. 427s Preparing to unpack .../131-r-cran-spatstat.geom_3.3-6-1_armhf.deb ... 427s Unpacking r-cran-spatstat.geom (3.3-6-1) ... 427s Selecting previously unselected package r-cran-spatstat.random. 427s Preparing to unpack .../132-r-cran-spatstat.random_3.3-3-1_armhf.deb ... 427s Unpacking r-cran-spatstat.random (3.3-3-1) ... 427s Selecting previously unselected package r-cran-tensor. 427s Preparing to unpack .../133-r-cran-tensor_1.5-4_all.deb ... 427s Unpacking r-cran-tensor (1.5-4) ... 427s Selecting previously unselected package r-cran-spatstat.sparse. 427s Preparing to unpack .../134-r-cran-spatstat.sparse_3.1-0-1_armhf.deb ... 427s Unpacking r-cran-spatstat.sparse (3.1-0-1) ... 427s Selecting previously unselected package r-cran-spatstat.explore. 427s Preparing to unpack .../135-r-cran-spatstat.explore_3.3-4-1_armhf.deb ... 427s Unpacking r-cran-spatstat.explore (3.3-4-1) ... 427s Selecting previously unselected package r-cran-spatstat.model. 427s Preparing to unpack .../136-r-cran-spatstat.model_3.3-4-1_armhf.deb ... 427s Unpacking r-cran-spatstat.model (3.3-4-1) ... 427s Selecting previously unselected package r-cran-spatstat.linnet. 427s Preparing to unpack .../137-r-cran-spatstat.linnet_3.2-5-1_armhf.deb ... 427s Unpacking r-cran-spatstat.linnet (3.2-5-1) ... 427s Selecting previously unselected package r-cran-spatstat. 427s Preparing to unpack .../138-r-cran-spatstat_3.3-1-1_armhf.deb ... 427s Unpacking r-cran-spatstat (3.3-1-1) ... 427s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 427s Setting up libpixman-1-0:armhf (0.44.0-3) ... 427s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 427s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 427s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 427s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 427s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 427s Setting up libdatrie1:armhf (0.2.13-3build1) ... 427s Setting up libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 427s Setting up libxcb-render0:armhf (1.17.0-2) ... 427s Setting up unzip (6.0-28ubuntu6) ... 427s Setting up x11-common (1:7.7+23ubuntu4) ... 428s Setting up libdeflate0:armhf (1.23-1) ... 428s Setting up linux-libc-dev:armhf (6.14.0-15.15) ... 428s Setting up libxcb-shm0:armhf (1.17.0-2) ... 428s Setting up libgomp1:armhf (15-20250404-0ubuntu1) ... 428s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 428s Setting up libpcre2-16-0:armhf (10.45-1) ... 428s Setting up zip (3.0-14ubuntu2) ... 428s Setting up libpcre2-32-0:armhf (10.45-1) ... 428s Setting up libblas3:armhf (3.12.1-2) ... 428s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 428s Setting up libtirpc-dev:armhf (1.3.4+ds-1.3) ... 428s Setting up libpkgconf3:armhf (1.8.1-4) ... 428s Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... 428s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 428s Setting up fonts-dejavu-mono (2.37-8) ... 428s Setting up libmpc3:armhf (1.3.1-1build2) ... 428s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 428s Setting up icu-devtools (76.1-1ubuntu2) ... 428s Setting up fonts-dejavu-core (2.37-8) ... 428s Setting up pkgconf-bin (1.8.1-4) ... 428s Setting up libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 428s Setting up libgfortran5:armhf (15-20250404-0ubuntu1) ... 428s Setting up libwebp7:armhf (1.5.0-0.1) ... 428s Setting up liblzma-dev:armhf (5.6.4-1ubuntu1) ... 428s Setting up libubsan1:armhf (15-20250404-0ubuntu1) ... 428s Setting up libpcre2-posix3:armhf (10.45-1) ... 428s Setting up libcrypt-dev:armhf (1:4.4.38-1) ... 428s Setting up libasan8:armhf (15-20250404-0ubuntu1) ... 428s Setting up libharfbuzz0b:armhf (10.2.0-1) ... 428s Setting up libthai-data (0.1.29-2build1) ... 428s Setting up libxss1:armhf (1:1.2.3-1build3) ... 428s Setting up libpaper2:armhf (2.2.5-0.3) ... 428s Setting up libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 428s Setting up libisl23:armhf (0.27-1) ... 428s Setting up libgsl28:armhf (2.8+dfsg-5ubuntu1) ... 428s Setting up libc-dev-bin (2.41-6ubuntu1) ... 428s Setting up libdeflate-dev:armhf (1.23-1) ... 428s Setting up xdg-utils (1.2.1-2ubuntu1) ... 428s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 428s Setting up libcc1-0:armhf (15-20250404-0ubuntu1) ... 428s Setting up libblas-dev:armhf (3.12.1-2) ... 428s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode 428s Setting up dctrl-tools (2.24-3build3) ... 428s Setting up cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 428s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 428s Setting up libgfortran-14-dev:armhf (14.2.0-19ubuntu2) ... 428s Setting up libice6:armhf (2:1.1.1-1) ... 428s Setting up liblapack3:armhf (3.12.1-2) ... 428s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 428s Setting up fontconfig-config (2.15.0-2.2ubuntu1) ... 428s Setting up gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 428s Setting up libpaper-utils (2.2.5-0.3) ... 428s Setting up pkgconf:armhf (1.8.1-4) ... 428s Setting up libthai0:armhf (0.1.29-2build1) ... 428s Setting up liblapack-dev:armhf (3.12.1-2) ... 428s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode 428s Setting up cpp-14 (14.2.0-19ubuntu2) ... 428s Setting up libtiff6:armhf (4.7.0-3ubuntu1) ... 428s Setting up libc6-dev:armhf (2.41-6ubuntu1) ... 428s Setting up libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 428s Setting up libstdc++-14-dev:armhf (14.2.0-19ubuntu2) ... 428s Setting up libsm6:armhf (2:1.2.4-1) ... 428s Setting up libicu-dev:armhf (76.1-1ubuntu2) ... 428s Setting up cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 428s Setting up gfortran-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 428s Setting up libbz2-dev:armhf (1.0.8-6) ... 428s Setting up gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 428s Setting up g++-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 428s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 430s Regenerating fonts cache... done. 430s Setting up libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 430s Setting up libxft2:armhf (2.3.6-1build1) ... 430s Setting up libncurses-dev:armhf (6.5+20250216-2) ... 430s Setting up libpcre2-dev:armhf (10.45-1) ... 430s Setting up libtk8.6:armhf (8.6.16-1) ... 430s Setting up libpango-1.0-0:armhf (1.56.3-1) ... 430s Setting up libreadline-dev:armhf (8.2-6) ... 430s Setting up libcairo2:armhf (1.18.4-1) ... 430s Setting up gcc-14 (14.2.0-19ubuntu2) ... 430s Setting up gfortran-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 430s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 430s Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 430s Setting up cpp (4:14.2.0-1ubuntu1) ... 430s Setting up g++-14 (14.2.0-19ubuntu2) ... 430s Setting up libpangoft2-1.0-0:armhf (1.56.3-1) ... 430s Setting up libjpeg8-dev:armhf (8c-2ubuntu11) ... 430s Setting up gfortran-14 (14.2.0-19ubuntu2) ... 430s Setting up libpangocairo-1.0-0:armhf (1.56.3-1) ... 430s Setting up g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 430s Setting up libpng-dev:armhf (1.6.47-1.1) ... 430s Setting up libjpeg-dev:armhf (8c-2ubuntu11) ... 430s Setting up gcc (4:14.2.0-1ubuntu1) ... 430s Setting up r-base-core (4.4.3-1) ... 431s Creating config file /etc/R/Renviron with new version 431s Setting up r-cran-lattice (0.22-6-1) ... 431s Setting up r-cran-nlme (3.1.168-1) ... 431s Setting up r-cran-spatstat.utils (3.1-3-1) ... 431s Setting up g++ (4:14.2.0-1ubuntu1) ... 431s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 431s Setting 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(of link group f95) doesn't exist 431s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 431s 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 431s Setting up r-cran-deldir (2.0-4-1build1) ... 431s Setting up r-cran-goftest (1.2-3-1) ... 431s Setting up r-cran-shape (1.4.6.1-1) ... 431s Setting up r-cran-matrix (1.7-3-1) ... 431s Setting up r-cran-spatstat.sparse (3.1-0-1) ... 431s Setting up r-cran-mgcv (1.9-1-1) ... 431s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ... 431s Setting up r-base-dev (4.4.3-1) ... 431s Setting up r-cran-survival (3.8-3-1) ... 431s Setting up r-cran-spatstat.data (3.1-6-1) ... 431s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 431s Setting up r-cran-spatstat.geom (3.3-6-1) ... 431s Setting up r-cran-glmnet (4.1-8-1) ... 431s Setting up r-cran-rpart (4.1.24-1) ... 431s Setting up r-cran-spatstat.random (3.3-3-1) ... 431s Setting up r-cran-spatstat.explore (3.3-4-1) ... 431s Setting up r-cran-spatstat.model (3.3-4-1) ... 431s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 431s Setting up r-cran-spatstat (3.3-1-1) ... 431s Processing triggers for install-info (7.1.1-1) ... 431s Processing triggers for libc-bin (2.41-6ubuntu1) ... 431s Processing triggers for man-db (2.13.0-1) ... 449s autopkgtest [02:38:53]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 449s autopkgtest [02:38:53]: test pkg-r-autopkgtest: [----------------------- 451s Test: Try to load the R library spatstat.model 451s 451s R version 4.4.3 (2025-02-28) -- "Trophy Case" 451s Copyright (C) 2025 The R Foundation for Statistical Computing 451s Platform: arm-unknown-linux-gnueabihf (32-bit) 451s 451s R is free software and comes with ABSOLUTELY NO WARRANTY. 451s You are welcome to redistribute it under certain conditions. 451s Type 'license()' or 'licence()' for distribution details. 451s 451s R is a collaborative project with many contributors. 451s Type 'contributors()' for more information and 451s 'citation()' on how to cite R or R packages in publications. 451s 451s Type 'demo()' for some demos, 'help()' for on-line help, or 451s 'help.start()' for an HTML browser interface to help. 451s Type 'q()' to quit R. 451s 451s > library('spatstat.model') 451s Loading required package: spatstat.data 452s Loading required package: spatstat.univar 452s spatstat.univar 3.1-2 452s Loading required package: spatstat.geom 452s spatstat.geom 3.3-6 452s Loading required package: spatstat.random 452s spatstat.random 3.3-3 452s Loading required package: spatstat.explore 452s Loading required package: nlme 452s spatstat.explore 3.3-4 452s Loading required package: rpart 452s spatstat.model 3.3-4 452s > 452s > 452s Other tests are currently unsupported! 452s They will be progressively added. 453s autopkgtest [02:38:57]: test pkg-r-autopkgtest: -----------------------] 456s pkg-r-autopkgtest PASS 456s autopkgtest [02:39:00]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 460s autopkgtest [02:39:04]: @@@@@@@@@@@@@@@@@@@@ summary 460s run-unit-test PASS 460s pkg-r-autopkgtest PASS