0s autopkgtest [02:31:23]: starting date and time: 2025-05-03 02:31:23+0000 0s autopkgtest [02:31:23]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [02:31:23]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x3zf6g8z/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.explore --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=nlme/3.1.168-1 -- lxd -r lxd-armhf-10.145.243.176 lxd-armhf-10.145.243.176:autopkgtest/ubuntu/questing/armhf 21s autopkgtest [02:31:44]: testbed dpkg architecture: armhf 23s autopkgtest [02:31:46]: testbed apt version: 3.0.0 27s autopkgtest [02:31:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [02:31:51]: testbed release detected to be: None 36s autopkgtest [02:31:59]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 38s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 38s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 38s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 38s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1920 kB] 38s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 38s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.3 kB] 38s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [204 kB] 38s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1378 kB] 38s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.5 kB] 38s Get:11 http://ftpmaster.internal/ubuntu questing/main Sources [1395 kB] 38s Get:12 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 38s Get:13 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 39s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 39s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [14.9 MB] 39s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 43s Fetched 43.3 MB in 5s (8178 kB/s) 44s Reading package lists... 49s autopkgtest [02:32:12]: upgrading testbed (apt dist-upgrade and autopurge) 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 52s Starting 2 pkgProblemResolver with broken count: 0 52s Done 53s Entering ResolveByKeep 54s 54s Calculating upgrade... 54s The following packages will be upgraded: 54s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 54s libftdi1-2 libfwupd3 libnpth0t64 libnvme1t64 libsensors-config libsensors5 54s liburcu8t64 motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n 54s usb.ids 55s 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 5431 kB of archives. 55s After this operation, 3722 kB disk space will be freed. 55s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 55s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 55s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 55s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 55s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 55s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 55s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 55s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 55s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 55s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 55s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 55s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 55s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 55s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 55s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 55s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 55s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 55s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 55s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 55s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libnvme1t64 armhf 1.13-2 [74.3 kB] 56s Fetched 5431 kB in 1s (6921 kB/s) 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 .../motd-news-config_13.7ubuntu1_all.deb ... 56s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 56s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 56s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 56s Setting up base-files (13.7ubuntu1) ... 56s Installing new version of config file /etc/issue ... 56s Installing new version of config file /etc/issue.net ... 56s Installing new version of config file /etc/lsb-release ... 57s motd-news.service is a disabled or a static unit not running, not starting it. 57s (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.) 57s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 57s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 57s Setting up dpkg (1.22.18ubuntu3) ... 57s (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.) 57s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 57s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 57s Setting up libnpth0t64:armhf (1.8-3) ... 58s (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.) 58s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 58s Unpacking distro-info-data (0.64) over (0.63) ... 58s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 58s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 58s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 58s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 58s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 58s Unpacking ed (1.21.1-1) over (1.21-1) ... 58s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 58s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 58s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 58s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 58s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 58s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 58s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 58s Unpacking nano (8.4-1) over (8.3-1) ... 58s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 58s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 58s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 58s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 58s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 58s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 58s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 59s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 59s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 59s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 59s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 59s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 59s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 59s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 59s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 59s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 59s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 59s Setting up motd-news-config (13.7ubuntu1) ... 59s Setting up liburcu8t64:armhf (0.15.2-2) ... 59s Setting up distro-info-data (0.64) ... 59s Setting up htop (3.4.1-4) ... 59s Setting up libsensors-config (1:3.6.2-2) ... 59s Installing new version of config file /etc/sensors3.conf ... 59s Setting up libfwupd3:armhf (2.0.8-3) ... 59s Setting up libftdi1-2:armhf (1.5-10) ... 59s Setting up libnvme1t64 (1.13-2) ... 59s Setting up ed (1.21.1-1) ... 59s Setting up usb.ids (2025.04.01-1) ... 59s Setting up libsensors5:armhf (1:3.6.2-2) ... 59s Setting up libdpkg-perl (1.22.18ubuntu3) ... 59s Setting up nano (8.4-1) ... 59s Installing new version of config file /etc/nanorc ... 59s Setting up ubuntu-pro-client (35.1ubuntu0) ... 59s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 59s 59s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 59s 59s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 59s 61s Setting up fwupd (2.0.8-3) ... 61s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 61s fwupd.service is a disabled or a static unit not running, not starting it. 61s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 61s Setting up dpkg-dev (1.22.18ubuntu3) ... 61s Processing triggers for dbus (1.16.2-2ubuntu1) ... 61s Processing triggers for install-info (7.1.1-1) ... 61s Processing triggers for libc-bin (2.41-6ubuntu1) ... 62s Processing triggers for man-db (2.13.0-1) ... 64s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 64s Processing triggers for initramfs-tools (0.147ubuntu1) ... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Starting pkgProblemResolver with broken count: 0 66s Starting 2 pkgProblemResolver with broken count: 0 66s Done 67s Solving dependencies... 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s autopkgtest [02:32:32]: rebooting testbed after setup commands that affected boot 109s autopkgtest [02:33:12]: 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 133s autopkgtest [02:33:36]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.explore 143s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (dsc) [2563 B] 143s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (tar) [668 kB] 143s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (diff) [3452 B] 143s gpgv: Signature made Fri Jan 31 07:56:43 2025 UTC 143s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 143s gpgv: issuer "plessy@debian.org" 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.explore_3.3-4-1.dsc: no acceptable signature found 144s autopkgtest [02:33:47]: testing package r-cran-spatstat.explore version 3.3-4-1 146s autopkgtest [02:33:49]: build not needed 149s autopkgtest [02:33:52]: test run-unit-test: preparing testbed 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Starting pkgProblemResolver with broken count: 0 152s Starting 2 pkgProblemResolver with broken count: 0 152s Done 153s The following NEW packages will be installed: 153s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 153s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libfreetype6 libgfortran5 153s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libice6 libjbig0 153s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 153s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 153s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 153s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 153s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 153s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 153s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 153s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 153s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 153s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 153s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 153s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. 153s Need to get 83.2 MB of archives. 153s After this operation, 128 MB of additional disk space will be used. 153s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 153s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 153s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 153s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 153s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 153s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig armhf 2.15.0-2.2ubuntu1 [190 kB] 153s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 153s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 153s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 153s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 153s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 153s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 154s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 154s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 154s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 154s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 154s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 154s Get:18 http://ftpmaster.internal/ubuntu questing/universe armhf libgslcblas0 armhf 2.8+dfsg-5ubuntu1 [84.4 kB] 154s Get:19 http://ftpmaster.internal/ubuntu questing/universe armhf libgsl28 armhf 2.8+dfsg-5ubuntu1 [876 kB] 154s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 154s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 154s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 154s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 154s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 154s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 154s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 154s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf libthai-data all 0.1.29-2build1 [158 kB] 154s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 154s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf libpango-1.0-0 armhf 1.56.3-1 [216 kB] 154s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf libpangoft2-1.0-0 armhf 1.56.3-1 [44.1 kB] 154s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf libpangocairo-1.0-0 armhf 1.56.3-1 [25.0 kB] 154s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 154s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 154s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 154s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 154s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 154s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 154s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 154s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 154s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 154s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 154s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 154s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 154s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 154s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 154s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 154s Get:47 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 155s Get:48 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 155s Get:49 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-deldir armhf 2.0-4-1build1 [268 kB] 155s Get:50 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-goftest armhf 1.2-3-1 [58.6 kB] 155s Get:51 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-gsl armhf 2.1-8-1build1 [481 kB] 155s Get:52 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 155s Get:53 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-locfit armhf 1.5-9.12-1 [495 kB] 155s Get:54 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 155s Get:55 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 155s Get:56 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 155s Get:57 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-polyclip armhf 1.10-7-1 [109 kB] 155s Get:58 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 155s Get:59 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 155s Get:60 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-sm armhf 2.2-6.0-1 [787 kB] 155s Get:61 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatial armhf 7.3-18-1 [131 kB] 155s Get:62 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.utils armhf 3.1-3-1 [384 kB] 155s Get:63 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.data all 3.1-6-1 [4153 kB] 155s Get:64 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.univar armhf 3.1-2-1 [310 kB] 155s Get:65 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.geom armhf 3.3-6-1 [3923 kB] 155s Get:66 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.random armhf 3.3-3-1 [1155 kB] 155s Get:67 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-tensor all 1.5-4 [15.7 kB] 155s Get:68 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.sparse armhf 3.1-0-1 [216 kB] 155s Get:69 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.explore armhf 3.3-4-1 [3271 kB] 156s Get:70 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.model armhf 3.3-4-1 [3397 kB] 156s Get:71 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.linnet armhf 3.2-5-1 [1505 kB] 156s Get:72 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat armhf 3.3-1-1 [4121 kB] 156s Preconfiguring packages ... 156s Fetched 83.2 MB in 3s (28.9 MB/s) 156s Selecting previously unselected package libfreetype6:armhf. 156s (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.) 156s Preparing to unpack .../00-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 156s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 156s Selecting previously unselected package fonts-dejavu-mono. 156s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-mono (2.37-8) ... 156s Selecting previously unselected package fonts-dejavu-core. 156s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 156s Unpacking fonts-dejavu-core (2.37-8) ... 157s Selecting previously unselected package fontconfig-config. 157s Preparing to unpack .../03-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 157s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 157s Selecting previously unselected package libfontconfig1:armhf. 157s Preparing to unpack .../04-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 157s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 157s Selecting previously unselected package fontconfig. 157s Preparing to unpack .../05-fontconfig_2.15.0-2.2ubuntu1_armhf.deb ... 157s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 157s Selecting previously unselected package libblas3:armhf. 157s Preparing to unpack .../06-libblas3_3.12.1-2_armhf.deb ... 157s Unpacking libblas3:armhf (3.12.1-2) ... 157s Selecting previously unselected package libpixman-1-0:armhf. 157s Preparing to unpack .../07-libpixman-1-0_0.44.0-3_armhf.deb ... 157s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 157s Selecting previously unselected package libxcb-render0:armhf. 157s Preparing to unpack .../08-libxcb-render0_1.17.0-2_armhf.deb ... 157s Unpacking libxcb-render0:armhf (1.17.0-2) ... 157s Selecting previously unselected package libxcb-shm0:armhf. 157s Preparing to unpack .../09-libxcb-shm0_1.17.0-2_armhf.deb ... 157s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 157s Selecting previously unselected package libxrender1:armhf. 157s Preparing to unpack .../10-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 157s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 157s Selecting previously unselected package libcairo2:armhf. 157s Preparing to unpack .../11-libcairo2_1.18.4-1_armhf.deb ... 157s Unpacking libcairo2:armhf (1.18.4-1) ... 157s Selecting previously unselected package libdatrie1:armhf. 157s Preparing to unpack .../12-libdatrie1_0.2.13-3build1_armhf.deb ... 157s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 157s Selecting previously unselected package libdeflate0:armhf. 157s Preparing to unpack .../13-libdeflate0_1.23-1_armhf.deb ... 157s Unpacking libdeflate0:armhf (1.23-1) ... 157s Selecting previously unselected package libgfortran5:armhf. 157s Preparing to unpack .../14-libgfortran5_15-20250404-0ubuntu1_armhf.deb ... 157s Unpacking libgfortran5:armhf (15-20250404-0ubuntu1) ... 157s Selecting previously unselected package libgomp1:armhf. 157s Preparing to unpack .../15-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 157s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 157s Selecting previously unselected package libgraphite2-3:armhf. 157s Preparing to unpack .../16-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 157s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 157s Selecting previously unselected package libgslcblas0:armhf. 157s Preparing to unpack .../17-libgslcblas0_2.8+dfsg-5ubuntu1_armhf.deb ... 157s Unpacking libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 157s Selecting previously unselected package libgsl28:armhf. 157s Preparing to unpack .../18-libgsl28_2.8+dfsg-5ubuntu1_armhf.deb ... 157s Unpacking libgsl28:armhf (2.8+dfsg-5ubuntu1) ... 157s Selecting previously unselected package libharfbuzz0b:armhf. 157s Preparing to unpack .../19-libharfbuzz0b_10.2.0-1_armhf.deb ... 157s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 157s Selecting previously unselected package x11-common. 157s Preparing to unpack .../20-x11-common_1%3a7.7+23ubuntu4_all.deb ... 157s Unpacking x11-common (1:7.7+23ubuntu4) ... 157s Selecting previously unselected package libice6:armhf. 157s Preparing to unpack .../21-libice6_2%3a1.1.1-1_armhf.deb ... 157s Unpacking libice6:armhf (2:1.1.1-1) ... 157s Selecting previously unselected package libjpeg-turbo8:armhf. 157s Preparing to unpack .../22-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 157s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 158s Selecting previously unselected package libjpeg8:armhf. 158s Preparing to unpack .../23-libjpeg8_8c-2ubuntu11_armhf.deb ... 158s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 158s Selecting previously unselected package liblapack3:armhf. 158s Preparing to unpack .../24-liblapack3_3.12.1-2_armhf.deb ... 158s Unpacking liblapack3:armhf (3.12.1-2) ... 158s Selecting previously unselected package liblerc4:armhf. 158s Preparing to unpack .../25-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 158s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 158s Selecting previously unselected package libthai-data. 158s Preparing to unpack .../26-libthai-data_0.1.29-2build1_all.deb ... 158s Unpacking libthai-data (0.1.29-2build1) ... 158s Selecting previously unselected package libthai0:armhf. 158s Preparing to unpack .../27-libthai0_0.1.29-2build1_armhf.deb ... 158s Unpacking libthai0:armhf (0.1.29-2build1) ... 158s Selecting previously unselected package libpango-1.0-0:armhf. 158s Preparing to unpack .../28-libpango-1.0-0_1.56.3-1_armhf.deb ... 158s Unpacking libpango-1.0-0:armhf (1.56.3-1) ... 158s Selecting previously unselected package libpangoft2-1.0-0:armhf. 158s Preparing to unpack .../29-libpangoft2-1.0-0_1.56.3-1_armhf.deb ... 158s Unpacking libpangoft2-1.0-0:armhf (1.56.3-1) ... 158s Selecting previously unselected package libpangocairo-1.0-0:armhf. 158s Preparing to unpack .../30-libpangocairo-1.0-0_1.56.3-1_armhf.deb ... 158s Unpacking libpangocairo-1.0-0:armhf (1.56.3-1) ... 158s Selecting previously unselected package libpaper2:armhf. 158s Preparing to unpack .../31-libpaper2_2.2.5-0.3_armhf.deb ... 158s Unpacking libpaper2:armhf (2.2.5-0.3) ... 158s Selecting previously unselected package libpaper-utils. 158s Preparing to unpack .../32-libpaper-utils_2.2.5-0.3_armhf.deb ... 158s Unpacking libpaper-utils (2.2.5-0.3) ... 158s Selecting previously unselected package libsharpyuv0:armhf. 158s Preparing to unpack .../33-libsharpyuv0_1.5.0-0.1_armhf.deb ... 158s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 158s Selecting previously unselected package libsm6:armhf. 158s Preparing to unpack .../34-libsm6_2%3a1.2.4-1_armhf.deb ... 158s Unpacking libsm6:armhf (2:1.2.4-1) ... 158s Selecting previously unselected package libtcl8.6:armhf. 158s Preparing to unpack .../35-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 158s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 158s Selecting previously unselected package libjbig0:armhf. 158s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 158s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 158s Selecting previously unselected package libwebp7:armhf. 158s Preparing to unpack .../37-libwebp7_1.5.0-0.1_armhf.deb ... 158s Unpacking libwebp7:armhf (1.5.0-0.1) ... 158s Selecting previously unselected package libtiff6:armhf. 158s Preparing to unpack .../38-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 158s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 158s Selecting previously unselected package libxft2:armhf. 158s Preparing to unpack .../39-libxft2_2.3.6-1build1_armhf.deb ... 158s Unpacking libxft2:armhf (2.3.6-1build1) ... 158s Selecting previously unselected package libxss1:armhf. 158s Preparing to unpack .../40-libxss1_1%3a1.2.3-1build3_armhf.deb ... 158s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 158s Selecting previously unselected package libtk8.6:armhf. 158s Preparing to unpack .../41-libtk8.6_8.6.16-1_armhf.deb ... 158s Unpacking libtk8.6:armhf (8.6.16-1) ... 158s Selecting previously unselected package libxt6t64:armhf. 158s Preparing to unpack .../42-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 158s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 158s Selecting previously unselected package zip. 158s Preparing to unpack .../43-zip_3.0-14ubuntu2_armhf.deb ... 158s Unpacking zip (3.0-14ubuntu2) ... 158s Selecting previously unselected package unzip. 158s Preparing to unpack .../44-unzip_6.0-28ubuntu6_armhf.deb ... 158s Unpacking unzip (6.0-28ubuntu6) ... 158s Selecting previously unselected package xdg-utils. 159s Preparing to unpack .../45-xdg-utils_1.2.1-2ubuntu1_all.deb ... 159s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 159s Selecting previously unselected package r-base-core. 159s Preparing to unpack .../46-r-base-core_4.4.3-1_armhf.deb ... 159s Unpacking r-base-core (4.4.3-1) ... 159s Selecting previously unselected package r-cran-abind. 159s Preparing to unpack .../47-r-cran-abind_1.4-8-1_all.deb ... 159s Unpacking r-cran-abind (1.4-8-1) ... 159s Selecting previously unselected package r-cran-deldir. 159s Preparing to unpack .../48-r-cran-deldir_2.0-4-1build1_armhf.deb ... 159s Unpacking r-cran-deldir (2.0-4-1build1) ... 159s Selecting previously unselected package r-cran-goftest. 159s Preparing to unpack .../49-r-cran-goftest_1.2-3-1_armhf.deb ... 159s Unpacking r-cran-goftest (1.2-3-1) ... 159s Selecting previously unselected package r-cran-gsl. 159s Preparing to unpack .../50-r-cran-gsl_2.1-8-1build1_armhf.deb ... 159s Unpacking r-cran-gsl (2.1-8-1build1) ... 159s Selecting previously unselected package r-cran-lattice. 159s Preparing to unpack .../51-r-cran-lattice_0.22-6-1_armhf.deb ... 159s Unpacking r-cran-lattice (0.22-6-1) ... 159s Selecting previously unselected package r-cran-locfit. 159s Preparing to unpack .../52-r-cran-locfit_1.5-9.12-1_armhf.deb ... 159s Unpacking r-cran-locfit (1.5-9.12-1) ... 159s Selecting previously unselected package r-cran-matrix. 159s Preparing to unpack .../53-r-cran-matrix_1.7-3-1_armhf.deb ... 159s Unpacking r-cran-matrix (1.7-3-1) ... 159s Selecting previously unselected package r-cran-nlme. 159s Preparing to unpack .../54-r-cran-nlme_3.1.168-1_armhf.deb ... 159s Unpacking r-cran-nlme (3.1.168-1) ... 159s Selecting previously unselected package r-cran-mgcv. 159s Preparing to unpack .../55-r-cran-mgcv_1.9-1-1_armhf.deb ... 159s Unpacking r-cran-mgcv (1.9-1-1) ... 159s Selecting previously unselected package r-cran-polyclip. 159s Preparing to unpack .../56-r-cran-polyclip_1.10-7-1_armhf.deb ... 159s Unpacking r-cran-polyclip (1.10-7-1) ... 160s Selecting previously unselected package r-cran-survival. 160s Preparing to unpack .../57-r-cran-survival_3.8-3-1_armhf.deb ... 160s Unpacking r-cran-survival (3.8-3-1) ... 160s Selecting previously unselected package r-cran-rpart. 160s Preparing to unpack .../58-r-cran-rpart_4.1.24-1_armhf.deb ... 160s Unpacking r-cran-rpart (4.1.24-1) ... 160s Selecting previously unselected package r-cran-sm. 160s Preparing to unpack .../59-r-cran-sm_2.2-6.0-1_armhf.deb ... 160s Unpacking r-cran-sm (2.2-6.0-1) ... 160s Selecting previously unselected package r-cran-spatial. 160s Preparing to unpack .../60-r-cran-spatial_7.3-18-1_armhf.deb ... 160s Unpacking r-cran-spatial (7.3-18-1) ... 160s Selecting previously unselected package r-cran-spatstat.utils. 160s Preparing to unpack .../61-r-cran-spatstat.utils_3.1-3-1_armhf.deb ... 160s Unpacking r-cran-spatstat.utils (3.1-3-1) ... 160s Selecting previously unselected package r-cran-spatstat.data. 160s Preparing to unpack .../62-r-cran-spatstat.data_3.1-6-1_all.deb ... 160s Unpacking r-cran-spatstat.data (3.1-6-1) ... 160s Selecting previously unselected package r-cran-spatstat.univar. 160s Preparing to unpack .../63-r-cran-spatstat.univar_3.1-2-1_armhf.deb ... 160s Unpacking r-cran-spatstat.univar (3.1-2-1) ... 160s Selecting previously unselected package r-cran-spatstat.geom. 160s Preparing to unpack .../64-r-cran-spatstat.geom_3.3-6-1_armhf.deb ... 160s Unpacking r-cran-spatstat.geom (3.3-6-1) ... 160s Selecting previously unselected package r-cran-spatstat.random. 160s Preparing to unpack .../65-r-cran-spatstat.random_3.3-3-1_armhf.deb ... 160s Unpacking r-cran-spatstat.random (3.3-3-1) ... 160s Selecting previously unselected package r-cran-tensor. 160s Preparing to unpack .../66-r-cran-tensor_1.5-4_all.deb ... 160s Unpacking r-cran-tensor (1.5-4) ... 160s Selecting previously unselected package r-cran-spatstat.sparse. 160s Preparing to unpack .../67-r-cran-spatstat.sparse_3.1-0-1_armhf.deb ... 160s Unpacking r-cran-spatstat.sparse (3.1-0-1) ... 160s Selecting previously unselected package r-cran-spatstat.explore. 160s Preparing to unpack .../68-r-cran-spatstat.explore_3.3-4-1_armhf.deb ... 160s Unpacking r-cran-spatstat.explore (3.3-4-1) ... 160s Selecting previously unselected package r-cran-spatstat.model. 160s Preparing to unpack .../69-r-cran-spatstat.model_3.3-4-1_armhf.deb ... 160s Unpacking r-cran-spatstat.model (3.3-4-1) ... 160s Selecting previously unselected package r-cran-spatstat.linnet. 160s Preparing to unpack .../70-r-cran-spatstat.linnet_3.2-5-1_armhf.deb ... 160s Unpacking r-cran-spatstat.linnet (3.2-5-1) ... 160s Selecting previously unselected package r-cran-spatstat. 160s Preparing to unpack .../71-r-cran-spatstat_3.3-1-1_armhf.deb ... 160s Unpacking r-cran-spatstat (3.3-1-1) ... 160s Setting up libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 160s Setting up libpixman-1-0:armhf (0.44.0-3) ... 160s Setting up libsharpyuv0:armhf (1.5.0-0.1) ... 160s Setting up liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 160s Setting up libxrender1:armhf (1:0.9.10-1.1build1) ... 160s Setting up libdatrie1:armhf (0.2.13-3build1) ... 160s Setting up libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 160s Setting up libxcb-render0:armhf (1.17.0-2) ... 160s Setting up unzip (6.0-28ubuntu6) ... 160s Setting up x11-common (1:7.7+23ubuntu4) ... 161s Setting up libdeflate0:armhf (1.23-1) ... 161s Setting up libxcb-shm0:armhf (1.17.0-2) ... 161s Setting up libgomp1:armhf (15-20250404-0ubuntu1) ... 161s Setting up libjbig0:armhf (2.1-6.1ubuntu2) ... 161s Setting up zip (3.0-14ubuntu2) ... 161s Setting up libblas3:armhf (3.12.1-2) ... 161s 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 161s Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... 161s Setting up fonts-dejavu-mono (2.37-8) ... 161s Setting up libtcl8.6:armhf (8.6.16+dfsg-1) ... 161s Setting up fonts-dejavu-core (2.37-8) ... 161s Setting up 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up libthai0:armhf (0.1.29-2build1) ... 161s Setting up libtiff6:armhf (4.7.0-3ubuntu1) ... 161s Setting up libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 161s Setting up libsm6:armhf (2:1.2.4-1) ... 161s Setting up fontconfig (2.15.0-2.2ubuntu1) ... 163s Regenerating fonts cache... done. 163s Setting up libxft2:armhf (2.3.6-1build1) ... 163s Setting up libtk8.6:armhf (8.6.16-1) ... 163s Setting up libpango-1.0-0:armhf (1.56.3-1) ... 163s Setting up libcairo2:armhf (1.18.4-1) ... 163s Setting up libxt6t64:armhf (1:1.2.1-1.2build1) ... 163s Setting up libpangoft2-1.0-0:armhf (1.56.3-1) ... 163s Setting up libpangocairo-1.0-0:armhf (1.56.3-1) ... 163s Setting up r-base-core (4.4.3-1) ... 163s Creating config file /etc/R/Renviron with new version 164s Setting up r-cran-lattice (0.22-6-1) ... 164s Setting up r-cran-nlme (3.1.168-1) ... 164s Setting up r-cran-spatstat.utils (3.1-3-1) ... 164s Setting up r-cran-locfit (1.5-9.12-1) ... 164s Setting up r-cran-tensor (1.5-4) ... 164s Setting up 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... 164s Processing triggers for libc-bin (2.41-6ubuntu1) ... 164s Processing triggers for man-db (2.13.0-1) ... 172s autopkgtest [02:34:15]: test run-unit-test: [----------------------- 174s BEGIN TEST testsAtoC.R 174s 174s R version 4.4.3 (2025-02-28) -- "Trophy Case" 174s Copyright (C) 2025 The R Foundation for Statistical Computing 174s Platform: arm-unknown-linux-gnueabihf (32-bit) 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 174s Loading required package: spatstat.explore 174s > Loading required package: spatstat.data 174s #' 174s > #' Header for all (concatenated) test files 174s > #' 174s > #' Require spatstat.explore 174s > #' Obtain environment variable controlling tests. 174s > #' 174s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 174s > 174s > require(spatstat.explore) 176s Loading required package: spatstat.univar 176s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 176s > ALWAYS <- TRUE 176s > cat(paste("--------- Executing", 176s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 176s + "test code -----------\n")) 176s --------- Executing **RESTRICTED** subset of test code ----------- 176s > ## tests/cdf.test.R 176s > 176s > 176s > local({ 176s + NSIM <- 9 176s + op <- spatstat.options(ndummy.min=16, npixel=32) 176s + AA <- split(ants, un=FALSE) 176s + AC <- AA[["Cataglyphis"]] 176s + AM <- AA[["Messor"]] 176s + DM <- distmap(AM) 176s + if(ALWAYS) { 176s + ## Check cdf.test with strange data 176s + ## Marked point patterns with some marks not represented 176s + ## should produce a warning, rather than a crash: 176s + cdf.test(AC, DM) 176s + } 176s + if(FULLTEST) { 176s + ## should be OK: 176s + cdf.test(unmark(AC), DM) 176s + cdf.test(unmark(AC), DM, "cvm") 176s + cdf.test(unmark(AC), DM, "ad") 176s + ## other code blocks 176s + cdf.test(finpines, "x") 176s + } 176s + }) 176s > 176s > 176s > #' tests/circular.R 176s > #' 176s > #' Circular data and periodic distributions 176s > #' 176s > #' $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 176s > 176s > 176s > local({ 176s + if(ALWAYS) { 176s + a <- pairorient(redwood, 0.05, 0.15, correction="none") 176s + rose(a) 176s + } 176s + if(FULLTEST) { 176s + b <- pairorient(redwood, 0.05, 0.15, correction="best") 176s + rose(b, start="N", clockwise=TRUE) 176s + } 176s + if(ALWAYS) { 176s + #' arcs on the circle 176s + #' (depends on numerical behaviour) 176s + set.seed(19171025) 176s + aa <- replicate(7, runif(1, 0, 2*pi) + c(0, runif(1, 0, pi)), 176s + simplify=FALSE) 176s + bb <- circunion(aa) 176s + 176s + assertsingle <- function(x, a, id) { 176s + y <- circunion(x) 176s + if(length(y) != 1 || max(abs(y[[1]] - a)) > .Machine$double.eps) 176s + stop(paste("Incorrect result from circunion in case", id), 176s + call.=FALSE) 176s + invisible(NULL) 176s + } 176s + 176s + assertsingle(list(c(pi/3, pi), c(pi/2, 3*pi/2)), 176s + c(pi/3, 3*pi/2), 176s + 1) 176s + assertsingle(list(c(0, pi/2), c(pi/4, pi)), 176s + c(0,pi), 176s + 2) 176s + assertsingle(list(c(-pi/4, pi/2), c(pi/4, pi)), 176s + c((2-1/4)*pi, pi), 176s + 3) 176s + } 176s + }) 176s > 176s > 176s > #' 176s > #' tests/closecore.R 176s > #' 176s > #' check 'closepairs/crosspairs' code 176s > #' invoked in core package 176s > #' 176s > #' $Revision: 1.4 $ $Date: 2021/04/17 04:16:43 $ 176s > #' 176s > #' ------- All this code must be run on every hardware ------- 176s > #' 176s > 176s > local({ 176s + #' weightedclosepairs is in wtdclosepair.R 176s + wi <- weightedclosepairs(redwood, 0.05, "isotropic") 176s + if(FULLTEST) { 176s + wt <- weightedclosepairs(redwood, 0.05, "translate") 176s + wp <- weightedclosepairs(redwood, 0.05, "periodic") 176s + } 176s + #' markmarkscatter uses closepairs.pp3 176s + X <- runifpoint3(100) 176s + marks(X) <- runif(100) 176s + markmarkscatter(X, 0.2) 176s + if(FULLTEST) { 176s + markmarkscatter(X[FALSE], 0.2) 176s + } 176s + }) 176s > 176s > #' 176s > #' contact.R 176s > #' 176s > #' Check machinery for first contact distributions 176s > #' 176s > #' $Revision: 1.8 $ $Date: 2021/04/17 02:25:55 $ 176s > 176s > local({ 176s + if(ALWAYS) { 176s + #' reduce complexity 176s + Y <- as.mask(heather$coarse, dimyx=c(50, 25)) 176s + 176s + X <- runifpoint(100, win = complement.owin(Y)) 176s + if(FULLTEST) G <- Gfox(X, Y) 176s + J <- Jfox(X, Y) 176s + 176s + Y <- as.polygonal(Y) 176s + X <- runifpoint(100, win = complement.owin(Y)) 176s + if(FULLTEST) G <- Gfox(X, Y) 176s + J <- Jfox(X, Y) 176s + 176s + op <- spatstat.options(exactdt.checks.data=TRUE) 176s + U <- exactdt(X) 176s + spatstat.options(op) 176s + } 176s + }) 176s spatstat.univar 3.1-2 176s Loading required package: spatstat.geom 176s spatstat.geom 3.3-6 176s Loading required package: spatstat.random 176s spatstat.random 3.3-3 176s Loading required package: nlme 176s spatstat.explore 3.3-4 176s Warning message: 176s In cdf.test.ppp(AC, DM) : 176s Ignoring marks, because some mark values have zero frequency 176s > 176s > reset.spatstat.options() 176s > 176s BEGIN TEST testsD.R 177s 177s R version 4.4.3 (2025-02-28) -- "Trophy Case" 177s Copyright (C) 2025 The R Foundation for Statistical Computing 177s Platform: arm-unknown-linux-gnueabihf (32-bit) 177s 177s R is free software and comes with ABSOLUTELY NO WARRANTY. 177s You are welcome to redistribute it under certain conditions. 177s Type 'license()' or 'licence()' for distribution details. 177s 177s R is a collaborative project with many contributors. 177s Type 'contributors()' for more information and 177s 'citation()' on how to cite R or R packages in publications. 177s 177s Type 'demo()' for some demos, 'help()' for on-line help, or 177s 'help.start()' for an HTML browser interface to help. 177s Type 'q()' to quit R. 177s 177s Loading required package: spatstat.explore 177s > #' 177s > #' Header for all (concatenated) test files 177s > #' 177s > #' Require spatstat.explore 177s > #' Obtain environment variable controlling tests. 177s > #' 177s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 177s > 177s > require(spatstat.explore) 177s Loading required package: spatstat.data 178s Loading required package: spatstat.univar 178s spatstat.univar 3.1-2 178s Loading required package: spatstat.geom 178s spatstat.geom 3.3-6 178s Loading required package: spatstat.random 178s spatstat.random 3.3-3 178s Loading required package: nlme 178s spatstat.explore 3.3-4 178s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 178s > ALWAYS <- TRUE 178s > cat(paste("--------- Executing", 178s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 178s + "test code -----------\n")) 178s --------- Executing **RESTRICTED** subset of test code ----------- 178s > #' 178s > #' tests/density.R 178s > #' 178s > #' Test behaviour of density() methods, 178s > #' relrisk(), Smooth() 178s > #' and inhomogeneous summary functions 178s > #' and idw, adaptive.density, intensity 178s > #' and SpatialMedian, SpatialQuantile 178s > #' 178s > #' $Revision: 1.67 $ $Date: 2024/01/29 07:07:16 $ 178s > #' 178s > 178s > if(!FULLTEST) 178s + spatstat.options(npixel=32, ndummy.min=16) 178s > 178s > 178s > local({ 178s + 178s + # test all cases of density.ppp and densityfun.ppp 178s + 178s + tryit <- function(..., do.fun=TRUE, badones=FALSE) { 178s + Z <- density(cells, ..., at="pixels") 178s + Z <- density(cells, ..., at="points") 178s + if(do.fun) { 178s + f <- densityfun(cells, ...) 178s + U <- f(0.1, 0.3) 178s + if(badones) { 178s + U2 <- f(1.1, 0.3) 178s + U3 <- f(1.1, 0.3, drop=FALSE) 178s + } 178s + } 178s + return(invisible(NULL)) 178s + } 178s + 178s + if(ALWAYS) { 178s + tryit(0.05) 178s + tryit(0.05, diggle=TRUE) 178s + tryit(0.05, se=TRUE) 178s + tryit(0.05, weights=expression(x)) 178s + tryit(0.07, kernel="epa") 178s + tryit(sigma=Inf) 178s + tryit(0.05, badones=TRUE) 178s + } 178s + if(FULLTEST) { 178s + tryit(0.07, kernel="quartic") 178s + tryit(0.07, kernel="disc") 178s + tryit(0.07, kernel="epa", weights=expression(x)) 178s + tryit(sigma=Inf, weights=expression(x)) 178s + } 178s + 178s + V <- diag(c(0.05^2, 0.07^2)) 178s + 178s + if(ALWAYS) { 178s + tryit(varcov=V) 178s + } 178s + if(FULLTEST) { 178s + tryit(varcov=V, diggle=TRUE) 178s + tryit(varcov=V, weights=expression(x)) 178s + tryit(varcov=V, weights=expression(x), diggle=TRUE) 178s + Z <- distmap(runifpoint(5, Window(cells))) 178s + tryit(0.05, weights=Z) 178s + tryit(0.05, weights=Z, diggle=TRUE) 178s + } 178s + 178s + trymost <- function(...) tryit(..., do.fun=FALSE) 178s + wdf <- data.frame(a=1:42,b=42:1) 178s + if(ALWAYS) { 178s + trymost(0.05, weights=wdf) 178s + trymost(sigma=Inf, weights=wdf) 178s + } 178s + if(FULLTEST) { 178s + trymost(0.05, weights=wdf, diggle=TRUE) 178s + trymost(varcov=V, weights=wdf) 178s + trymost(varcov=V, weights=expression(cbind(x,y))) 178s + } 178s + 178s + ## check conservation of mass 178s + checkconserve <- function(X, xname, sigma, toler=0.01) { 178s + veritas <- npoints(X) 178s + vino <- integral(density(X, sigma, diggle=TRUE)) 178s + relerr <- abs(vino - veritas)/veritas 178s + if(relerr > toler) 178s + stop(paste("density.ppp(diggle=TRUE) fails to conserve mass:", 178s + vino, "!=", veritas, 178s + "for", sQuote(xname)), 178s + call.=FALSE) 178s + return(relerr) 178s + } 178s + if(FULLTEST) { 178s + checkconserve(cells, "cells", 0.15) 178s + } 178s + if(ALWAYS) { 178s + checkconserve(split(chorley)[["lung"]], "lung", 2) 178s + } 178s + 178s + ## run C algorithm 'denspt' 178s + opa <- spatstat.options(densityC=TRUE, densityTransform=FALSE) 178s + if(ALWAYS) { 178s + tryit(varcov=V) 178s + } 178s + if(FULLTEST) { 178s + tryit(varcov=V, weights=expression(x)) 178s + trymost(varcov=V, weights=wdf) 178s + } 178s + spatstat.options(opa) 178s + 178s + crossit <- function(..., sigma=NULL) { 178s + U <- runifpoint(20, Window(cells)) 178s + a <- densitycrossEngine(cells, U, ..., sigma=sigma) 178s + a <- densitycrossEngine(cells, U, ..., sigma=sigma, diggle=TRUE) 178s + invisible(NULL) 178s + } 178s + if(ALWAYS) { 178s + crossit(varcov=V, weights=cells$x) 178s + crossit(sigma=Inf) 178s + } 178s + if(FULLTEST) { 178s + crossit(varcov=V, weights=wdf) 178s + crossit(sigma=0.1, weights=wdf) 178s + crossit(sigma=0.1, kernel="epa", weights=wdf) 178s + } 178s + 178s + ## apply different discretisation rules 178s + if(ALWAYS) { 178s + Z <- density(cells, 0.05, fractional=TRUE) 178s + } 178s + if(FULLTEST) { 178s + Z <- density(cells, 0.05, preserve=TRUE) 178s + Z <- density(cells, 0.05, fractional=TRUE, preserve=TRUE) 178s + } 178s + 178s + ## compare results with different algorithms 178s + crosscheque <- function(expr) { 178s + e <- as.expression(substitute(expr)) 178s + ename <- sQuote(deparse(substitute(expr))) 178s + ## interpreted R 178s + opa <- spatstat.options(densityC=FALSE, densityTransform=FALSE) 178s + val.interpreted <- eval(e) 178s + ## established C algorithm 'denspt' 178s + spatstat.options(densityC=TRUE, densityTransform=FALSE) 178s + val.C <- eval(e) 178s + ## new C algorithm 'Gdenspt' using transformed coordinates 178s + spatstat.options(densityC=TRUE, densityTransform=TRUE) 178s + val.Transform <- eval(e) 178s + spatstat.options(opa) 178s + if(max(abs(val.interpreted - val.C)) > 0.001) 178s + stop(paste("Numerical discrepancy between R and C algorithms in", 178s + ename)) 178s + if(max(abs(val.C - val.Transform)) > 0.001) 178s + stop(paste("Numerical discrepancy between C algorithms", 178s + "using transformed and untransformed coordinates in", 178s + ename)) 178s + invisible(NULL) 178s + } 178s + 178s + ## execute & compare results of density(at="points") with different algorithms 178s + wdfr <- cbind(1:npoints(redwood), 2) 178s + if(ALWAYS) { 178s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE)) 178s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 178s + weights=wdfr[,1])) 178s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 178s + weights=wdfr)) 178s + } 178s + 178s + ## correctness of non-Gaussian kernel calculation 178s + leavein <- function(ker, maxd=0.025) { 178s + ZI <- density(redwood, 0.12, kernel=ker, edge=FALSE, 178s + dimyx=256)[redwood] 178s + ZP <- density(redwood, 0.12, kernel=ker, edge=FALSE, 178s + at="points", leaveoneout=FALSE) 178s + discrep <- max(abs(ZP - ZI))/npoints(redwood) 178s + if(discrep > maxd) 178s + stop(paste("Discrepancy", 178s + signif(discrep, 3), 178s + "in calculation for", ker, "kernel")) 178s + return(invisible(NULL)) 178s + } 178s + if(ALWAYS) { 178s + leavein("epanechnikov", 0.015) 178s + } 178s + if(FULLTEST) { 178s + leavein("quartic", 0.010) 178s + leavein("disc", 0.100) 178s + } 178s + 178s + ## bandwidth selection code blocks 178s + sigvec <- 0.01 * 2:15 178s + sigran <- range(sigvec) 178s + if(ALWAYS) { 178s + bw.ppl(redwood, sigma=sigvec) 178s + bw.CvL(redwood, sigma=sigvec) 178s + } 178s + if(FULLTEST) { 178s + bw.ppl(redwood, srange=sigran, ns=5) 178s + bw.CvL(redwood, srange=sigran, ns=5) 178s + } 178s + ## adaptive bandwidth 178s + if(ALWAYS) { 178s + a <- bw.abram(redwood) 178s + } 178s + if(FULLTEST) { 178s + a <- bw.abram(redwood, pilot=density(redwood, 0.2)) 178s + a <- bw.abram(redwood, smoother="densityVoronoi", at="pixels") 178s + } 178s + 178s + ## Kinhom 178s + if(ALWAYS) { 178s + lam <- density(redwood) 178s + K <- Kinhom(redwood, lam) 178s + 178s + lamX <- density(redwood, at="points") 178s + KX <- Kinhom(redwood, lamX) 178s + } 178s + 178s + ## test all code cases of new 'relrisk.ppp' algorithm 178s + pants <- function(..., X=ants, sigma=100, se=TRUE) { 178s + a <- relrisk(X, sigma=sigma, se=se, ...) 178s + return(TRUE) 178s + } 178s + if(ALWAYS) { 178s + pants() 178s + pants(diggle=TRUE) 178s + pants(edge=FALSE) 178s + pants(at="points") 178s + pants(casecontrol=FALSE) 178s + pants(relative=TRUE) 178s + pants(sigma=Inf) 178s + pants(sigma=NULL, varcov=diag(c(100,100)^2)) 178s + f <- 1/area(Window(ants)) 178s + pants(fudge=f) 178s + } 178s + if(FULLTEST) { 178s + pants(diggle=TRUE, at="points") 178s + pants(edge=FALSE, at="points", fudge=f) 178s + pants(casecontrol=FALSE, relative=TRUE) 178s + pants(casecontrol=FALSE,at="points") 178s + pants(relative=TRUE,at="points", fudge=f) 178s + pants(casecontrol=FALSE, relative=TRUE,at="points") 178s + pants(relative=TRUE, control="Cataglyphis", case="Messor", fudge=f) 178s + pants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 178s + pants(casecontrol=FALSE, case="Messor", se=FALSE) 178s + pants(case=2, at="pixels", relative=TRUE) 178s + pants(case=2, at="points", relative=TRUE) 178s + pants(case=2, at="pixels", relative=FALSE) 178s + pants(case=2, at="points", relative=FALSE) 178s + } 178s + if(ALWAYS) { 178s + ## underflow example from stackoverflow! 178s + funky <- scanpp("funky.tab", owin(c(4, 38), c(0.3, 17))) 178s + P <- relrisk(funky, 0.5) 178s + R <- relrisk(funky, 0.5, relative=TRUE) 178s + } 178s + ## more than 2 types 178s + if(ALWAYS) { 178s + pants(X=sporophores) 178s + pants(X=sporophores, sigma=20, at="points") 178s + pants(X=sporophores, sigma=20, at="points", fudge=f) 178s + bw.relrisk(sporophores, method="leastsquares") 178s + } 178s + if(FULLTEST) { 178s + pants(X=sporophores, sigma=20, relative=TRUE, at="points", fudge=f) 178s + pants(X=sporophores, sigma=20, at="pixels", se=FALSE) 178s + pants(X=sporophores, sigma=20, relative=TRUE, at="pixels", se=FALSE) 178s + bw.relrisk(sporophores, method="weightedleastsquares") 178s + } 178s + 178s + ## execute Smooth.ppp and Smoothfun.ppp in all cases 178s + stroke <- function(..., Y = longleaf, FUN=TRUE) { 178s + Z <- Smooth(Y, ..., at="pixels") 178s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 178s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 178s + if(FUN) { 178s + f <- Smoothfun(Y, ...) 178s + f(120, 80) 178s + f(Y[1:2]) 178s + f(Y[FALSE]) 178s + U <- as.im(f) 178s + } 178s + return(invisible(NULL)) 178s + } 178s + if(ALWAYS) { 178s + stroke() 178s + stroke(5, diggle=TRUE) 178s + stroke(5, geometric=TRUE) 178s + stroke(1e-6) # generates warning about small bandwidth 178s + stroke(5, weights=expression(x)) 178s + stroke(5, kernel="epa") 178s + stroke(sigma=Inf) 178s + stroke(varcov1=diag(c(1,1))) # 'anisotropic' code 178s + } 178s + if(FULLTEST) { 178s + Z <- as.im(function(x,y){abs(x)+1}, Window(longleaf)) 178s + stroke(5, weights=Z) 178s + stroke(5, weights=runif(npoints(longleaf))) 178s + stroke(varcov=diag(c(25, 36))) 178s + stroke(varcov=diag(c(25, 36)), weights=runif(npoints(longleaf))) 178s + stroke(5, Y=longleaf %mark% 1) 178s + stroke(5, Y=cut(longleaf,breaks=3)) 178s + stroke(5, weights=Z, geometric=TRUE) 178s + g <- function(x,y) { dnorm(x, sd=10) * dnorm(y, sd=10) } 178s + stroke(kernel=g, cutoff=30, FUN=FALSE) 178s + stroke(kernel=g, cutoff=30, scalekernel=TRUE, sigma=1, FUN=FALSE) 178s + } 178s + if(FULLTEST) { 178s + ## standard errors - single column of marks 178s + stroke(sigma=5, se=TRUE) 178s + stroke(sigma=5, se=TRUE, loctype="f") 178s + w <- runif(npoints(longleaf)) 178s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="i") 178s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="m") 178s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="i") 178s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="m") 178s + } 178s + 178s + niets <- markmean(longleaf, 9) 178s + 178s + strike <- function(..., Y=finpines) { 178s + Z <- Smooth(Y, ..., at="pixels") 178s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 178s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 178s + f <- Smoothfun(Y, ...) 178s + f(4, 1) 178s + f(Y[1:2]) 178s + f(Y[FALSE]) 178s + U <- as.im(f) 178s + return(invisible(NULL)) 178s + } 178s + if(ALWAYS) { 178s + strike() 178s + strike(sigma=1.5, kernel="epa") 178s + strike(varcov=diag(c(1.2, 2.1))) 178s + strike(sigma=1e-6) 178s + strike(sigma=Inf) 178s + } 178s + if(FULLTEST) { 178s + strike(sigma=1e-6, kernel="epa") 178s + strike(1.5, weights=runif(npoints(finpines))) 178s + strike(1.5, weights=expression(y)) 178s + strike(1.5, geometric=TRUE) 178s + strike(1.5, Y=finpines[FALSE]) 178s + flatfin <- finpines %mark% data.frame(a=rep(1, npoints(finpines)), b=2) 178s + strike(1.5, Y=flatfin) 178s + strike(1.5, Y=flatfin, geometric=TRUE) 178s + } 178s + if(FULLTEST) { 178s + ## standard errors - multivariate marks 178s + strike(sigma=1.5, se=TRUE) 178s + strike(sigma=1.5, se=TRUE, loctype="f") 178s + w <- runif(npoints(finpines)) 178s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="i") 178s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="m") 178s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="i") 178s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="m") 178s + } 178s + opx <- spatstat.options(densityTransform=FALSE) 178s + if(ALWAYS) { 178s + stroke(5, Y=longleaf[order(longleaf$x)], sorted=TRUE) 178s + } 178s + if(FULLTEST) { 178s + strike(1.5, Y=finpines[order(finpines$x)], sorted=TRUE) 178s + } 178s + spatstat.options(opx) 178s + 178s + ## detect special cases 178s + if(ALWAYS) { 178s + Smooth(longleaf[FALSE]) 178s + Smooth(longleaf, minnndist(longleaf)) 178s + Xconst <- cells %mark% 1 178s + Smooth(Xconst, 0.1) 178s + Smooth(Xconst, 0.1, at="points") 178s + Smooth(cells %mark% runif(42), sigma=Inf) 178s + Smooth(cells %mark% runif(42), sigma=Inf, at="points") 178s + Smooth(cells %mark% runif(42), sigma=Inf, at="points", leaveoneout=FALSE) 178s + Smooth(cut(longleaf, breaks=4)) 178s + } 178s + 178s + ## code not otherwise reached 178s + if(ALWAYS) { 178s + smoothpointsEngine(cells, values=rep(1, npoints(cells)), sigma=0.2) 178s + } 178s + if(FULLTEST) { 178s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=Inf) 178s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=1e-16) 178s + } 178s + 178s + ## validity of Smooth.ppp(at='points') 178s + Y <- longleaf %mark% runif(npoints(longleaf), min=41, max=43) 178s + Z <- Smooth(Y, 5, at="points", leaveoneout=TRUE) 178s + rZ <- range(Z) 178s + if(rZ[1] < 40 || rZ[2] > 44) 178s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=TRUE)") 178s + 178s + Z <- Smooth(Y, 5, at="points", leaveoneout=FALSE) 178s + rZ <- range(Z) 178s + if(rZ[1] < 40 || rZ[2] > 44) 178s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=FALSE)") 178s + 178s + ## compare Smooth.ppp results with different algorithms 178s + if(ALWAYS) { 178s + crosscheque(Smooth(longleaf, at="points", sigma=6)) 178s + wt <- runif(npoints(longleaf)) 178s + crosscheque(Smooth(longleaf, at="points", sigma=6, weights=wt)) 178s + } 178s + if(FULLTEST) { 178s + vc <- diag(c(25,36)) 178s + crosscheque(Smooth(longleaf, at="points", varcov=vc)) 178s + crosscheque(Smooth(longleaf, at="points", varcov=vc, weights=wt)) 178s + } 178s + ## drop-dimension coding errors 178s + if(FULLTEST) { 178s + X <- longleaf 178s + marks(X) <- cbind(marks(X), 1) 178s + Z <- Smooth(X, 5) 178s + 178s + ZZ <- bw.smoothppp(finpines, hmin=0.01, hmax=0.012, nh=2) # reshaping problem 178s + } 178s + 178s + ## geometric-mean smoothing 178s + if(ALWAYS) { 178s + U <- Smooth(longleaf, 5, geometric=TRUE) 178s + } 178s + if(FULLTEST) { 178s + UU <- Smooth(X, 5, geometric=TRUE) 178s + V <- Smooth(longleaf, 5, geometric=TRUE, at="points") 178s + VV <- Smooth(X, 5, geometric=TRUE, at="points") 178s + } 178s + 178s + if(FULLTEST) { 178s + ## isotropic and anisotropic cases of bw.smoothppp 178s + bi <- bw.smoothppp(longleaf) 178s + ba <- bw.smoothppp(longleaf, varcov1=diag(c(1,1))) 178s + ## should be equal 178s + if(abs(bi-ba) > 0.001) 178s + stop(paste("Inconsistency in bw.smoothppp: isotropic =", bi, 178s + "!=", ba, "= anisotropic")) 178s + } 178s + }) 183s There were 22 warnings (use warnings() to see them) 183s > 183s > reset.spatstat.options() 183s > 183s > local({ 183s + if(ALWAYS) { 183s + #' Kmeasure, second.moment.engine 183s + #' Expansion of window 183s + Zno <- Kmeasure(redwood, sigma=0.2, expand=FALSE) 183s + Zyes <- Kmeasure(redwood, sigma=0.2, expand=TRUE) 183s + #' All code blocks 183s + sigmadouble <- rep(0.1, 2) 183s + diagmat <- diag(sigmadouble^2) 183s + generalmat <- matrix(c(1, 0.5, 0.5, 1)/100, 2, 2) 183s + Z <- Kmeasure(redwood, sigma=sigmadouble) 183s + Z <- Kmeasure(redwood, varcov=diagmat) 183s + Z <- Kmeasure(redwood, varcov=generalmat) 183s + A <- second.moment.calc(redwood, 0.1, what="all", debug=TRUE) 183s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 183s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 183s + D <- second.moment.calc(redwood, varcov=generalmat, what="all") 183s + PR <- pixellate(redwood) 183s + DRno <- second.moment.calc(PR, 0.2, debug=TRUE, expand=FALSE, 183s + npts=npoints(redwood), obswin=Window(redwood)) 183s + DRyes <- second.moment.calc(PR, 0.2, debug=TRUE, expand=TRUE, 183s + npts=npoints(redwood), obswin=Window(redwood)) 183s + DR2 <- second.moment.calc(solist(PR, PR), 0.2, debug=TRUE, expand=TRUE, 183s + npts=npoints(redwood), obswin=Window(redwood)) 183s + Gmat <- generalmat * 100 183s + isoGauss <- function(x,y) {dnorm(x) * dnorm(y)} 183s + ee <- evaluate2Dkernel(isoGauss, runif(10), runif(10), 183s + varcov=Gmat, scalekernel=TRUE) 183s + isoGaussIm <- as.im(isoGauss, square(c(-3,3))) 183s + gg <- evaluate2Dkernel(isoGaussIm, runif(10), runif(10), 183s + varcov=Gmat, scalekernel=TRUE) 183s + ## experimental code 183s + op <- spatstat.options(developer=TRUE) 183s + DR <- density(redwood, 0.1) 183s + spatstat.options(op) 183s + } 183s + }) 183s smooth: maximum imaginary part= 5.32e-18 183s smooth: mass error= 3e-12 183s 2nd moment measure: maximum imaginary part= 1.28e-16 183s 2nd moment measure: mass error= 2.28e-10 184s smooth: maximum imaginary part= 2.64e-18 184s smooth: mass error= -1.8e-12 184s 2nd moment measure: maximum imaginary part= 8.4e-17 184s 2nd moment measure: mass error= -9.37e-11 184s smooth: maximum imaginary part= 6.97e-18 184s smooth: mass error= 1.11e-12 184s 2nd moment measure: maximum imaginary part= 4.06e-16 184s 2nd moment measure: mass error= 1.2e-10 184s smooth component 1 : maximum imaginary part= 6.97e-18 184s smooth component 1 : mass error= 1.11e-12 184s smooth component 2 : maximum imaginary part= 6.97e-18 184s smooth component 2 : mass error= 1.11e-12 184s 2nd moment measure: maximum imaginary part= 4.06e-16 184s 2nd moment measure: mass error= 1.2e-10 184s 2nd moment measure: maximum imaginary part= 4.06e-16 184s 2nd moment measure: mass error= 1.2e-10 184s > 184s > local({ 184s + if(FULLTEST) { 184s + #' bandwidth selection 184s + op <- spatstat.options(n.bandwidth=8) 184s + bw.diggle(cells) 184s + bw.diggle(cells, method="interpreted") # undocumented test 184s + ## bw.relrisk(urkiola, hmax=20) is tested in man/bw.relrisk.Rd 184s + bw.relrisk(urkiola, hmax=20, method="leastsquares") 184s + bw.relrisk(urkiola, hmax=20, method="weightedleastsquares") 184s + ZX <- density(swedishpines, at="points") 184s + bw.pcf(swedishpines, lambda=ZX) 184s + bw.pcf(swedishpines, lambda=ZX, 184s + bias.correct=FALSE, simple=FALSE, cv.method="leastSQ") 184s + spatstat.options(op) 184s + } 184s + }) 184s > 184s > local({ 184s + if(FULLTEST) { 184s + ## idw 184s + Z <- idw(longleaf, power=4) 184s + Z <- idw(longleaf, power=4, se=TRUE) 184s + ZX <- idw(longleaf, power=4, at="points") 184s + ZX <- idw(longleaf, power=4, at="points", se=TRUE) 184s + } 184s + if(ALWAYS) { 184s + ## former bug in densityVoronoi.ppp 184s + X <- redwood[1:2] 184s + A <- densityVoronoi(X, f=0.51, counting=FALSE, fixed=FALSE, nrep=50, verbose=FALSE) 184s + ## dodgy code blocks in densityVoronoi.R 184s + A <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE) 184s + B <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE, fixed=TRUE) 184s + D <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE) 184s + E <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE, fixed=TRUE) 184s + } 184s + if(FULLTEST) { 184s + #' adaptive kernel estimation 184s + d10 <- nndist(nztrees, k=10) 184s + d10fun <- distfun(nztrees, k=10) 184s + d10im <- as.im(d10fun) 185s + uN <- 2 * runif(npoints(nztrees)) 185s + AA <- densityAdaptiveKernel(nztrees, bw=d10) 185s + BB <- densityAdaptiveKernel(nztrees, bw=d10, weights=uN) 185s + DD <- densityAdaptiveKernel(nztrees, bw=d10fun, weights=uN) 185s + EE <- densityAdaptiveKernel(nztrees, bw=d10im, weights=uN) 185s + } 185s + }) 185s Computing 2 intensity estimates...1, 185s 2. 185s Done. 185s Computing 2 intensity estimates...1, 185s 2. 185s Done. 185s Computing 2 intensity estimates...1, 185s 2. 185s Done. 185s Computing 2 intensity estimates...1, 185s 2. 185s Done. 185s > 185s > local({ 185s + if(FULLTEST) { 185s + ## cases of 'intensity' etc 185s + a <- intensity(amacrine, weights=expression(x)) 185s + SA <- split(amacrine) 185s + a <- intensity(SA, weights=expression(x)) 185s + a <- intensity(SA, weights=amacrine$x) 185s + 185s + ## check infrastructure for 'densityfun' 185s + f <- densityfun(cells, 0.05) 185s + Z <- as.im(f) 185s + Z <- as.im(f, W=square(0.5)) 185s + } 185s + }) 185s > 185s > local({ 185s + if(FULLTEST) { 185s + ## other cases of SpatialQuantile.ppp 185s + X <- longleaf 185s + marks(X) <- round(marks(X), -1) 185s + Z <- SpatialMedian(X, 30, type=4) 185s + ZX <- SpatialMedian(X, 30, type=4, at="points") 185s + ZXP <- SpatialMedian(X, 30, at="points", leaveoneout=FALSE) 185s + } 185s + }) 185s > 185s > 185s > 185s > reset.spatstat.options() 185s > 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 186s > #' 186s > #' Header for all (concatenated) test files 186s > #' 186s > #' Require spatstat.explore 186s > #' Obtain environment variable controlling tests. 186s > #' 186s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 186s > 186s > require(spatstat.explore) 186s Loading required package: spatstat.explore 186s Loading required package: spatstat.data 187s Loading required package: spatstat.univar 187s spatstat.univar 3.1-2 187s Loading required package: spatstat.geom 187s spatstat.geom 3.3-6 187s Loading required package: spatstat.random 187s spatstat.random 3.3-3 187s Loading required package: nlme 187s spatstat.explore 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 + 187s + ## check envelope calls from 'alltypes' 187s + if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE) 187s + if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE) 187s + ## check 'transform' idioms 187s + if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x)) 187s + if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x)) 187s + 187s + 187s + # check conditional simulation 187s + if(FULLTEST) { 187s + e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE) 187s + e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE) 187s + e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE) 187s + e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks 187s + e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE) 187s + } 187s + 187s + 187s + ## check pooling of envelopes in global case 187s + E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE) 187s + E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE) 187s + p12 <- pool(E1, E2) 187s + p12 <- pool(E1, E2, savefuns=TRUE) 187s + if(FULLTEST) { 187s + F1 <- envelope(cells, Kest, nsim=5, 187s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 187s + F2 <- envelope(cells, Kest, nsim=12, 187s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 187s + p12 <- pool(F1, F2) 187s + p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE) 187s + E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE, 187s + ginterval=c(0.05, 0.15)) 187s + E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE, 187s + ginterval=c(0.05, 0.15)) 187s + p12r <- pool(E1r, E2r) 187s + } 187s + 187s + if(FULLTEST) { 187s + #' as.data.frame.envelope 187s + Nsim <- 5 187s + E <- envelope(cells, nsim=Nsim, savefuns=TRUE) 187s + A <- as.data.frame(E) 187s + B <- as.data.frame(E, simfuns=TRUE) 187s + stopifnot(ncol(B) - ncol(A) == Nsim) 187s + } 187s + 187s + if(FULLTEST) { 187s + #' cases not covered elsewhere 187s + A <- envelope(cells, nsim=5, alternative="less", 187s + do.pwrong=TRUE, use.theory=FALSE, 187s + savepatterns=TRUE, savefuns=TRUE) 187s + print(A) 187s + B <- envelope(A, nsim=5, savefuns=TRUE) 187s + D <- envelope(cells, "Lest", nsim=5) 187s + 187s + UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE) 187s + 187s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE) 187s + AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE) 187s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 187s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 187s + 187s + #' spotted by Art Stock - bugs in ratfv class support 187s + BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="border") 187s + CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border") 187s + DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="trans") 187s + EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans") 187s + 187s + #' envelopes based on sample variance 187s + E <- envelope(cells, nsim=8, VARIANCE=TRUE) 187s + G <- envelope(cells, nsim=8, VARIANCE=TRUE, 187s + use.theory=FALSE, do.pwrong=TRUE) 187s + print(G) 187s + #' summary method 187s + summary(E) 187s + summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42)))) 187s + #' weights argument 187s + H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 187s + H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 187s + J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 187s + J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 187s + #' pooling with weights 187s + H <- pool(H1, H2) 187s + J <- pool(J1, J2) 187s + #' pooling envelopes with non-identical attributes 187s + H0 <- envelope(cells, nsim=4, savefuns=TRUE) 187s + HH <- pool(H0, H1) 187s + #' malformed argument 'simulate' 187s + A <- replicate(3, list(list(runifpoint(ex=cells)))) # list(list(ppp), list(ppp), list(ppp)) 187s + E <- envelope(cells, simulate=A, nsim=3) 187s + #' undocumented/secret 187s + K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE) 187s + #' so secret I've even forgotten how to do it 187s + M <- envelope(cells, nsim=4, internal=list(eject="patterns")) 187s + } 187s + 187s + 187s + if(ALWAYS) { 187s + #' Test robustness of envelope() sorting procedure when NA's are present 187s + #' Fails with spatstat.utils 1.12-0 187s + set.seed(42) 187s + EP <- envelope(longleaf, pcf, nsim=10, nrank=2) 187s + 187s + #' Test case when the maximum permitted number of failures is exceeded 187s + X <- amacrine[1:153] # contains exactly one point with mark='off' 187s + #' High probability of generating a pattern with no marks = 'off' 187s + E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn") 187s + A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2) 187s + } 187s + 187s + if(ALWAYS) { 187s + #' Internals: envelope.matrix 187s + Y <- matrix(rnorm(200), 10, 20) 187s + rr <- 1:10 187s + oo <- rnorm(10) 187s + zz <- numeric(10) 187s + E <- envelope(Y, rvals=rr, observed=oo, nsim=10) 187s + E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10) 187s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 187s + type="global", use.theory=TRUE) 187s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 187s + type="global", use.theory=TRUE, nsim=10) 187s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 187s + type="global", use.theory=FALSE, nsim=10) 187s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 187s + nsim=10, nsim2=10) 187s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 187s + jsim=1:10, jsim.mean=11:20) 187s + if(FULLTEST) print(E) 187s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 187s + nsim=10, jsim.mean=11:20) 187s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 187s + jsim=1:10, nsim2=10) 187s + } 187s + 187s + if(ALWAYS) { 187s + #' quirk with handmade summary functions ('conserve' attribute) 187s + Kdif <- function(X, r=NULL) { # note no ellipsis 187s + Y <- split(X) 187s + K1 <- Kest(Y[[1]], r=r) 187s + K2 <- Kest(Y[[2]], r=r) 187s + D <- eval.fv(K1-K2) 187s + return(D) 187s + } 187s + envelope(amacrine, Kdif, nsim=3) 187s + } 187s + 187s + 187s + ## close 'local' 187s + }) 188s Generating 4 simulations of CSR ... 188s 1, 2, 3, 188s 4. 188s 188s Done. 188s Generating 5 simulations of CSR ... 188s 1, 2, 3, 4, 188s 5. 188s 188s Done. 188s Generating 12 simulations of CSR ... 188s 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 188s 12. 188s 188s Done. 188s Generating 10 simulations of CSR ... 188s 1, 2, 3, 4, 5, 6, 7, 8, 9, 188s 10. 188s 188s Done. 188s Generating 39 simulations of CSR ... 188s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 188s No points have mark i = off 188s [retrying] 188s 1, 2, 3, 4, [retrying] 188s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 188s No points have mark i = off 188s 5, 6, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 188s No points have mark i = off 188s 188s Done. 189s Generating 3 simulations of CSR ... 189s 1, 2, 189s 3. 189s 189s Done. 189s Pointwise critical envelopes for K1(r)-K2(r) 189s and observed value for ‘amacrine’ 189s Edge correction: “iso” 189s Obtained from 3 simulations of CSR 189s Alternative: two.sided 189s Significance level of pointwise Monte Carlo test: 2/4 = 0.5 189s ................................................................................ 189s Math.label 189s r r 189s obs hat((K1-K2))[obs](r) 189s theo (K1-K2)[theo](r) 189s lo hat((K1-K2))[lo](r) 189s hi hat((K1-K2))[hi](r) 189s Description 189s r distance argument r 189s obs observed value of K1(r)-K2(r) for data pattern 189s theo theoretical value of K1(r)-K2(r) for CSR 189s lo lower pointwise envelope of K1(r)-K2(r) from simulations 189s hi upper pointwise envelope of K1(r)-K2(r) from simulations 189s ................................................................................ 189s Default plot formula: .~r 189s where “.” stands for ‘obs’, ‘theo’, ‘hi’, ‘lo’ 189s Columns ‘lo’ and ‘hi’ will be plotted as shading (by default) 189s Recommended range of argument r: [0, 0.25] 189s Available range of argument r: [0, 0.25] 189s Warning messages: 189s 1: Exceeded maximum permissible number of (maxnerr = 2) when evaluating summary function for simulated point patterns 189s 2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) : 189s 3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns 189s Unit of length: 662 microns 189s > # 189s > # tests/fastK.R 189s > # 189s > # check fast and slow code for Kest 189s > # and options not tested elsewhere 189s > # 189s > # $Revision: 1.5 $ $Date: 2020/04/28 12:58:26 $ 189s > # 189s > if(ALWAYS) { 189s + local({ 189s + ## fast code 189s + Kb <- Kest(cells, nlarge=0) 189s + Ku <- Kest(cells, correction="none") 189s + Kbu <- Kest(cells, correction=c("none", "border")) 189s + ## slow code, full set of corrections, sqrt transformation, ratios 189s + Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE) 189s + ## Lotwick-Silverman var approx (rectangular window) 189s + Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE) 189s + ## Code for large dataset 189s + nbig <- .Machine$integer.max 189s + if(!is.null(nbig)) { 189s + nn <- ceiling(sqrt(nbig)) 189s + if(nn < 1e6) Kbig <- Kest(runifpoint(nn), 189s + correction=c("border", "bord.modif", "none"), 189s + ratio=TRUE) 189s + } 189s + 189s + ## Kinhom 189s number of data points exceeds 0 - computing border correction estimate only 189s + lam <- density(cells, at="points", leaveoneout=TRUE) 189s + ## fast code 189s + Kib <- Kinhom(cells, lam, nlarge=0) 189s + Kiu <- Kest(cells, lam, correction="none") 189s + Kibu <- Kest(cells, lam, correction=c("none", "border")) 189s + ## slow code 189s + Lidd <- Linhom(unmark(demopat), sigma=bw.scott) 189s + }) 189s + 189s + } 192s number of data points exceeds 0 - computing border correction estimate only 192s > ## 192s > ## tests/fvproblems.R 192s > ## 192s > ## problems with fv, ratfv and fasp code 192s > ## 192s > ## $Revision: 1.15 $ $Date: 2020/04/28 12:58:26 $ 192s > 192s > #' This appears in the workshop notes 192s > #' Problem detected by Martin Bratschi 192s > 192s > if(FULLTEST) { 192s + local({ 192s + Jdif <- function(X, ..., i) { 192s + Jidot <- Jdot(X, ..., i=i) 192s + J <- Jest(X, ...) 192s + dif <- eval.fv(Jidot - J) 192s + return(dif) 192s + } 192s + Z <- Jdif(amacrine, i="on") 192s + }) 192s + } 192s > #' 192s > #' Test mathlegend code 192s > #' 192s > local({ 192s + K <- Kest(cells) 192s + if(FULLTEST) { 192s + plot(K) 192s + plot(K, . ~ r) 192s + plot(K, . - theo ~ r) 192s + } 192s + if(ALWAYS) { 192s + plot(K, sqrt(./pi) ~ r) 192s + } 192s + if(FULLTEST) { 192s + plot(K, cbind(iso, theo) ~ r) 192s + plot(K, cbind(iso, theo) - theo ~ r) 192s + plot(K, sqrt(cbind(iso, theo)/pi) ~ r) 192s + plot(K, cbind(iso/2, -theo) ~ r) 192s + plot(K, cbind(iso/2, trans/2) - theo ~ r) 192s + } 192s + if(FULLTEST) { 192s Warning message: 192s Periodic correction is not defined for non-rectangular windows 192s + ## test expansion of .x and .y 192s + plot(K, . ~ .x) 192s + plot(K, . - theo ~ .x) 192s + plot(K, .y - theo ~ .x) 192s + } 192s + if(ALWAYS) { 192s + plot(K, sqrt(.y) - sqrt(theo) ~ .x) 192s + } 192s + 192s + # problems with parsing weird strings in levels(marks(X)) 192s + # noted by Ulf Mehlig 192s + if(ALWAYS) { 192s + levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis") 192s + plot(Kcross(amacrine)) 192s + plot(alltypes(amacrine, "K")) 192s + } 192s + if(FULLTEST) { 192s + plot(alltypes(amacrine, "J")) 192s + plot(alltypes(amacrine, pcfcross)) 192s + } 192s + }) 192s > 192s > #' 192s > #' Test quirks related to 'alim' attribute 192s > 192s > if(FULLTEST) { 192s + local({ 192s + K <- Kest(cells) 192s + attr(K, "alim") <- NULL 192s + plot(K) 192s + attr(K, "alim") <- c(0, 0.1) 192s + plot(tail(K)) 192s + }) 192s + } 192s > 192s > #' 192s > #' Check that default 'r' vector passes the test for fine spacing 192s > 192s > if(ALWAYS) { 192s + local({ 192s + a <- Fest(cells) 192s + A <- Fest(cells, r=a$r) 192s + b <- Hest(heather$coarse) 192s + B <- Hest(heather$coarse, r=b$r) 192s + # from Cenk Icos 192s + X <- runifpoint(100, owin(c(0,3), c(0,10))) 192s + FX <- Fest(X) 192s + FXr <- Fest(X, r=FX$r) 192s + JX <- Jest(X) 192s + }) 192s + } 192s > 192s > ##' various functionality in fv.R 192s > 192s > if(ALWAYS) { 192s + local({ 192s + M <- cbind(1:20, matrix(runif(100), 20, 5)) 192s + A <- as.fv(M) 192s + fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)") 192s + A <- rename.fv(A, "M", quote(M(r))) 192s + A <- tweak.fv.entry(A, "V1", new.tag="r") 192s + A[,3] <- NULL 192s + A$hogwash <- runif(nrow(A)) 192s + fvnames(A, ".") <- NULL 192s + #' bind.fv with qualitatively different functions 192s + GK <- harmonise(G=Gest(cells), K=Kest(cells)) 192s + G <- GK$G 192s + K <- GK$K 192s + ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10)) 192s + U <- bind.fv(G, K[ss, ], clip=TRUE) 192s + #' 192s + H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2) 192s + H <- rebadge.as.dotfun(K, "H", "inhom", 3) 192s + #' text layout 192s + op <- options(width=27) 192s + print(K) 192s + options(width=18) 192s + print(K) 192s + options(op) 192s + #' collapse.fv 192s + Kb <- Kest(cells, correction="border") 192s + Ki <- Kest(cells, correction="isotropic") 192s + collapse.fv(Kb, Ki, same="theo") 192s + collapse.fv(anylist(B=Kb, I=Ki), same="theo") 192s + collapse.fv(anylist(B=Kb), I=Ki, same="theo") 192s + Xlist <- replicate(3, runifpoint(30), simplify=FALSE) 192s + Klist <- anylapply(Xlist, Kest) 192s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 192s + names(Klist) <- LETTERS[24:26] 192s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 193s Warning message: 193s In bind.fv(G, K[ss, ], clip = TRUE) : 193s The column name ‘theo’ was duplicated. Unique names were generated 193s + }) 193s + } 193s Function value object 193s (class ‘fv’) 193s for the function r -> K(r) 193s ........................... 193s Math.label 193s r r 193s theo K[pois](r) 193s border hat(K)[bord](r) 193s trans hat(K)[trans](r) 193s iso hat(K)[iso](r) 193s Description 193s r distance argument r 193s theo theoretical [..] 193s border [..] 193s trans [..] 193s iso [..] 193s ........................... 193s Default plot formula: .~r 193s where “.” stands for 193s ‘iso’, ‘trans’, 193s ‘border’, ‘theo’ 193s Recommended range of 193s argument r: [0, 0.25] 193s Available range of 193s argument r: [0, 0.25] 193s Function value 193s object (class 193s ‘fv’) 193s for the function 193s r -> K(r) 193s .................. 193s Math.label 193s r r 193s theo K[pois](r) 193s border hat(K)[bord](r) 193s trans hat(K)[trans](r) 193s iso hat(K)[iso](r) 193s Description 193s r [..] 193s theo [..] 193s border [..] 193s trans [..] 193s iso [..] 193s .................. 193s Default plot 193s formula: .~r 193s where “.” 193s stands for 193s ‘iso’, 193s ‘trans’, 193s ‘border’, 193s ‘theo’ 193s Recommended range 193s of argument r: 193s [0, 0.25] 193s Available range 193s of argument r: 193s [0, 0.25] 193s Function value object (class ‘fv’) 193s for the function r -> K(r) 193s ................................................................ 193s Math.label Description 193s r r distance argument r 193s theo K[pois](r) theoretical Poisson K(r) 193s Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r) 193s Xiso X~hat(K)[iso](r) X isotropic-corrected estimate of K(r) 193s Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r) 193s Yiso Y~hat(K)[iso](r) Y isotropic-corrected estimate of K(r) 193s Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r) 193s Ziso Z~hat(K)[iso](r) Z isotropic-corrected estimate of K(r) 193s ................................................................ 193s Default plot formula: .~.x 193s where “.” stands for ‘theo’, ‘Xborder’, ‘Xiso’, ‘Yborder’, 193s ‘Yiso’, ‘Zborder’, ‘Ziso’ 193s Recommended range of argument r: [0, 0.25] 193s Available range of argument r: [0, 0.25] 193s > 193s > if(FULLTEST) { 193s + local({ 193s + ## rat 193s + K <- Kest(cells, ratio=TRUE) 193s + G <- Gest(cells, ratio=TRUE) 193s + print(K) 193s + compatible(K, K) 193s + compatible(K, G) 193s + H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE) 193s + }) 193s + } 193s > 193s > if(FULLTEST) { 193s + local({ 193s + ## bug in Jmulti.R colliding with breakpts.R 193s + B <- owin(c(0,3), c(0,10)) 193s + Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B)) 193s + JDX <- Jdot(Y) 193s + JCX <- Jcross(Y) 193s + Jdif <- function(X, ..., i) { 193s + Jidot <- Jdot(X, ..., i=i) 193s + J <- Jest(X, ...) 193s + dif <- eval.fv(Jidot - J) 193s + return(dif) 193s + } 193s + E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y))) 193s + }) 193s + } 193s > 193s > if(FULLTEST) { 193s + local({ 193s + #' fasp axes, title, dimnames 193s + a <- alltypes(amacrine) 193s + a$title <- NULL 193s + plot(a, samex=TRUE, samey=TRUE) 193s + dimnames(a) <- lapply(dimnames(a), toupper) 193s + 193s + b <- as.fv(a) 193s + }) 193s + } 193s > 193s > if(FULLTEST) { 193s + local({ 193s + ## plot.anylist (fv) 193s + b <- anylist(A=Kcross(amacrine), B=Kest(amacrine)) 193s + plot(b, equal.scales=TRUE, main=expression(sqrt(pi))) 193s + plot(b, arrange=FALSE) 193s + }) 193s + } 193s > 193s BEGIN TEST testsGtoJ.R 193s 193s R version 4.4.3 (2025-02-28) -- "Trophy Case" 193s Copyright (C) 2025 The R Foundation for Statistical Computing 193s Platform: arm-unknown-linux-gnueabihf (32-bit) 193s 193s R is free software and comes with ABSOLUTELY NO WARRANTY. 193s You are welcome to redistribute it under certain conditions. 193s Type 'license()' or 'licence()' for distribution details. 193s 193s R is a collaborative project with many contributors. 193s Type 'contributors()' for more information and 193s 'citation()' on how to cite R or R packages in publications. 193s 193s Type 'demo()' for some demos, 'help()' for on-line help, or 193s 'help.start()' for an HTML browser interface to help. 193s Type 'q()' to quit R. 193s 193s > #' 193s > #' Header for all (concatenated) test files 193s > #' 193s > #' Require spatstat.explore 193s > #' Obtain environment variable controlling tests. 193s > #' 193s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 193s > 193s > require(spatstat.explore) 193s Loading required package: spatstat.explore 193s Loading required package: spatstat.data 194s Loading required package: spatstat.univar 194s spatstat.univar 3.1-2 194s Loading required package: spatstat.geom 194s spatstat.geom 3.3-6 194s Loading required package: spatstat.random 194s spatstat.random 3.3-3 194s Loading required package: nlme 195s spatstat.explore 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/gcc323.R 195s > ## 195s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 195s > ## 195s > if(ALWAYS) { # depends on hardware 195s + local({ 195s + # critical R values that provoke GCC bug #323 195s + a <- marktable(lansing, R=0.25) 195s + a <- marktable(lansing, R=0.21) 195s + a <- marktable(lansing, R=0.20) 195s + a <- marktable(lansing, R=0.10) 195s + }) 195s + } 195s > #' tests/hypotests.R 195s > #' Hypothesis tests 195s > #' 195s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 195s > 195s > if(FULLTEST) { 195s + local({ 195s + 195s + hopskel.test(redwood, method="MonteCarlo", nsim=5) 195s + 195s + #' quadrat test - spatial methods 195s + a <- quadrat.test(redwood, 3) 195s + domain(a) 195s + shift(a, c(1,1)) 195s + 195s + #' quadrat test - correctness of mapping from table to quadrats 195s + Q2 <- quadratcount(humberside, 2, 3) 195s + T2 <- suppressWarnings(quadrat.test(Q2)) 195s + R2 <- cbind(as.numeric(t(Q2)), round(10 * residuals(T2))) 195s + R2correct <- cbind(c(2, 20, 13, 11, 34, 123), 195s + c(-46, -12, -62, -41, 50, 134)) 195s + if(!all(R2 == R2correct)) 195s + stop("Incorrect count-residual map for quadrat.test(2,3)") 195s + 195s + Q5 <- quadratcount(humberside, 5, 3) 195s + T5 <- suppressWarnings(quadrat.test(Q5)) 195s + R5 <- cbind(as.numeric(t(Q5)), round(10 * residuals(T5))) 195s + R5correct <- cbind( 195s + c( 0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3), 195s + c(-19, -33, -42, 16, -37, -49, -28, -35, -5, -21, 295, 40, -32)) 195s + if(!all(R5 == R5correct)) 195s + stop("Incorrect count-residual map for quadrat.test(5,3)") 195s + 195s + #' cases of studpermu.test 195s + #' X is a hyperframe 195s + b <- studpermu.test(pyramidal, nperm=9) 195s + b <- studpermu.test(pyramidal, nperm=9, use.Tbar=TRUE) 195s + #' X is a list of lists of ppp 195s + ZZ <- split(pyramidal$Neurons, pyramidal$group) 195s + bb <- studpermu.test(ZZ, nperm=9) 195s + 195s + #' Issue #115 195s + X <- runifpoint(50, nsim = 3) 195s + Y <- runifpoint(3000, nsim = 3) 195s + h <- hyperframe(ppp = c(X, Y), group = rep(1:2, 3)) 195s + studpermu.test(h, ppp ~ group) 195s + 195s + #' scan test 195s + Z <- scanmeasure(cells, 0.1, method="fft") 195s + rr <- c(0.05, 1) 195s + scan.test(amacrine, rr, nsim=5, 195s + method="binomial", alternative="less") 195s + }) 195s + } 195s > # 195s > # tests/imageops.R 195s > # 195s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 195s > # 195s > 195s > 195s > if(FULLTEST) { 195s + local({ 195s + #' case of "[.im" and "[<-.im" where index is an ssf 195s + d <- distmap(cells, dimyx=32) 195s + Empty <- cells[FALSE] 195s + EmptyFun <- ssf(Empty, numeric(0)) 195s + ff <- d[EmptyFun] 195s + d[EmptyFun] <- 42 195s + 195s + #' Smooth.im -> blur.im with sigma=NULL 195s + Z <- as.im(function(x,y) { x - y }, letterR, dimyx=32) 195s + ZS <- Smooth(Z) 195s + 195s + #' deprecated -> im.apply(DA, which.max) 195s + Z <- which.max.im(bei.extra) 195s + 195s + #' rotmean 195s + U <- rotmean(Z, origin="midpoint", result="im", padzero=FALSE) 195s + 195s + #' cases of distcdf 195s + distcdf(cells[1:5]) 195s + distcdf(W=cells[1:5], dW=1:5) 195s + distcdf(W=Window(cells), V=cells[1:5]) 195s + distcdf(W=Window(cells), V=cells[1:5], dV=1:5) 195s + }) 195s + } 195s > 195s > 195s BEGIN TEST testsK.R 195s 195s R version 4.4.3 (2025-02-28) -- "Trophy Case" 195s Copyright (C) 2025 The R Foundation for Statistical Computing 195s Platform: arm-unknown-linux-gnueabihf (32-bit) 195s 195s R is free software and comes with ABSOLUTELY NO WARRANTY. 195s You are welcome to redistribute it under certain conditions. 195s Type 'license()' or 'licence()' for distribution details. 195s 195s R is a collaborative project with many contributors. 195s Type 'contributors()' for more information and 195s 'citation()' on how to cite R or R packages in publications. 195s 195s Type 'demo()' for some demos, 'help()' for on-line help, or 195s 'help.start()' for an HTML browser interface to help. 195s Type 'q()' to quit R. 195s 195s > #' 195s > #' Header for all (concatenated) test files 195s > #' 195s > #' Require spatstat.explore 195s > #' Obtain environment variable controlling tests. 195s > #' 195s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 195s > 195s > require(spatstat.explore) 195s Loading required package: spatstat.explore 195s Loading required package: spatstat.data 197s Loading required package: spatstat.univar 197s spatstat.univar 3.1-2 197s Loading required package: spatstat.geom 197s spatstat.geom 3.3-6 197s Loading required package: spatstat.random 197s spatstat.random 3.3-3 197s Loading required package: nlme 197s spatstat.explore 3.3-4 197s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 197s > ALWAYS <- TRUE 197s > cat(paste("--------- Executing", 197s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 197s + "test code -----------\n")) 197s --------- Executing **RESTRICTED** subset of test code ----------- 197s > #' 197s > #' tests/kernelstuff.R 197s > #' 197s > #' $Revision: 1.2 $ $Date: 2023/11/05 01:49:45 $ 197s > 197s > local({ 197s + if(FULLTEST) { 197s + #' test all cases in kernels.R 197s + kernames <- c("gaussian", "rectangular", "triangular", 197s + "epanechnikov", "biweight", "cosine", "optcosine") 197s + X <- rnorm(20) 197s + U <- runif(20) 197s + for(ker in kernames) { 197s + dX <- dkernel(X, ker) 197s + fX <- pkernel(X, ker) 197s + qU <- qkernel(U, ker) 197s + m0 <- kernel.moment(0, 0, ker) 197s + m1 <- kernel.moment(1, 0, ker) 197s + m2 <- kernel.moment(2, 0, ker) 197s + m3 <- kernel.moment(3, 0, ker) 197s + } 197s + } 197s + }) 197s > 197s > #' 197s > #' tests/Kfuns.R 197s > #' 197s > #' Various K and L functions and pcf 197s > #' 197s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 197s > #' 197s > #' Assumes 'EveryStart.R' was run 197s > 197s > if(FULLTEST) { 197s + Cells <- cells 197s + Amacrine <- amacrine 197s + Redwood <- redwood 197s + } else { 197s + ## reduce numbers of data + dummy points 197s + spatstat.options(npixel=32, ndummy.min=16) 197s + Cells <- cells[c(FALSE, TRUE)] 197s + Amacrine <- amacrine[c(FALSE, TRUE)] 197s + Redwood <- redwood[c(FALSE, TRUE)] 197s + } 197s > 197s > 197s > myfun <- function(x,y){(x+1) * y } # must be outside 197s > 197s > local({ 197s + if(FULLTEST) { 197s + #' supporting code 197s + rmax.rule("Kscaled", owin(), 42) 197s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 197s + "polygonal", TRUE) 197s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 197s + "mask", TRUE) 197s + implemented.for.K(c("border", "isotropic"), "mask", TRUE) 197s + implemented.for.K(c("border", "isotropic"), "mask", FALSE) 197s + #' shortcuts 197s + D <- density(Cells) 197s + K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 197s + K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 197s + allcor <- c("none", "border", "bord.modif","isotropic", "translate") 197s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor) 197s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 197s + weights=D) 197s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 197s + use.integers=FALSE) 197s + #' Kest special code blocks 197s + K <- Kest(Cells, var.approx=TRUE, ratio=FALSE) 197s + Z <- distmap(Cells) + 1 197s + Kb <- Kest(Cells, correction=c("border","bord.modif"), 197s + weights=Z, ratio=TRUE) 197s + Kn <- Kest(Cells, correction="none", 197s + weights=Z, ratio=TRUE) 197s + Knb <- Kest(Cells, correction=c("border","bord.modif","none"), 197s + weights=Z, ratio=TRUE) 197s + } 197s + if(ALWAYS) { 197s + bigint <- 50000 # This is only "big" on a 32-bit system where 197s + # sqrt(.Machine$integer.max) = 46340.9 197s + X <- runifpoint(bigint) 197s + Z <- as.im(1/bigint, owin()) 197s + Kb <- Kest(X, correction=c("border","bord.modif"), 197s + rmax=0.02, weights=Z, ratio=TRUE) 197s + } 197s + if(FULLTEST) { 197s + Kn <- Kest(X, correction="none", 197s + rmax=0.02, weights=Z, ratio=TRUE) 197s + Knb <- Kest(X, correction=c("border","bord.modif","none"), 197s + rmax=0.02, weights=Z, ratio=TRUE) 197s + #' pcf.ppp special code blocks 197s + pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE) 197s + pc <- pcf(Cells, domain=square(0.5)) 197s + pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE) 197s + pw <- pcf(Redwood, correction="none") 197s + pwr <- pcf(Redwood, correction="none", ratio=TRUE) 197s + pv <- pcf(Redwood, kernel="rectangular") 197s + p1 <- pcf(Redwood[1]) 197s + #' pcf.fv 197s + K <- Kest(Redwood) 197s + g <- pcf(K, method="a") 197s + g <- pcf(K, method="c") 197s + g <- pcf(K, method="d") 197s + #' Kinhom code blocks 197s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 197s + lambda <- 100 * X$x 197s + Kin <- Kinhom(X, lambda, correction=c("none", "border")) 197s + lambda2 <- outer(lambda, lambda, "*") 197s + Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE, 197s + correction=c("translate", "isotropic")) 197s + } 197s + if(ALWAYS) { 197s + #' edge corrections 197s + rr <- rep(0.1, npoints(Cells)) 197s + eC <- edge.Ripley(Cells, rr) 197s + eI <- edge.Ripley(Cells, rr, method="interpreted") 197s + if(max(abs(eC-eI)) > 0.1) 197s + stop("Ripley edge correction results do not match") 197s + } 197s + if(FULLTEST) { 197s + a <- rmax.Ripley(square(1)) 197s + a <- rmax.Rigid(square(1)) 197s + a <- rmax.Ripley(as.polygonal(square(1))) 197s + a <- rmax.Rigid(as.polygonal(square(1))) 197s + a <- rmax.Ripley(letterR) 197s + a <- rmax.Rigid(letterR) 197s + } 197s + if(ALWAYS) { 197s + #' run slow code for edge correction and compare results 197s + op <- spatstat.options(npixel=128) 197s + X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)] 197s + Window(X) <- as.polygonal(Window(X)) 197s + Eapprox <- edge.Trans(X) 197s + Eexact <- edge.Trans(X, exact=TRUE) 197s + maxrelerr <- max(abs(1 - range(Eapprox/Eexact))) 197s + if(maxrelerr > 0.1) 197s + stop(paste("Exact and approximate algorithms for edge.Trans disagree by", 197s + paste0(round(100*maxrelerr), "%")), 197s + call.=FALSE) 197s + spatstat.options(op) 197s + } 197s + }) 197s > 197s > local({ 197s + if(FULLTEST) { 197s + #' ---- multitype ------ 197s + K <- Kcross(Amacrine, correction=c("none", "bord.modif")) 197s + K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"), 197s + ratio=TRUE) 197s + #' inhomogeneous multitype 197s + K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine)) 197s + K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points")) 197s + K5 <- Kcross.inhom(Amacrine, correction="bord.modif") 197s + #' markconnect, markcorr 197s + M <- markconnect(Amacrine, "on", "off", normalise=TRUE) 197s + M <- markcorr(longleaf, normalise=TRUE, 197s + correction=c("isotropic", "translate", "border", "none")) 197s + M <- markcorr(longleaf, normalise=TRUE, fargs=list()) 197s + #' Kmark (=markcorrint) 197s + X <- runifpoint(100) %mark% runif(100) 197s + km <- Kmark(X, f=atan2) 197s + km <- Kmark(X, f1=sin) 197s + km <- Kmark(X, f="myfun") 197s + aa <- Kmark(X, normalise=FALSE, returnL=FALSE) 197s + aa <- Kmark(X, normalise=FALSE, returnL=TRUE) 197s + aa <- Kmark(X, normalise=TRUE, returnL=FALSE) 197s + aa <- Kmark(X, normalise=TRUE, returnL=TRUE) 197s + } 197s + }) 197s > 197s > local({ 197s + if(FULLTEST) { 197s + #' various modified K functions 197s + #' 197s + #' directional K functions 197s + #' 197s + a <- Ksector(swedishpines, 197s + -pi/2, pi/2, units="radians", 197s + correction=c("none", "border", "bord.modif", 197s + "Ripley", "translate"), 197s + ratio=TRUE) 197s + plot(a) 197s + #' 197s + #' local K functions 197s + #' 197s + Z <- as.im(intensity(swedishpines), W=Window(swedishpines)) 197s + ZX <- Z[swedishpines] 197s + a <- localLinhom(swedishpines, lambda=Z) 197s + a <- localLinhom(swedishpines, lambda=ZX) 197s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 197s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 197s discrepancy in isotropic edge correction at interior point of rectangle is 2.22e-16, within tolerance of 1e-06 197s discrepancy in isotropic edge correction near corner of rectangle is 8.882e-16, within tolerance of 1e-06 197s discrepancy in isotropic edge correction at interior point of polygon (debug on) is 7.55e-15, within tolerance of 1e-06 197s discrepancy in isotropic edge correction at interior point of polygon (debug off) is 7.55e-15, within tolerance of 1e-06 197s + a <- localLcross(Amacrine) 197s + a <- localLcross(Amacrine, from="off", to="off") 197s + a <- localKdot(Amacrine) 197s + a <- localLdot(Amacrine) 197s + a <- localKcross.inhom(Amacrine) 197s + a <- localLcross.inhom(Amacrine) 197s + Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine)) 197s + Lum <- evaluateCovariateAtPoints(Zed, Amacrine) 197s + moff <- (marks(Amacrine) == "off") 197s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 197s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 197s + a <- localLcross.inhom(Amacrine, from="off", to="on", 197s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 197s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 197s + correction="none") 197s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 197s + correction="translate") 197s + #' 197s + #' cases of resolve.lambdacross 197s + #' 197s + h <- resolve.lambdacross(Amacrine, moff, !moff) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, 197s + lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, 197s + lambdaI=Lum[moff], lambdaJ=Lum[!moff]) 197s + d <- densityfun(unmark(Amacrine), sigma=0.1) 197s + dm <- lapply(split(Amacrine), densityfun, sigma=0.1) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=d) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, 197s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 197s + h <- resolve.lambdacross(Amacrine, moff, !moff, 197s + lambdaX=function(x,y,m){ d(x,y) }) 197s + #' 197s + #' multitype inhomogeneous pcf 197s + #' 197s + g <- pcfcross.inhom(Amacrine, 197s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 197s + 197s + #' 197s + #' lohboot code blocks 197s + #' 197s + Ared <- lohboot(Redwood, fun="Kest", block=TRUE, 197s + Vcorrection=TRUE, global=FALSE, correction="none") 197s + Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE) 197s + Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE, 197s + correction="translate") 197s + Dred <- lohboot(Redwood, Lest) 197s + Kred <- lohboot(Redwood, Kinhom) 197s + Lred <- lohboot(Redwood, Linhom) 197s + gred <- lohboot(Redwood, pcfinhom, sigma=0.1) 197s + #' 197s + X <- runifpoint(100, letterR) 197s + AX <- lohboot(X, block=TRUE, nx=7, ny=10) 197s + #' multitype 197s + b <- lohboot(Amacrine, Kcross) 197s + b <- lohboot(Amacrine, Lcross) 197s + b <- lohboot(Amacrine, Kdot) 197s + b <- lohboot(Amacrine, Ldot) 197s + b <- lohboot(Amacrine, Kcross.inhom) 197s + b <- lohboot(Amacrine, Lcross.inhom) 197s + 197s + ## Kscaled 197s + A <- Lscaled(japanesepines, renormalise=TRUE, correction="all") 197s + } 197s + }) 197s > 197s > local({ 197s + if(ALWAYS) { 197s + #' From Ege, in response to a stackoverflow question. 197s + #' The following example has two points separated by r = 1 with 1/4 of the 197s + #' circumference outside the 10x10 window (i.e. area 100). 197s + #' Thus the value of K^(r) should jump from 0 to 197s + #' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333. 197s + x <- c(4.5,5.5) 197s + y <- c(10,10)-sqrt(2)/2 197s + W <- square(10) 197s + X <- ppp(x, y, W) 197s + compere <- function(a, b, where, tol=1e-6) { 197s + descrip <- paste("discrepancy in isotropic edge correction", where) 197s + err <- as.numeric(a) - as.numeric(b) 197s + maxerr <- max(abs(err)) 197s + blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","), 197s + if(maxerr > tol) "exceeding" else "within", 197s + "tolerance of", tol) 197s + message(blurb) 197s + if(maxerr > tol) { 197s + message(paste("Discrepancies:", paste(err, collapse=", "))) 197s + stop(paste("excessive", descrip), call.=FALSE) 197s + } 197s + invisible(TRUE) 197s + } 197s + ## Testing: 197s + eX <- edge.Ripley(X, c(1,1)) 197s + compere(eX, c(4/3,4/3), "at interior point of rectangle") 197s + ## Corner case: 197s + Y <- X 197s + Y$x <- X$x-4.5+sqrt(2)/2 197s + eY <- edge.Ripley(Y, c(1,1)) 197s + compere(eY, c(2,4/3), "near corner of rectangle") 197s + ## Invoke polygonal code 197s + Z <- rotate(Y, pi/4) 197s + eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE)) 197s + compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)") 197s + ## test validity without debugger,in case of quirks of compiler optimisation 197s + eZ <- edge.Ripley(Z, c(1,1)) 197s + compere(eZ, c(2,4/3), "at interior point of polygon (debug off)") 197s + } 197s + }) 197s /// Debug level 3 /// 197s ------- centre[0] = (-6.071068, 7.071068) ------ 197s boundary distance 0.707107 197s radius[0] = 1.000000 197s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 197s Left: det = -35.857864 197s Right: det = -171.715729 197s Top: det = -34143.145751 197s Finished cutting; ncut = 0 197s contrib = -0.000000 197s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 197s Left: det = -171.715729 197s Right: det = -35.857864 197s Top: det = -34143.145751 197s Finished cutting; ncut = 0 197s contrib = 0.000000 197s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 197s Left: det = -35.857864 197s Right: det = 0.000000 197s det = 0 197s Top: det = 200.000000 197s det > 0 197s hits + segment: t = 1.000000, theta = 3.141593 197s hits - segment: t = 0.858579, theta = 1.570796 197s Finished cutting; ncut = 2 197s theta[0] = 1.570796 197s theta[1] = 3.141593 197s Interval 0, width 1.570796:inside 197s Interval 1, width 1.570796:outside 197s Interval 2, width 3.141593:inside 197s contrib = 4.712389 197s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 197s Left: det = 0.000000 197s det = 0 197s Right: det = -35.857864 197s Top: det = 200.000000 197s det > 0 197s hits + segment: t = 0.141421, theta = -1.570796 197s hits - segment: t = 0.000000, theta = 3.141593 197s Finished cutting; ncut = 2 197s theta[0] = 3.141593 197s theta[1] = 4.712389 197s Interval 0, width 3.141593:outside 197s Interval 1, width 1.570796:inside 197s Interval 2, width 1.570796:outside 197s contrib = -1.570796 197s 197s Total = 3.141593 = 0.500000 * (2 * pi) 197s ------- centre[1] = (-5.363961, 7.778175) ------ 197s boundary distance 0.707107 197s radius[0] = 1.000000 197s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 197s Left: det = -27.772078 197s Right: det = -153.629942 197s Top: det = -34143.145751 197s Finished cutting; ncut = 0 197s contrib = -0.000000 197s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 197s Left: det = -153.629942 197s Right: det = -27.772078 197s Top: det = -27108.831175 197s Finished cutting; ncut = 0 197s contrib = 0.000000 197s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 197s Left: det = -27.772078 197s Right: det = -1.914214 197s Top: det = 200.000000 197s det > 0 197s hits + segment: t = 0.900000, theta = 3.141593 197s hits - segment: t = 0.758579, theta = 1.570796 197s Finished cutting; ncut = 2 197s theta[0] = 1.570796 197s theta[1] = 3.141593 197s Interval 0, width 1.570796:inside 197s Interval 1, width 1.570796:outside 197s Interval 2, width 3.141593:inside 197s contrib = 4.712389 197s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 197s Left: det = -1.914214 197s Right: det = -27.772078 197s Top: det = -765.685425 197s Finished cutting; ncut = 0 197s contrib = -0.000000 197s 197s Total = 4.712389 = 0.750000 * (2 * pi) 197s > 197s > 197s > 197s > reset.spatstat.options() 197s > 197s BEGIN TEST testsL.R 197s 197s R version 4.4.3 (2025-02-28) -- "Trophy Case" 197s Copyright (C) 2025 The R Foundation for Statistical Computing 197s Platform: arm-unknown-linux-gnueabihf (32-bit) 197s 197s R is free software and comes with ABSOLUTELY NO WARRANTY. 197s You are welcome to redistribute it under certain conditions. 197s Type 'license()' or 'licence()' for distribution details. 197s 197s R is a collaborative project with many contributors. 197s Type 'contributors()' for more information and 197s 'citation()' on how to cite R or R packages in publications. 197s 197s Type 'demo()' for some demos, 'help()' for on-line help, or 197s 'help.start()' for an HTML browser interface to help. 197s Type 'q()' to quit R. 197s 197s > #' 197s > #' Header for all (concatenated) test files 197s > #' 197s > #' Require spatstat.explore 197s > #' Obtain environment variable controlling tests. 197s > #' 197s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 197s > 197s > require(spatstat.explore) 197s Loading required package: spatstat.explore 197s Loading required package: spatstat.data 199s Loading required package: spatstat.univar 199s spatstat.univar 3.1-2 199s Loading required package: spatstat.geom 199s spatstat.geom 3.3-6 199s Loading required package: spatstat.random 199s spatstat.random 3.3-3 199s Loading required package: nlme 199s spatstat.explore 3.3-4 199s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 199s > ALWAYS <- TRUE 199s > cat(paste("--------- Executing", 199s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 199s + "test code -----------\n")) 199s --------- Executing **RESTRICTED** subset of test code ----------- 199s > ## 199s > ## tests/localpcf.R 199s > ## 199s > ## temporary test file for localpcfmatrix 199s > ## $Revision: 1.2 $ $Date: 2015/12/29 08:54:49 $ 199s > 199s > local({ 199s + a <- localpcfmatrix(redwood) 199s + if(FULLTEST) { 199s + a 199s + plot(a) 199s + a[, 3:5] 199s + } 199s + }) 199s > 199s BEGIN TEST testsM.R 199s 199s R version 4.4.3 (2025-02-28) -- "Trophy Case" 199s Copyright (C) 2025 The R Foundation for Statistical Computing 199s Platform: arm-unknown-linux-gnueabihf (32-bit) 199s 199s R is free software and comes with ABSOLUTELY NO WARRANTY. 199s You are welcome to redistribute it under certain conditions. 199s Type 'license()' or 'licence()' for distribution details. 199s 199s R is a collaborative project with many contributors. 199s Type 'contributors()' for more information and 199s 'citation()' on how to cite R or R packages in publications. 199s 199s Type 'demo()' for some demos, 'help()' for on-line help, or 199s 'help.start()' for an HTML browser interface to help. 199s Type 'q()' to quit R. 199s 199s Loading required package: spatstat.explore 199s > #' 199s > #' Header for all (concatenated) test files 199s > #' 199s > #' Require spatstat.explore 199s > #' Obtain environment variable controlling tests. 199s > #' 199s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 199s > 199s > require(spatstat.explore) 199s Loading required package: spatstat.data 200s Loading required package: spatstat.univar 200s spatstat.univar 3.1-2 200s Loading required package: spatstat.geom 201s spatstat.geom 3.3-6 201s Loading required package: spatstat.random 201s spatstat.random 3.3-3 201s Loading required package: nlme 201s spatstat.explore 3.3-4 201s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 201s > ALWAYS <- TRUE 201s > cat(paste("--------- Executing", 201s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 201s + "test code -----------\n")) 201s --------- Executing **RESTRICTED** subset of test code ----------- 201s > ## 201s > ## tests/markcor.R 201s > ## 201s > ## Tests of mark correlation code (etc) 201s > ## 201s > ## $Revision: 1.7 $ $Date: 2020/11/25 01:23:32 $ 201s > 201s > local({ 201s + if(ALWAYS) { 201s + ## check.testfun checks equality of functions 201s + ## and is liable to break if the behaviour of all.equal is changed 201s + fe <- function(m1, m2) {m1 == m2} 201s + fm <- function(m1, m2) {m1 * m2} 201s + fs <- function(m1, m2) {sqrt(m1)} 201s + if(check.testfun(fe, X=amacrine)$ftype != "equ") 201s + warning("check.testfun fails to recognise mark equality function") 201s + if(check.testfun(fm, X=longleaf)$ftype != "mul") 201s + warning("check.testfun fails to recognise mark product function") 201s + check.testfun(fs, X=longleaf) 201s + check.testfun("mul") 201s + check.testfun("equ") 201s + } 201s + 201s + if(FULLTEST) { 201s + ## test all is well in Kmark -> Kinhom 201s + MA <- Kmark(amacrine,function(m1,m2){m1==m2}) 201s + set.seed(42) 201s + AR <- rlabel(amacrine) 201s + MR <- Kmark(AR,function(m1,m2){m1==m2}) 201s + if(isTRUE(all.equal(MA,MR))) 201s + stop("Kmark unexpectedly ignores marks") 201s + 201s + ## cover code blocks in markcorr() 201s + X <- runifpoint(100) %mark% runif(100) 201s + Y <- X %mark% data.frame(u=runif(100), v=runif(100)) 201s + ww <- runif(100) 201s + fone <- function(x) { x/2 } 201s + ffff <- function(x,y) { fone(x) * fone(y) } 201s + aa <- markcorr(Y) 201s + bb <- markcorr(Y, ffff, weights=ww, normalise=TRUE) 201s + bb <- markcorr(Y, ffff, weights=ww, normalise=FALSE) 201s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=TRUE) 201s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=FALSE) 201s Warning messages: 201s 1: In eval(quote({ : 201s check.testfun fails to recognise mark equality function 201s 2: In eval(quote({ : 201s check.testfun fails to recognise mark product function 201s + 201s + ## markcrosscorr 201s + a <- markcrosscorr(betacells, normalise=FALSE) 201s + if(require(sm)) { 201s + b <- markcrosscorr(betacells, method="sm") 201s + } 201s + 201s + ## Vmark with normalisation 201s + v <- Vmark(spruces, normalise=TRUE) 201s + v <- Vmark(finpines, normalise=TRUE) 201s + } 201s + }) 201s > #' tests/mctests.R 201s > #' Monte Carlo tests 201s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 201s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 201s > 201s > local({ 201s + if(FULLTEST) { 201s + envelopeTest(cells, Lest, exponent=1, nsim=9, savepatterns=TRUE) 201s + (a3 <- envelopeTest(cells, Lest, exponent=3, nsim=9, savepatterns=TRUE)) 201s + 201s + envelopeTest(a3, Lest, exponent=3, nsim=9, alternative="less") 201s + 201s + envelopeTest(redwood, Lest, exponent=1, nsim=19, 201s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 201s + envelopeTest(redwood, pcf, exponent=Inf, nsim=19, 201s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 201s + } 201s + }) 201s > 201s > 201s > 201s BEGIN TEST testsNtoO.R 201s 201s R version 4.4.3 (2025-02-28) -- "Trophy Case" 201s Copyright (C) 2025 The R Foundation for Statistical Computing 201s Platform: arm-unknown-linux-gnueabihf (32-bit) 201s 201s R is free software and comes with ABSOLUTELY NO WARRANTY. 201s You are welcome to redistribute it under certain conditions. 201s Type 'license()' or 'licence()' for distribution details. 201s 201s R is a collaborative project with many contributors. 201s Type 'contributors()' for more information and 201s 'citation()' on how to cite R or R packages in publications. 201s 201s Type 'demo()' for some demos, 'help()' for on-line help, or 201s 'help.start()' for an HTML browser interface to help. 201s Type 'q()' to quit R. 201s 201s > #' 201s > #' Header for all (concatenated) test files 201s > #' 201s > #' Require spatstat.explore 201s > #' Obtain environment variable controlling tests. 201s > #' 201s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 201s > 201s > require(spatstat.explore) 201s Loading required package: spatstat.explore 201s Loading required package: spatstat.data 202s Loading required package: spatstat.univar 202s spatstat.univar 3.1-2 202s Loading required package: spatstat.geom 202s spatstat.geom 3.3-6 202s Loading required package: spatstat.random 202s spatstat.random 3.3-3 202s Loading required package: nlme 202s spatstat.explore 3.3-4 202s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 202s > ALWAYS <- TRUE 202s > cat(paste("--------- Executing", 202s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 202s + "test code -----------\n")) 202s --------- Executing **RESTRICTED** subset of test code ----------- 202s > # 202s > # tests/nnstat.R 202s > # 202s > # Check code that uses nndist/nnwhich 202s > # 202s > # nnorient() 202s > # stienen() 202s > # 202s > # $Revision: 1.1 $ $Date: 2020/12/04 03:45:44 $ 202s > # 202s > 202s > 202s > local({ 202s + if(FULLTEST) { 202s + #' test nnorient 202s + nnorient(cells, domain=erosion(Window(cells), 0.1)) 202s + #' degenerate case 202s + X <- cells[nndist(cells) > bdist.points(cells)] 202s + f <- nnorient(X) 202s + #' nnclean 202s + A <- nnclean(shapley, k=17, edge.correct=TRUE) 202s + B <- nnclean(runifpoint3(300), 3) 202s + #' stienen set 202s + #' bug when disc radius is zero 202s + Y <- unmark(humberside)[40:100] # contains duplicated points 202s + stienen(Y) 202s + Z <- stienenSet(Y) 202s + #' other cases 202s + U <- stienen(cells[1]) 202s + V <- stienenSet(cells, edge=FALSE) 202s + } 202s + }) 202s > 202s > 202s > 202s > 202s BEGIN TEST testsP1.R 202s 202s R version 4.4.3 (2025-02-28) -- "Trophy Case" 202s Copyright (C) 2025 The R Foundation for Statistical Computing 202s Platform: arm-unknown-linux-gnueabihf (32-bit) 202s 202s R is free software and comes with ABSOLUTELY NO WARRANTY. 202s You are welcome to redistribute it under certain conditions. 202s Type 'license()' or 'licence()' for distribution details. 202s 202s R is a collaborative project with many contributors. 202s Type 'contributors()' for more information and 202s 'citation()' on how to cite R or R packages in publications. 202s 202s Type 'demo()' for some demos, 'help()' for on-line help, or 202s 'help.start()' for an HTML browser interface to help. 202s Type 'q()' to quit R. 202s 203s > #' 203s > #' Header for all (concatenated) test files 203s > #' 203s > #' Require spatstat.explore 203s > #' Obtain environment variable controlling tests. 203s > #' 203s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 203s > 203s > require(spatstat.explore) 203s Loading required package: spatstat.explore 203s Loading required package: spatstat.data 204s Loading required package: spatstat.univar 204s spatstat.univar 3.1-2 204s Loading required package: spatstat.geom 204s spatstat.geom 3.3-6 204s Loading required package: spatstat.random 204s spatstat.random 3.3-3 204s Loading required package: nlme 204s spatstat.explore 3.3-4 204s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 204s > ALWAYS <- TRUE 204s > cat(paste("--------- Executing", 204s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 204s + "test code -----------\n")) 204s --------- Executing **RESTRICTED** subset of test code ----------- 204s > ## 204s > ## tests/pixelgripes.R 204s > ## Problems related to pixellation of windows 204s > ## 204s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 204s > 204s > if(FULLTEST) { 204s + local({ 204s + 204s + 204s + }) 204s + } 204s > 204s BEGIN TEST testsP2.R 204s 204s R version 4.4.3 (2025-02-28) -- "Trophy Case" 204s Copyright (C) 2025 The R Foundation for Statistical Computing 204s Platform: arm-unknown-linux-gnueabihf (32-bit) 204s 204s R is free software and comes with ABSOLUTELY NO WARRANTY. 204s You are welcome to redistribute it under certain conditions. 204s Type 'license()' or 'licence()' for distribution details. 204s 204s R is a collaborative project with many contributors. 204s Type 'contributors()' for more information and 204s 'citation()' on how to cite R or R packages in publications. 204s 204s Type 'demo()' for some demos, 'help()' for on-line help, or 204s 'help.start()' for an HTML browser interface to help. 204s Type 'q()' to quit R. 204s 204s > #' 204s > #' Header for all (concatenated) test files 204s > #' 204s > #' Require spatstat.explore 204s > #' Obtain environment variable controlling tests. 204s > #' 204s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 204s > 204s > require(spatstat.explore) 204s Loading required package: spatstat.explore 204s Loading required package: spatstat.data 205s Loading required package: spatstat.univar 205s spatstat.univar 3.1-2 205s Loading required package: spatstat.geom 205s spatstat.geom 3.3-6 205s Loading required package: spatstat.random 205s spatstat.random 3.3-3 205s Loading required package: nlme 205s spatstat.explore 3.3-4 205s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 205s > ALWAYS <- TRUE 205s > cat(paste("--------- Executing", 205s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 205s + "test code -----------\n")) 205s --------- Executing **RESTRICTED** subset of test code ----------- 205s > 205s BEGIN TEST testsQ.R 206s 206s R version 4.4.3 (2025-02-28) -- "Trophy Case" 206s Copyright (C) 2025 The R Foundation for Statistical Computing 206s Platform: arm-unknown-linux-gnueabihf (32-bit) 206s 206s R is free software and comes with ABSOLUTELY NO WARRANTY. 206s You are welcome to redistribute it under certain conditions. 206s Type 'license()' or 'licence()' for distribution details. 206s 206s R is a collaborative project with many contributors. 206s Type 'contributors()' for more information and 206s 'citation()' on how to cite R or R packages in publications. 206s 206s Type 'demo()' for some demos, 'help()' for on-line help, or 206s 'help.start()' for an HTML browser interface to help. 206s Type 'q()' to quit R. 206s 206s > #' 206s > #' Header for all (concatenated) test files 206s > #' 206s > #' Require spatstat.explore 206s > #' Obtain environment variable controlling tests. 206s > #' 206s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 206s > 206s > require(spatstat.explore) 206s Loading required package: spatstat.explore 206s Loading required package: spatstat.data 207s Loading required package: spatstat.univar 207s spatstat.univar 3.1-2 207s Loading required package: spatstat.geom 207s spatstat.geom 3.3-6 207s Loading required package: spatstat.random 207s spatstat.random 3.3-3 207s Loading required package: nlme 207s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 207s > ALWAYS <- TRUE 207s > cat(paste("--------- Executing", 207s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 207s + "test code -----------\n")) 207s --------- Executing **RESTRICTED** subset of test code ----------- 207s > 207s spatstat.explore 3.3-4 207s BEGIN TEST testsR1.R 207s 207s R version 4.4.3 (2025-02-28) -- "Trophy Case" 207s Copyright (C) 2025 The R Foundation for Statistical Computing 207s Platform: arm-unknown-linux-gnueabihf (32-bit) 207s 207s R is free software and comes with ABSOLUTELY NO WARRANTY. 207s You are welcome to redistribute it under certain conditions. 207s Type 'license()' or 'licence()' for distribution details. 207s 207s R is a collaborative project with many contributors. 207s Type 'contributors()' for more information and 207s 'citation()' on how to cite R or R packages in publications. 207s 207s Type 'demo()' for some demos, 'help()' for on-line help, or 207s 'help.start()' for an HTML browser interface to help. 207s Type 'q()' to quit R. 207s 207s > #' 207s > #' Header for all (concatenated) test files 207s > #' 207s > #' Require spatstat.explore 207s > #' Obtain environment variable controlling tests. 207s > #' 207s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 207s > 207s > require(spatstat.explore) 207s Loading required package: spatstat.explore 207s Loading required package: spatstat.data 208s Loading required package: spatstat.univar 208s spatstat.univar 3.1-2 208s Loading required package: spatstat.geom 208s spatstat.geom 3.3-6 208s Loading required package: spatstat.random 208s spatstat.random 3.3-3 208s Loading required package: nlme 209s spatstat.explore 3.3-4 209s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 209s > ALWAYS <- TRUE 209s > cat(paste("--------- Executing", 209s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 209s + "test code -----------\n")) 209s --------- Executing **RESTRICTED** subset of test code ----------- 209s > ## 209s > ## tests/rhohat.R 209s > ## 209s > ## Test all combinations of options for rhohatCalc 209s > ## 209s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 209s > 209s > local({ 209s + if(FULLTEST) { 209s + X <- rpoispp(function(x,y){exp(3+3*x)}) 209s + Z <- as.im(function(x,y) { x }, Window(X)) 209s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 209s + 209s + ## rhohat.ppp 209s + ## done in example(rhohat): 209s + ## rhoA <- rhohat(X, "x") 209s + ## rhoB <- rhohat(X, "x", method="reweight") 209s + ## rhoC <- rhohat(X, "x", method="transform") 209s + ## alternative smoother (if package locfit available) 209s + rhoA <- rhohat(X, "x", smoother="local") 209s + rhoB <- rhohat(X, "x", smoother="local", method="reweight") 209s + rhoC <- rhohat(X, "x", smoother="local", method="transform") 209s + 209s + #' code blocks 209s + rhoD <- rhohat(X, "y", positiveCI=TRUE) 209s + rhoE <- rhohat(X, Z, positiveCI=TRUE) 209s + #' weights 209s + rhoF <- rhohat(X, Z, weights=f(X)) 209s + rhoG <- rhohat(X, Z, weights=f) 209s + rhoH <- rhohat(X, Z, weights=as.im(f)) 209s + 209s + lam <- as.im(function(x,y) {exp(3+2*x)}, W=Window(Z)) 209s + 209s + ## Baseline 209s + rhoAb <- rhohat(X, "x", baseline=lam) 209s + rhoBb <- rhohat(X, "x", method="reweight", baseline=lam) 209s + rhoCb <- rhohat(X, "x", method="transform", baseline=lam) 209s + 209s + ## Horvitz-Thompson 209s + rhoAH <- rhohat(X, "x", horvitz=TRUE) 209s + rhoBH <- rhohat(X, "x", method="reweight", horvitz=TRUE) 209s + rhoCH <- rhohat(X, "x", method="transform", horvitz=TRUE) 209s + 209s + ## class support 209s + plot(rhoA) 209s + plot(rhoA, rho ~ x, shade=NULL) 209s + plot(rhoA, log(rho) ~ x, shade=NULL) 209s + plot(rhoA, log(.) ~ x) 209s + 209s + ## rho2hat 209s + r2xy <- rho2hat(X, "x", "y") 209s + r2xyw <- rho2hat(X, "x", "y", method="reweight") 209s + print(r2xyw) 209s + plot(r2xy, do.points=TRUE) 209s + xcoord <- function(x,y) x 209s + ycoord <- function(x,y) y 209s + xim <- as.im(xcoord, W=Window(X)) 209s + r2fi <- rho2hat(X, ycoord, xim) 209s + r2if <- rho2hat(X, xim, ycoord) 209s + } 209s + }) 209s > 209s BEGIN TEST testsR2.R 209s 209s R version 4.4.3 (2025-02-28) -- "Trophy Case" 209s Copyright (C) 2025 The R Foundation for Statistical Computing 209s Platform: arm-unknown-linux-gnueabihf (32-bit) 209s 209s R is free software and comes with ABSOLUTELY NO WARRANTY. 209s You are welcome to redistribute it under certain conditions. 209s Type 'license()' or 'licence()' for distribution details. 209s 209s R is a collaborative project with many contributors. 209s Type 'contributors()' for more information and 209s 'citation()' on how to cite R or R packages in publications. 209s 209s Type 'demo()' for some demos, 'help()' for on-line help, or 209s 'help.start()' for an HTML browser interface to help. 209s Type 'q()' to quit R. 209s 209s > #' 209s > #' Header for all (concatenated) test files 209s > #' 209s > #' Require spatstat.explore 209s > #' Obtain environment variable controlling tests. 209s > #' 209s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 209s > 209s > require(spatstat.explore) 209s Loading required package: spatstat.explore 209s Loading required package: spatstat.data 210s Loading required package: spatstat.univar 210s spatstat.univar 3.1-2 210s Loading required package: spatstat.geom 210s spatstat.geom 3.3-6 210s Loading required package: spatstat.random 210s spatstat.random 3.3-3 210s Loading required package: nlme 210s spatstat.explore 3.3-4 210s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 210s > ALWAYS <- TRUE 210s > cat(paste("--------- Executing", 210s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 210s + "test code -----------\n")) 210s --------- Executing **RESTRICTED** subset of test code ----------- 210s > 210s BEGIN TEST testsS.R 210s 210s R version 4.4.3 (2025-02-28) -- "Trophy Case" 210s Copyright (C) 2025 The R Foundation for Statistical Computing 210s Platform: arm-unknown-linux-gnueabihf (32-bit) 210s 210s R is free software and comes with ABSOLUTELY NO WARRANTY. 210s You are welcome to redistribute it under certain conditions. 210s Type 'license()' or 'licence()' for distribution details. 210s 210s R is a collaborative project with many contributors. 210s Type 'contributors()' for more information and 210s 'citation()' on how to cite R or R packages in publications. 210s 210s Type 'demo()' for some demos, 'help()' for on-line help, or 210s 'help.start()' for an HTML browser interface to help. 210s Type 'q()' to quit R. 210s 210s > #' 210s > #' Header for all (concatenated) test files 210s > #' 210s > #' Require spatstat.explore 210s > #' Obtain environment variable controlling tests. 210s > #' 210s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 210s > 210s > require(spatstat.explore) 210s Loading required package: spatstat.explore 210s Loading required package: spatstat.data 212s Loading required package: spatstat.univar 212s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 212s > ALWAYS <- TRUE 212s > cat(paste("--------- Executing", 212s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 212s + "test code -----------\n")) 212s --------- Executing **RESTRICTED** subset of test code ----------- 212s > #' tests/sdr.R 212s > #' 212s > #' $Revision: 1.2 $ $Date: 2020/05/01 09:59:59 $ 212s > 212s > if(FULLTEST) { 212s + local({ 212s + AN <- sdr(bei, bei.extra, method="NNIR") 212s + AV <- sdr(bei, bei.extra, method="SAVE") 212s + AI <- sdr(bei, bei.extra, method="SIR") 212s + AT <- sdr(bei, bei.extra, method="TSE") 212s + subspaceDistance(AN$B, AV$B) 212s + dimhat(AN$M) 212s + }) 212s + } 212s > ## 212s > ## tests/segments.R 212s > ## Tests of psp class and related code 212s > ## [SEE ALSO: tests/xysegment.R] 212s > ## 212s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 212s > 212s > 212s > local({ 212s + if(ALWAYS) { # C code 212s + #' tests of density.psp 212s + Y <- edges(letterR) 212s + Window(Y) <- grow.rectangle(Frame(Y), 0.4) 212s + YC <- density(Y, 0.2, method="C", edge=FALSE, dimyx=64) 212s + YI <- density(Y, 0.2, method="interpreted", edge=FALSE, dimyx=64) 212s + YF <- density(Y, 0.2, method="FFT", edge=FALSE, dimyx=64) 212s + xCI <- max(abs(YC/YI - 1)) 212s + xFI <- max(abs(YF/YI - 1)) 212s + cat(paste("xCI =", xCI, "\txFI =", signif(xFI, 5)), fill=TRUE) 212s + if(xCI > 0.01) stop(paste("density.psp C algorithm relative error =", xCI)) 212s + if(xFI > 0.1) stop(paste("density.psp FFT algorithm relative error =", xFI)) 212s + 212s + B <- square(0.3) 212s + density(Y, 0.2, at=B) 212s + density(Y, 0.2, at=B, edge=TRUE, method="C") 212s + Z <- runifrect(3, B) 212s + density(Y, 0.2, at=Z) 212s + density(Y, 0.2, at=Z, edge=TRUE, method="C") 212s + } 212s + 212s + if(FULLTEST) { 212s + #' segment clipping in window (bug found by Rolf) 212s + set.seed(42) 212s + X <- runifpoint(50, letterR) 212s + SP <- dirichletEdges(X) #' clip to polygonal window 212s + Window(X) <- as.mask(Window(X)) 212s + SM <- dirichletEdges(X) #' clip to mask window 212s + } 212s + 212s + if(FULLTEST) { 212s + #' test rshift.psp and append.psp with marks (Ute Hahn) 212s + m <- data.frame(A=1:10, B=letters[1:10]) 212s + g <- gl(3, 3, length=10) 212s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 212s + Y <- rshift(X, radius = 0.1) 212s + Y <- rshift(X, radius = 0.1, group=g) 212s + #' mark management 212s + b <- data.frame(A=1:10) 212s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=b) 212s + stopifnot(is.data.frame(marks(X))) 212s + Y <- rshift(X, radius = 0.1) 212s + Y <- rshift(X, radius = 0.1, group=g) 212s + } 212s + 212s + }) 212s spatstat.univar 3.1-2 212s Loading required package: spatstat.geom 212s spatstat.geom 3.3-6 212s Loading required package: spatstat.random 212s spatstat.random 3.3-3 212s Loading required package: nlme 212s spatstat.explore 3.3-4 212s xCI = 0 xFI = 0.073128 214s > 214s > 214s > 214s > # 214s > ## tests/sigtraceprogress.R 214s > # 214s > ## Tests of *.sigtrace and *.progress 214s > # 214s > ## $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 214s > 214s > if(FULLTEST) { 214s + local({ 214s + plot(dclf.sigtrace(redwood, nsim=19, alternative="greater", rmin=0.02, 214s + verbose=FALSE)) 214s + plot(dclf.progress(redwood, nsim=19, alternative="greater", rmin=0.02, 214s + verbose=FALSE)) 214s + plot(dg.sigtrace(redwood, nsim=5, alternative="greater", rmin=0.02, 214s + verbose=FALSE)) 214s + plot(dg.progress(redwood, nsim=5, alternative="greater", rmin=0.02, 214s + verbose=FALSE)) 214s + ## test 'leave-two-out' algorithm 214s + a <- dclf.sigtrace(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 214s Warning message: 214s the images ‘dens’ and ‘edg’ were not compatible 214s + verbose=FALSE) 214s + aa <- dclf.progress(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 214s + verbose=FALSE) 214s + b <- dg.sigtrace(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2) 214s + bb <- dg.progress(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2, 214s + verbose=FALSE) 214s + ## other code blocks 214s + e <- mad.progress(redwood, nsim=5) 214s + e <- mad.progress(redwood, nsim=19, alpha=0.05) 214s + f <- dclf.progress(redwood, nsim=5, scale=function(x) x^2) 214s + f <- dclf.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 214s + g <- dg.progress(redwood, nsim=5, scale=function(x) x^2) 214s + g <- dg.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 214s + }) 214s + } 214s > #' 214s > #' tests/ssf.R 214s > #' 214s > #' Tests of 'ssf' class 214s > #' 214s > #' $Revision: 1.5 $ $Date: 2020/12/04 08:02:25 $ 214s > #' 214s > 214s > if(FULLTEST) { 214s + local({ 214s + Y <- cells[1:5] 214s + X <- rsyst(Window(Y), 5) 214s + Z <- runifpoint(3, Window(Y)) 214s + f1 <- ssf(X, nncross(X,Y,what="dist")) 214s + f2 <- ssf(X, nncross(X,Y,what="dist", k=1:2)) 214s + image(f1) 214s + g1 <- as.function(f1) 214s + g1(Z) 214s + g2 <- as.function(f2) 214s + g2(Z) 214s + plot(f1, style="contour") 214s + plot(f1, style="imagecontour") 214s + contour(f1) 214s + apply.ssf(f2, 1, sum) 214s + range(f1) 214s + min(f1) 214s + max(f1) 214s + integral(f1, weights=tile.areas(dirichlet(X))) 214s + }) 214s + } 214s > #' 214s > #' tests/sumfun.R 214s > #' 214s > #' Tests of code for summary functions 214s > #' 214s > #' $Revision: 1.9 $ $Date: 2022/05/22 08:45:23 $ 214s > 214s > if(ALWAYS) { # involves C code 214s + local({ 214s + W <- owin(c(0,1), c(-1/2, 0)) 214s + Gr <- Gest(redwood, correction="all",domain=W) 214s + Fr <- Fest(redwood, correction="all",domain=W) 214s + Jr <- Jest(redwood, correction="all",domain=W) 214s + 214s + F0 <- Fest(redwood[FALSE], correction="all") 214s + Fh <- Fest(humberside, domain=erosion(Window(humberside), 100)) 214s + 214s + FIr <- Finhom(redwood, savelambda=TRUE, ratio=TRUE) 214s + JIr <- Jinhom(redwood, savelambda=TRUE, ratio=TRUE) 214s + 214s + Ga <- Gcross(amacrine, correction="all") 214s + Ia <- Iest(amacrine, correction="all") 214s + lam <- intensity(amacrine) 214s + lmin <- 0.9 * min(lam) 214s + nJ <- sum(marks(amacrine) == "off") 214s + FM <- FmultiInhom(amacrine, marks(amacrine) == "off", 214s + lambdaJ=rep(lam["off"], nJ), 214s + lambdamin = lmin) 214s + GM <- GmultiInhom(amacrine, marks(amacrine) == "on", 214s + marks(amacrine) == "off", 214s + lambda=lam[marks(amacrine)], 214s + lambdamin=lmin, 214s + ReferenceMeasureMarkSetI=42) 214s + 214s + a <- compileCDF(D=nndist(redwood), 214s + B=bdist.points(redwood), 214s + r=seq(0, 1, length=256)) 214s + 214s + #' Tstat (triplet) function, all code blocks 214s + a <- Tstat(redwood, ratio=TRUE, 214s + correction=c("none", "border", "bord.modif", "translate")) 214s + 214s + ## distance argument spacing and breakpoints 214s + e <- check.finespacing(c(0,1,2), eps=0.1, action="silent") 214s + b <- as.breakpts(pi, 20) 214s + b <- as.breakpts(42, max=pi, npos=20) 214s + b <- even.breaks.owin(letterR) 214s + }) 214s + } 216s Searching 59340 potential triangles; estimated time 0.000426 sec 216s > 216s BEGIN TEST testsT.R 216s 216s R version 4.4.3 (2025-02-28) -- "Trophy Case" 216s Copyright (C) 2025 The R Foundation for Statistical Computing 216s Platform: arm-unknown-linux-gnueabihf (32-bit) 216s 216s R is free software and comes with ABSOLUTELY NO WARRANTY. 216s You are welcome to redistribute it under certain conditions. 216s Type 'license()' or 'licence()' for distribution details. 216s 216s R is a collaborative project with many contributors. 216s Type 'contributors()' for more information and 216s 'citation()' on how to cite R or R packages in publications. 216s 216s Type 'demo()' for some demos, 'help()' for on-line help, or 216s 'help.start()' for an HTML browser interface to help. 216s Type 'q()' to quit R. 216s 216s > #' 216s > #' Header for all (concatenated) test files 216s > #' 216s > #' Require spatstat.explore 216s > #' Obtain environment variable controlling tests. 216s > #' 216s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 216s > 216s > require(spatstat.explore) 216s Loading required package: spatstat.explore 216s Loading required package: spatstat.data 217s Loading required package: spatstat.univar 217s spatstat.univar 3.1-2 217s Loading required package: spatstat.geom 217s spatstat.geom 3.3-6 217s Loading required package: spatstat.random 217s spatstat.random 3.3-3 217s Loading required package: nlme 217s spatstat.explore 3.3-4 217s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 217s > ALWAYS <- TRUE 217s > cat(paste("--------- Executing", 217s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 217s + "test code -----------\n")) 217s --------- Executing **RESTRICTED** subset of test code ----------- 217s > #' 217s > #' tests/threedee.R 217s > #' 217s > #' Tests of 3D code 217s > #' 217s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 217s > #' 217s > 217s > local({ 217s + X <- runifpoint3(30) 217s + Y <- runifpoint3(20) 217s + if(FULLTEST) { 217s + A <- runifpoint3(10, nsim=2) 217s + Z <- ppsubset(X, 2:4) 217s + } 217s + ## 217s + if(ALWAYS) { # includes C code 217s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 217s + d <- crossdist(X, Y, squared=TRUE) 217s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 217s + #' 217s + h <- has.close(X, 0.2) 217s + h <- has.close(X, 0.2, periodic=TRUE) 217s + h <- has.close(X, 0.2, Y=Y) 218s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 218s + #' code blocks not otherwise reached 218s + rmax <- 0.6 * max(nndist(X)) 218s + g <- G3est(X, rmax=rmax, correction="rs") 218s + g <- G3est(X, rmax=rmax, correction="km") 218s + g <- G3est(X, rmax=rmax, correction="Hanisch") 218s + g <- G3est(X, rmax=rmax, sphere="ideal") 218s + g <- G3est(X, rmax=rmax, sphere="digital") 218s + v <- sphere.volume() 218s + v <- digital.volume() 218s + #' older code 218s + co <- coords(X) 218s + xx <- co$x 218s + yy <- co$y 218s + zz <- co$z 218s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 218s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 218s + ff1 <- f3engine(xx, yy, zz, correction="no") 218s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 218s + } 218s + ## 218s + if(ALWAYS) { 218s + #'class support 218s + X <- runifpoint3(10) 218s + print(X) 218s + print(X %mark% runif(10)) 218s + print(X %mark% factor(letters[c(1:5,5:1)])) 218s + print(X %mark% data.frame(a=1:10, b=runif(10))) 218s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 218s + print(X %mark% da) 218s + print(X %mark% data.frame(a=1:10, b=da)) 218s + } 218s + }) 218s Three-dimensional point pattern: 10 points 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Marked three-dimensional point pattern: 10 points 218s marks are numeric, of storage type ‘double’ 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Marked three-dimensional point pattern: 10 points 218s Multitype, with levels = a, b, c, d, e 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Marked three-dimensional point pattern: 10 points 218s Mark variables: a, b 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Marked three-dimensional point pattern: 10 points 218s marks are dates, of class ‘Date’ 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Marked three-dimensional point pattern: 10 points 218s Mark variables: a, b 218s Box: [0, 1] x [0, 1] x [0, 1] units 218s Warning messages: 218s 1: In G3est: unrecognised argument ‘sphere’ was ignored 218s 2: In G3est: unrecognised argument ‘sphere’ was ignored 218s > 218s BEGIN TEST testsUtoZ.R 218s 218s R version 4.4.3 (2025-02-28) -- "Trophy Case" 218s Copyright (C) 2025 The R Foundation for Statistical Computing 218s Platform: arm-unknown-linux-gnueabihf (32-bit) 218s 218s R is free software and comes with ABSOLUTELY NO WARRANTY. 218s You are welcome to redistribute it under certain conditions. 218s Type 'license()' or 'licence()' for distribution details. 218s 218s R is a collaborative project with many contributors. 218s Type 'contributors()' for more information and 218s 'citation()' on how to cite R or R packages in publications. 218s 218s Type 'demo()' for some demos, 'help()' for on-line help, or 218s 'help.start()' for an HTML browser interface to help. 218s Type 'q()' to quit R. 218s 218s > #' 218s > #' Header for all (concatenated) test files 218s > #' 218s > #' Require spatstat.explore 218s > #' Obtain environment variable controlling tests. 218s > #' 218s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 218s > 218s > require(spatstat.explore) 218s Loading required package: spatstat.explore 218s Loading required package: spatstat.data 219s Loading required package: spatstat.univar 219s spatstat.univar 3.1-2 219s Loading required package: spatstat.geom 219s spatstat.geom 3.3-6 219s Loading required package: spatstat.random 219s spatstat.random 3.3-3 219s Loading required package: nlme 219s spatstat.explore 3.3-4 219s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 219s > ALWAYS <- TRUE 219s > cat(paste("--------- Executing", 219s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 219s + "test code -----------\n")) 219s --------- Executing **RESTRICTED** subset of test code ----------- 219s > 219s autopkgtest [02:35:02]: test run-unit-test: -----------------------] 223s run-unit-test PASS 223s autopkgtest [02:35:06]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 227s autopkgtest [02:35:10]: test pkg-r-autopkgtest: preparing testbed 249s autopkgtest [02:35:32]: testbed dpkg architecture: armhf 251s autopkgtest [02:35:34]: testbed apt version: 3.0.0 254s autopkgtest [02:35:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 256s autopkgtest [02:35:39]: testbed release detected to be: questing 263s autopkgtest [02:35:46]: updating testbed package index (apt update) 265s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 266s Get:2 http://ftpmaster.internal/ubuntu questing InRelease [110 kB] 266s Get:3 http://ftpmaster.internal/ubuntu questing-updates InRelease [110 kB] 266s Get:4 http://ftpmaster.internal/ubuntu questing-security InRelease [110 kB] 266s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [168 kB] 266s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1920 kB] 266s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [43.3 kB] 266s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main armhf Packages [204 kB] 266s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf Packages [1378 kB] 266s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse armhf Packages [12.5 kB] 266s Get:11 http://ftpmaster.internal/ubuntu questing/main Sources [1395 kB] 266s Get:12 http://ftpmaster.internal/ubuntu questing/multiverse Sources [299 kB] 266s Get:13 http://ftpmaster.internal/ubuntu questing/universe Sources [21.1 MB] 267s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf Packages [1358 kB] 267s Get:15 http://ftpmaster.internal/ubuntu questing/universe armhf Packages [14.9 MB] 267s Get:16 http://ftpmaster.internal/ubuntu questing/multiverse armhf Packages [173 kB] 271s Fetched 43.3 MB in 5s (8025 kB/s) 272s Reading package lists... 278s autopkgtest [02:36:01]: upgrading testbed (apt dist-upgrade and autopurge) 279s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 281s Entering ResolveByKeep 282s 282s Calculating upgrade... 283s The following packages will be upgraded: 283s base-files distro-info-data dpkg dpkg-dev ed fwupd htop libdpkg-perl 283s libftdi1-2 libfwupd3 libnpth0t64 libnvme1t64 libsensors-config libsensors5 283s liburcu8t64 motd-news-config nano ubuntu-pro-client ubuntu-pro-client-l10n 283s usb.ids 283s 20 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 283s Need to get 5431 kB of archives. 283s After this operation, 3722 kB disk space will be freed. 283s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf motd-news-config all 13.7ubuntu1 [5260 B] 283s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf base-files armhf 13.7ubuntu1 [75.4 kB] 283s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf dpkg armhf 1.22.18ubuntu3 [1254 kB] 283s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf libnpth0t64 armhf 1.8-3 [7716 B] 283s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf distro-info-data all 0.64 [6664 B] 283s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client-l10n armhf 35.1ubuntu0 [19.7 kB] 283s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf ubuntu-pro-client armhf 35.1ubuntu0 [258 kB] 283s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf ed armhf 1.21.1-1 [53.0 kB] 283s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf libsensors-config all 1:3.6.2-2 [6756 B] 283s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf libsensors5 armhf 1:3.6.2-2 [26.8 kB] 283s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf liburcu8t64 armhf 0.15.2-2 [57.3 kB] 283s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf nano armhf 8.4-1 [278 kB] 283s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf usb.ids all 2025.04.01-1 [223 kB] 283s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf dpkg-dev all 1.22.18ubuntu3 [1089 kB] 283s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libdpkg-perl all 1.22.18ubuntu3 [281 kB] 283s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf fwupd armhf 2.0.8-3 [1414 kB] 284s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf libfwupd3 armhf 2.0.8-3 [126 kB] 284s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf htop armhf 3.4.1-4 [147 kB] 284s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf libftdi1-2 armhf 1.5-10 [27.8 kB] 284s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf libnvme1t64 armhf 1.13-2 [74.3 kB] 284s Fetched 5431 kB in 1s (6486 kB/s) 284s (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.) 284s Preparing to unpack .../motd-news-config_13.7ubuntu1_all.deb ... 284s Unpacking motd-news-config (13.7ubuntu1) over (13.6ubuntu2) ... 284s Preparing to unpack .../base-files_13.7ubuntu1_armhf.deb ... 284s Unpacking base-files (13.7ubuntu1) over (13.6ubuntu2) ... 284s Setting up base-files (13.7ubuntu1) ... 284s Installing new version of config file /etc/issue ... 284s Installing new version of config file /etc/issue.net ... 284s Installing new version of config file /etc/lsb-release ... 285s motd-news.service is a disabled or a static unit not running, not starting it. 285s (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.) 285s Preparing to unpack .../dpkg_1.22.18ubuntu3_armhf.deb ... 285s Unpacking dpkg (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 285s Setting up dpkg (1.22.18ubuntu3) ... 286s (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.) 286s Preparing to unpack .../libnpth0t64_1.8-3_armhf.deb ... 286s Unpacking libnpth0t64:armhf (1.8-3) over (1.8-2) ... 286s Setting up libnpth0t64:armhf (1.8-3) ... 286s (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.) 286s Preparing to unpack .../00-distro-info-data_0.64_all.deb ... 286s Unpacking distro-info-data (0.64) over (0.63) ... 286s Preparing to unpack .../01-ubuntu-pro-client-l10n_35.1ubuntu0_armhf.deb ... 286s Unpacking ubuntu-pro-client-l10n (35.1ubuntu0) over (35) ... 286s Preparing to unpack .../02-ubuntu-pro-client_35.1ubuntu0_armhf.deb ... 286s Unpacking ubuntu-pro-client (35.1ubuntu0) over (35) ... 286s Preparing to unpack .../03-ed_1.21.1-1_armhf.deb ... 286s Unpacking ed (1.21.1-1) over (1.21-1) ... 286s Preparing to unpack .../04-libsensors-config_1%3a3.6.2-2_all.deb ... 286s Unpacking libsensors-config (1:3.6.2-2) over (1:3.6.0-10) ... 286s Preparing to unpack .../05-libsensors5_1%3a3.6.2-2_armhf.deb ... 286s Unpacking libsensors5:armhf (1:3.6.2-2) over (1:3.6.0-10) ... 286s Preparing to unpack .../06-liburcu8t64_0.15.2-2_armhf.deb ... 286s Unpacking liburcu8t64:armhf (0.15.2-2) over (0.15.1-1) ... 286s Preparing to unpack .../07-nano_8.4-1_armhf.deb ... 286s Unpacking nano (8.4-1) over (8.3-1) ... 286s Preparing to unpack .../08-usb.ids_2025.04.01-1_all.deb ... 286s Unpacking usb.ids (2025.04.01-1) over (2025.01.14-1) ... 286s Preparing to unpack .../09-dpkg-dev_1.22.18ubuntu3_all.deb ... 286s Unpacking dpkg-dev (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 287s Preparing to unpack .../10-libdpkg-perl_1.22.18ubuntu3_all.deb ... 287s Unpacking libdpkg-perl (1.22.18ubuntu3) over (1.22.18ubuntu2) ... 287s Preparing to unpack .../11-fwupd_2.0.8-3_armhf.deb ... 287s Unpacking fwupd (2.0.8-3) over (2.0.7-1) ... 287s dpkg: warning: unable to delete old directory '/etc/grub.d': Directory not empty 287s Preparing to unpack .../12-libfwupd3_2.0.8-3_armhf.deb ... 287s Unpacking libfwupd3:armhf (2.0.8-3) over (2.0.7-1) ... 287s Preparing to unpack .../13-htop_3.4.1-4_armhf.deb ... 287s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 287s Preparing to unpack .../14-libftdi1-2_1.5-10_armhf.deb ... 287s Unpacking libftdi1-2:armhf (1.5-10) over (1.5-8build1) ... 287s Preparing to unpack .../15-libnvme1t64_1.13-2_armhf.deb ... 287s Unpacking libnvme1t64 (1.13-2) over (1.11.1-2) ... 287s Setting up motd-news-config (13.7ubuntu1) ... 287s Setting up liburcu8t64:armhf (0.15.2-2) ... 287s Setting up distro-info-data (0.64) ... 287s Setting up htop (3.4.1-4) ... 287s Setting up libsensors-config (1:3.6.2-2) ... 287s Installing new version of config file /etc/sensors3.conf ... 287s Setting up libfwupd3:armhf (2.0.8-3) ... 287s Setting up libftdi1-2:armhf (1.5-10) ... 287s Setting up libnvme1t64 (1.13-2) ... 287s Setting up ed (1.21.1-1) ... 287s Setting up usb.ids (2025.04.01-1) ... 287s Setting up libsensors5:armhf (1:3.6.2-2) ... 287s Setting up libdpkg-perl (1.22.18ubuntu3) ... 287s Setting up nano (8.4-1) ... 287s Installing new version of config file /etc/nanorc ... 287s Setting up ubuntu-pro-client (35.1ubuntu0) ... 287s apparmor_parser: Unable to replace "ubuntu_pro_apt_news". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 287s 288s apparmor_parser: Unable to replace "apt_methods". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 288s 288s apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 288s 289s Setting up fwupd (2.0.8-3) ... 290s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 290s fwupd.service is a disabled or a static unit not running, not starting it. 290s Setting up ubuntu-pro-client-l10n (35.1ubuntu0) ... 290s Setting up dpkg-dev (1.22.18ubuntu3) ... 290s Processing triggers for dbus (1.16.2-2ubuntu1) ... 290s Processing triggers for install-info (7.1.1-1) ... 290s Processing triggers for libc-bin (2.41-6ubuntu1) ... 290s Processing triggers for man-db (2.13.0-1) ... 292s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu7) ... 292s Processing triggers for initramfs-tools (0.147ubuntu1) ... 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 295s Solving dependencies... 296s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 298s autopkgtest [02:36:21]: rebooting testbed after setup commands that affected boot 361s Reading package lists... 361s Building dependency tree... 361s Reading state information... 361s Starting pkgProblemResolver with broken count: 0 362s Starting 2 pkgProblemResolver with broken count: 0 362s Done 363s The following NEW packages will be installed: 363s build-essential cpp cpp-14 cpp-14-arm-linux-gnueabihf 363s cpp-arm-linux-gnueabihf dctrl-tools fontconfig fontconfig-config 363s fonts-dejavu-core fonts-dejavu-mono g++ g++-14 g++-14-arm-linux-gnueabihf 363s g++-arm-linux-gnueabihf gcc gcc-14 gcc-14-arm-linux-gnueabihf 363s gcc-arm-linux-gnueabihf gfortran gfortran-14 gfortran-14-arm-linux-gnueabihf 363s gfortran-arm-linux-gnueabihf icu-devtools libasan8 libblas-dev libblas3 363s libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0 libcrypt-dev libdatrie1 363s libdeflate-dev libdeflate0 libfontconfig1 libfreetype6 libgcc-14-dev 363s libgfortran-14-dev libgfortran5 libgomp1 libgraphite2-3 libgsl28 363s libgslcblas0 libharfbuzz0b libice6 libicu-dev libisl23 libjbig0 libjpeg-dev 363s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev 363s liblapack3 liblerc4 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0 363s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 363s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 363s libpng-dev libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 363s libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libubsan1 libwebp7 363s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 363s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 363s r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl r-cran-lattice 363s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-polyclip r-cran-rpart r-cran-sm 363s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 363s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 363s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.univar 363s r-cran-spatstat.utils r-cran-survival r-cran-tensor rpcsvc-proto unzip 363s x11-common xdg-utils zip zlib1g-dev 363s 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. 363s Need to get 161 MB of archives. 363s After this operation, 370 MB of additional disk space will be used. 363s Get:1 http://ftpmaster.internal/ubuntu questing/main armhf libc-dev-bin armhf 2.41-6ubuntu1 [21.7 kB] 363s Get:2 http://ftpmaster.internal/ubuntu questing/main armhf linux-libc-dev armhf 6.14.0-15.15 [1687 kB] 363s Get:3 http://ftpmaster.internal/ubuntu questing/main armhf libcrypt-dev armhf 1:4.4.38-1 [120 kB] 363s Get:4 http://ftpmaster.internal/ubuntu questing/main armhf rpcsvc-proto armhf 1.4.2-0ubuntu7 [62.2 kB] 363s Get:5 http://ftpmaster.internal/ubuntu questing/main armhf libc6-dev armhf 2.41-6ubuntu1 [1396 kB] 363s Get:6 http://ftpmaster.internal/ubuntu questing/main armhf libisl23 armhf 0.27-1 [546 kB] 363s Get:7 http://ftpmaster.internal/ubuntu questing/main armhf libmpc3 armhf 1.3.1-1build2 [47.1 kB] 363s Get:8 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9221 kB] 364s Get:9 http://ftpmaster.internal/ubuntu questing/main armhf cpp-14 armhf 14.2.0-19ubuntu2 [1032 B] 364s Get:10 http://ftpmaster.internal/ubuntu questing/main armhf cpp-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [5578 B] 364s Get:11 http://ftpmaster.internal/ubuntu questing/main armhf cpp armhf 4:14.2.0-1ubuntu1 [22.4 kB] 364s Get:12 http://ftpmaster.internal/ubuntu questing/main armhf libcc1-0 armhf 15-20250404-0ubuntu1 [43.3 kB] 364s Get:13 http://ftpmaster.internal/ubuntu questing/main armhf libgomp1 armhf 15-20250404-0ubuntu1 [128 kB] 364s Get:14 http://ftpmaster.internal/ubuntu questing/main armhf libasan8 armhf 15-20250404-0ubuntu1 [2951 kB] 364s Get:15 http://ftpmaster.internal/ubuntu questing/main armhf libubsan1 armhf 15-20250404-0ubuntu1 [1188 kB] 364s Get:16 http://ftpmaster.internal/ubuntu questing/main armhf libgcc-14-dev armhf 14.2.0-19ubuntu2 [897 kB] 364s Get:17 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [18.0 MB] 364s Get:18 http://ftpmaster.internal/ubuntu questing/main armhf gcc-14 armhf 14.2.0-19ubuntu2 [510 kB] 364s Get:19 http://ftpmaster.internal/ubuntu questing/main armhf gcc-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1218 B] 364s Get:20 http://ftpmaster.internal/ubuntu questing/main armhf gcc armhf 4:14.2.0-1ubuntu1 [5004 B] 364s Get:21 http://ftpmaster.internal/ubuntu questing/main armhf libstdc++-14-dev armhf 14.2.0-19ubuntu2 [2576 kB] 364s Get:22 http://ftpmaster.internal/ubuntu questing/main armhf g++-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [10.5 MB] 365s Get:23 http://ftpmaster.internal/ubuntu questing/main armhf g++-14 armhf 14.2.0-19ubuntu2 [23.0 kB] 365s Get:24 http://ftpmaster.internal/ubuntu questing/main armhf g++-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [966 B] 365s Get:25 http://ftpmaster.internal/ubuntu questing/main armhf g++ armhf 4:14.2.0-1ubuntu1 [1084 B] 365s Get:26 http://ftpmaster.internal/ubuntu questing/main armhf build-essential armhf 12.12ubuntu1 [5088 B] 365s Get:27 http://ftpmaster.internal/ubuntu questing/main armhf dctrl-tools armhf 2.24-3build3 [94.7 kB] 365s Get:28 http://ftpmaster.internal/ubuntu questing/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [330 kB] 365s Get:29 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-mono all 2.37-8 [502 kB] 365s Get:30 http://ftpmaster.internal/ubuntu questing/main armhf fonts-dejavu-core all 2.37-8 [835 kB] 365s Get:31 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig-config armhf 2.15.0-2.2ubuntu1 [37.9 kB] 365s Get:32 http://ftpmaster.internal/ubuntu questing/main armhf libfontconfig1 armhf 2.15.0-2.2ubuntu1 [114 kB] 365s Get:33 http://ftpmaster.internal/ubuntu questing/main armhf fontconfig armhf 2.15.0-2.2ubuntu1 [190 kB] 365s Get:34 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran5 armhf 15-20250404-0ubuntu1 [331 kB] 365s Get:35 http://ftpmaster.internal/ubuntu questing/main armhf libgfortran-14-dev armhf 14.2.0-19ubuntu2 [370 kB] 365s Get:36 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14-arm-linux-gnueabihf armhf 14.2.0-19ubuntu2 [9763 kB] 365s Get:37 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-14 armhf 14.2.0-19ubuntu2 [14.2 kB] 365s Get:38 http://ftpmaster.internal/ubuntu questing/main armhf gfortran-arm-linux-gnueabihf armhf 4:14.2.0-1ubuntu1 [1026 B] 365s Get:39 http://ftpmaster.internal/ubuntu questing/main armhf gfortran armhf 4:14.2.0-1ubuntu1 [1166 B] 365s Get:40 http://ftpmaster.internal/ubuntu questing/main armhf icu-devtools armhf 76.1-1ubuntu2 [206 kB] 365s Get:41 http://ftpmaster.internal/ubuntu questing/main armhf libblas3 armhf 3.12.1-2 [132 kB] 365s Get:42 http://ftpmaster.internal/ubuntu questing/main armhf libblas-dev armhf 3.12.1-2 [141 kB] 365s Get:43 http://ftpmaster.internal/ubuntu questing/main armhf libbz2-dev armhf 1.0.8-6 [30.9 kB] 365s Get:44 http://ftpmaster.internal/ubuntu questing/main armhf libpixman-1-0 armhf 0.44.0-3 [183 kB] 365s Get:45 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-render0 armhf 1.17.0-2 [15.3 kB] 365s Get:46 http://ftpmaster.internal/ubuntu questing/main armhf libxcb-shm0 armhf 1.17.0-2 [5774 B] 365s Get:47 http://ftpmaster.internal/ubuntu questing/main armhf libxrender1 armhf 1:0.9.10-1.1build1 [16.0 kB] 365s Get:48 http://ftpmaster.internal/ubuntu questing/main armhf libcairo2 armhf 1.18.4-1 [483 kB] 365s Get:49 http://ftpmaster.internal/ubuntu questing/main armhf libdatrie1 armhf 0.2.13-3build1 [15.7 kB] 365s Get:50 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 365s Get:51 http://ftpmaster.internal/ubuntu questing/main armhf libdeflate-dev armhf 1.23-1 [45.0 kB] 365s Get:52 http://ftpmaster.internal/ubuntu questing/main armhf libgraphite2-3 armhf 1.3.14-2ubuntu1 [64.8 kB] 365s Get:53 http://ftpmaster.internal/ubuntu questing/universe armhf libgslcblas0 armhf 2.8+dfsg-5ubuntu1 [84.4 kB] 365s Get:54 http://ftpmaster.internal/ubuntu questing/universe armhf libgsl28 armhf 2.8+dfsg-5ubuntu1 [876 kB] 365s Get:55 http://ftpmaster.internal/ubuntu questing/main armhf libharfbuzz0b armhf 10.2.0-1 [464 kB] 365s Get:56 http://ftpmaster.internal/ubuntu questing/main armhf x11-common all 1:7.7+23ubuntu4 [21.8 kB] 365s Get:57 http://ftpmaster.internal/ubuntu questing/main armhf libice6 armhf 2:1.1.1-1 [36.5 kB] 365s Get:58 http://ftpmaster.internal/ubuntu questing/main armhf libicu-dev armhf 76.1-1ubuntu2 [12.0 MB] 366s Get:59 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8 armhf 2.1.5-3ubuntu2 [127 kB] 366s Get:60 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-turbo8-dev armhf 2.1.5-3ubuntu2 [265 kB] 366s Get:61 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 366s Get:62 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg8-dev armhf 8c-2ubuntu11 [1484 B] 366s Get:63 http://ftpmaster.internal/ubuntu questing/main armhf libjpeg-dev armhf 8c-2ubuntu11 [1482 B] 366s Get:64 http://ftpmaster.internal/ubuntu questing/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 366s Get:65 http://ftpmaster.internal/ubuntu questing/main armhf liblapack-dev armhf 3.12.1-2 [2207 kB] 366s Get:66 http://ftpmaster.internal/ubuntu questing/main armhf liblerc4 armhf 4.0.0+ds-5ubuntu1 [160 kB] 366s Get:67 http://ftpmaster.internal/ubuntu questing/main armhf libncurses-dev armhf 6.5+20250216-2 [345 kB] 366s Get:68 http://ftpmaster.internal/ubuntu questing/main armhf libthai-data all 0.1.29-2build1 [158 kB] 366s Get:69 http://ftpmaster.internal/ubuntu questing/main armhf libthai0 armhf 0.1.29-2build1 [15.2 kB] 366s Get:70 http://ftpmaster.internal/ubuntu questing/main armhf libpango-1.0-0 armhf 1.56.3-1 [216 kB] 366s Get:71 http://ftpmaster.internal/ubuntu questing/main armhf libpangoft2-1.0-0 armhf 1.56.3-1 [44.1 kB] 366s Get:72 http://ftpmaster.internal/ubuntu questing/main armhf libpangocairo-1.0-0 armhf 1.56.3-1 [25.0 kB] 366s Get:73 http://ftpmaster.internal/ubuntu questing/main armhf libpaper2 armhf 2.2.5-0.3 [16.3 kB] 366s Get:74 http://ftpmaster.internal/ubuntu questing/main armhf libpaper-utils armhf 2.2.5-0.3 [14.2 kB] 366s Get:75 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-16-0 armhf 10.45-1 [207 kB] 366s Get:76 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-32-0 armhf 10.45-1 [197 kB] 366s Get:77 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-posix3 armhf 10.45-1 [6300 B] 366s Get:78 http://ftpmaster.internal/ubuntu questing/main armhf libpcre2-dev armhf 10.45-1 [752 kB] 366s Get:79 http://ftpmaster.internal/ubuntu questing/main armhf libpkgconf3 armhf 1.8.1-4 [26.6 kB] 366s Get:80 http://ftpmaster.internal/ubuntu questing/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1ubuntu1 [880 kB] 366s Get:81 http://ftpmaster.internal/ubuntu questing/main armhf libpng-dev armhf 1.6.47-1.1 [251 kB] 366s Get:82 http://ftpmaster.internal/ubuntu questing/main armhf libreadline-dev armhf 8.2-6 [153 kB] 366s Get:83 http://ftpmaster.internal/ubuntu questing/main armhf libsharpyuv0 armhf 1.5.0-0.1 [16.4 kB] 366s Get:84 http://ftpmaster.internal/ubuntu questing/main armhf libsm6 armhf 2:1.2.4-1 [15.1 kB] 366s Get:85 http://ftpmaster.internal/ubuntu questing/main armhf libtcl8.6 armhf 8.6.16+dfsg-1 [909 kB] 366s Get:86 http://ftpmaster.internal/ubuntu questing/main armhf libjbig0 armhf 2.1-6.1ubuntu2 [24.9 kB] 366s Get:87 http://ftpmaster.internal/ubuntu questing/main armhf libwebp7 armhf 1.5.0-0.1 [188 kB] 366s Get:88 http://ftpmaster.internal/ubuntu questing/main armhf libtiff6 armhf 4.7.0-3ubuntu1 [184 kB] 366s Get:89 http://ftpmaster.internal/ubuntu questing/main armhf libxft2 armhf 2.3.6-1build1 [37.4 kB] 366s Get:90 http://ftpmaster.internal/ubuntu questing/main armhf libxss1 armhf 1:1.2.3-1build3 [6500 B] 366s Get:91 http://ftpmaster.internal/ubuntu questing/main armhf libtk8.6 armhf 8.6.16-1 [686 kB] 366s Get:92 http://ftpmaster.internal/ubuntu questing/main armhf libxt6t64 armhf 1:1.2.1-1.2build1 [145 kB] 366s Get:93 http://ftpmaster.internal/ubuntu questing/main armhf zip armhf 3.0-14ubuntu2 [164 kB] 366s Get:94 http://ftpmaster.internal/ubuntu questing/main armhf unzip armhf 6.0-28ubuntu6 [167 kB] 366s Get:95 http://ftpmaster.internal/ubuntu questing/main armhf xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 366s Get:96 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-core armhf 4.4.3-1 [28.2 MB] 367s Get:97 http://ftpmaster.internal/ubuntu questing/main armhf liblzma-dev armhf 5.6.4-1ubuntu1 [166 kB] 367s Get:98 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf-bin armhf 1.8.1-4 [21.2 kB] 367s Get:99 http://ftpmaster.internal/ubuntu questing/main armhf pkgconf armhf 1.8.1-4 [16.8 kB] 367s Get:100 http://ftpmaster.internal/ubuntu questing/main armhf libtirpc-dev armhf 1.3.4+ds-1.3 [184 kB] 367s Get:101 http://ftpmaster.internal/ubuntu questing/universe armhf r-base-dev all 4.4.3-1 [4176 B] 367s Get:102 http://ftpmaster.internal/ubuntu questing/universe armhf pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 367s Get:103 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-abind all 1.4-8-1 [66.9 kB] 368s Get:104 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-deldir armhf 2.0-4-1build1 [268 kB] 368s Get:105 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-goftest armhf 1.2-3-1 [58.6 kB] 368s Get:106 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-gsl armhf 2.1-8-1build1 [481 kB] 368s Get:107 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-lattice armhf 0.22-6-1 [1363 kB] 368s Get:108 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-matrix armhf 1.7-3-1 [4039 kB] 368s Get:109 http://ftpmaster.internal/ubuntu questing-proposed/universe armhf r-cran-nlme armhf 3.1.168-1 [2304 kB] 368s Get:110 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-mgcv armhf 1.9-1-1 [3205 kB] 368s Get:111 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-polyclip armhf 1.10-7-1 [109 kB] 368s Get:112 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-survival armhf 3.8-3-1 [8196 kB] 369s Get:113 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-rpart armhf 4.1.24-1 [661 kB] 369s Get:114 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-sm armhf 2.2-6.0-1 [787 kB] 369s Get:115 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatial armhf 7.3-18-1 [131 kB] 369s Get:116 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.utils armhf 3.1-3-1 [384 kB] 369s Get:117 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.data all 3.1-6-1 [4153 kB] 369s Get:118 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.univar armhf 3.1-2-1 [310 kB] 369s Get:119 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.geom armhf 3.3-6-1 [3923 kB] 369s Get:120 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.random armhf 3.3-3-1 [1155 kB] 369s Get:121 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-tensor all 1.5-4 [15.7 kB] 369s Get:122 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.sparse armhf 3.1-0-1 [216 kB] 369s Get:123 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.explore armhf 3.3-4-1 [3271 kB] 369s Get:124 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.model armhf 3.3-4-1 [3397 kB] 369s Get:125 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat.linnet armhf 3.2-5-1 [1505 kB] 370s Get:126 http://ftpmaster.internal/ubuntu questing/universe armhf r-cran-spatstat armhf 3.3-1-1 [4121 kB] 370s Preconfiguring packages ... 370s Fetched 161 MB in 7s (22.4 MB/s) 370s Selecting previously unselected package libc-dev-bin. 371s (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.) 371s Preparing to unpack .../000-libc-dev-bin_2.41-6ubuntu1_armhf.deb ... 371s Unpacking libc-dev-bin (2.41-6ubuntu1) ... 371s Selecting previously unselected package linux-libc-dev:armhf. 371s Preparing to unpack .../001-linux-libc-dev_6.14.0-15.15_armhf.deb ... 371s Unpacking linux-libc-dev:armhf (6.14.0-15.15) ... 371s Selecting previously unselected package libcrypt-dev:armhf. 371s Preparing to unpack .../002-libcrypt-dev_1%3a4.4.38-1_armhf.deb ... 371s Unpacking libcrypt-dev:armhf (1:4.4.38-1) ... 371s Selecting previously unselected package rpcsvc-proto. 371s Preparing to unpack .../003-rpcsvc-proto_1.4.2-0ubuntu7_armhf.deb ... 371s Unpacking rpcsvc-proto (1.4.2-0ubuntu7) ... 371s Selecting previously unselected package libc6-dev:armhf. 371s Preparing to unpack .../004-libc6-dev_2.41-6ubuntu1_armhf.deb ... 371s Unpacking libc6-dev:armhf (2.41-6ubuntu1) ... 371s Selecting previously unselected package libisl23:armhf. 371s Preparing to unpack .../005-libisl23_0.27-1_armhf.deb ... 371s Unpacking libisl23:armhf (0.27-1) ... 371s Selecting previously unselected package libmpc3:armhf. 371s Preparing to unpack .../006-libmpc3_1.3.1-1build2_armhf.deb ... 371s Unpacking libmpc3:armhf (1.3.1-1build2) ... 371s Selecting previously unselected package cpp-14-arm-linux-gnueabihf. 371s Preparing to unpack .../007-cpp-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 371s Unpacking cpp-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 371s Selecting previously unselected package cpp-14. 371s Preparing to unpack .../008-cpp-14_14.2.0-19ubuntu2_armhf.deb ... 371s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 371s Selecting previously unselected package cpp-arm-linux-gnueabihf. 371s Preparing to unpack .../009-cpp-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 371s Unpacking cpp-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 371s Selecting previously unselected package cpp. 371s Preparing to unpack .../010-cpp_4%3a14.2.0-1ubuntu1_armhf.deb ... 371s Unpacking cpp (4:14.2.0-1ubuntu1) ... 371s Selecting previously unselected package libcc1-0:armhf. 371s Preparing to unpack .../011-libcc1-0_15-20250404-0ubuntu1_armhf.deb ... 371s Unpacking libcc1-0:armhf (15-20250404-0ubuntu1) ... 371s Selecting previously unselected package libgomp1:armhf. 371s Preparing to unpack .../012-libgomp1_15-20250404-0ubuntu1_armhf.deb ... 371s Unpacking libgomp1:armhf (15-20250404-0ubuntu1) ... 371s Selecting previously unselected package libasan8:armhf. 371s Preparing to unpack .../013-libasan8_15-20250404-0ubuntu1_armhf.deb ... 371s Unpacking libasan8:armhf (15-20250404-0ubuntu1) ... 372s Selecting previously unselected package libubsan1:armhf. 372s Preparing to unpack .../014-libubsan1_15-20250404-0ubuntu1_armhf.deb ... 372s Unpacking libubsan1:armhf (15-20250404-0ubuntu1) ... 372s Selecting previously unselected package libgcc-14-dev:armhf. 372s Preparing to unpack .../015-libgcc-14-dev_14.2.0-19ubuntu2_armhf.deb ... 372s Unpacking libgcc-14-dev:armhf (14.2.0-19ubuntu2) ... 372s Selecting previously unselected package gcc-14-arm-linux-gnueabihf. 372s Preparing to unpack .../016-gcc-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 372s Unpacking gcc-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 372s Selecting previously unselected package gcc-14. 372s Preparing to unpack .../017-gcc-14_14.2.0-19ubuntu2_armhf.deb ... 372s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 372s Selecting previously unselected package gcc-arm-linux-gnueabihf. 372s Preparing to unpack .../018-gcc-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 372s Unpacking gcc-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 372s Selecting previously unselected package gcc. 372s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_armhf.deb ... 372s Unpacking gcc (4:14.2.0-1ubuntu1) ... 372s Selecting previously unselected package libstdc++-14-dev:armhf. 372s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-19ubuntu2_armhf.deb ... 372s Unpacking libstdc++-14-dev:armhf (14.2.0-19ubuntu2) ... 372s Selecting previously unselected package g++-14-arm-linux-gnueabihf. 372s Preparing to unpack .../021-g++-14-arm-linux-gnueabihf_14.2.0-19ubuntu2_armhf.deb ... 372s Unpacking g++-14-arm-linux-gnueabihf (14.2.0-19ubuntu2) ... 373s Selecting previously unselected package g++-14. 373s Preparing to unpack .../022-g++-14_14.2.0-19ubuntu2_armhf.deb ... 373s Unpacking g++-14 (14.2.0-19ubuntu2) ... 373s Selecting previously unselected package g++-arm-linux-gnueabihf. 373s Preparing to unpack .../023-g++-arm-linux-gnueabihf_4%3a14.2.0-1ubuntu1_armhf.deb ... 373s Unpacking g++-arm-linux-gnueabihf (4:14.2.0-1ubuntu1) ... 373s Selecting previously unselected package g++. 373s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_armhf.deb ... 373s Unpacking g++ (4:14.2.0-1ubuntu1) ... 373s Selecting previously unselected package build-essential. 373s Preparing to unpack .../025-build-essential_12.12ubuntu1_armhf.deb ... 373s Unpacking build-essential (12.12ubuntu1) ... 373s Selecting previously unselected package dctrl-tools. 373s Preparing to unpack .../026-dctrl-tools_2.24-3build3_armhf.deb ... 373s Unpacking dctrl-tools (2.24-3build3) ... 373s Selecting previously unselected package libfreetype6:armhf. 373s Preparing to unpack .../027-libfreetype6_2.13.3+dfsg-1_armhf.deb ... 373s Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ... 373s Selecting previously unselected package fonts-dejavu-mono. 373s Preparing to unpack .../028-fonts-dejavu-mono_2.37-8_all.deb ... 373s Unpacking fonts-dejavu-mono (2.37-8) ... 373s Selecting previously unselected package fonts-dejavu-core. 373s Preparing to unpack .../029-fonts-dejavu-core_2.37-8_all.deb ... 373s Unpacking fonts-dejavu-core (2.37-8) ... 373s Selecting previously unselected package fontconfig-config. 373s Preparing to unpack .../030-fontconfig-config_2.15.0-2.2ubuntu1_armhf.deb ... 373s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 373s Selecting previously unselected package libfontconfig1:armhf. 373s Preparing to unpack .../031-libfontconfig1_2.15.0-2.2ubuntu1_armhf.deb ... 373s Unpacking libfontconfig1:armhf (2.15.0-2.2ubuntu1) ... 373s Selecting previously unselected package fontconfig. 373s Preparing to unpack .../032-fontconfig_2.15.0-2.2ubuntu1_armhf.deb ... 373s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 373s Selecting previously unselected package libgfortran5:armhf. 373s Preparing to unpack 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374s Selecting previously unselected package gfortran. 374s Preparing to unpack .../038-gfortran_4%3a14.2.0-1ubuntu1_armhf.deb ... 374s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 374s Selecting previously unselected package icu-devtools. 374s Preparing to unpack .../039-icu-devtools_76.1-1ubuntu2_armhf.deb ... 374s Unpacking icu-devtools (76.1-1ubuntu2) ... 374s Selecting previously unselected package libblas3:armhf. 374s Preparing to unpack .../040-libblas3_3.12.1-2_armhf.deb ... 374s Unpacking libblas3:armhf (3.12.1-2) ... 374s Selecting previously unselected package libblas-dev:armhf. 374s Preparing to unpack .../041-libblas-dev_3.12.1-2_armhf.deb ... 374s Unpacking libblas-dev:armhf (3.12.1-2) ... 374s Selecting previously unselected package libbz2-dev:armhf. 374s Preparing to unpack .../042-libbz2-dev_1.0.8-6_armhf.deb ... 374s Unpacking libbz2-dev:armhf (1.0.8-6) ... 374s Selecting previously unselected package libpixman-1-0:armhf. 374s Preparing to unpack .../043-libpixman-1-0_0.44.0-3_armhf.deb ... 374s Unpacking libpixman-1-0:armhf (0.44.0-3) ... 374s Selecting previously unselected package libxcb-render0:armhf. 374s Preparing to unpack .../044-libxcb-render0_1.17.0-2_armhf.deb ... 374s Unpacking libxcb-render0:armhf (1.17.0-2) ... 374s Selecting previously unselected package libxcb-shm0:armhf. 374s Preparing to unpack .../045-libxcb-shm0_1.17.0-2_armhf.deb ... 374s Unpacking libxcb-shm0:armhf (1.17.0-2) ... 374s Selecting previously unselected package libxrender1:armhf. 374s Preparing to unpack .../046-libxrender1_1%3a0.9.10-1.1build1_armhf.deb ... 374s Unpacking libxrender1:armhf (1:0.9.10-1.1build1) ... 374s Selecting previously unselected package libcairo2:armhf. 374s Preparing to unpack .../047-libcairo2_1.18.4-1_armhf.deb ... 374s Unpacking libcairo2:armhf (1.18.4-1) ... 374s Selecting previously unselected package libdatrie1:armhf. 374s Preparing to unpack .../048-libdatrie1_0.2.13-3build1_armhf.deb ... 374s Unpacking libdatrie1:armhf (0.2.13-3build1) ... 374s Selecting previously unselected package libdeflate0:armhf. 374s Preparing to unpack .../049-libdeflate0_1.23-1_armhf.deb ... 374s Unpacking libdeflate0:armhf (1.23-1) ... 374s Selecting previously unselected package libdeflate-dev:armhf. 374s Preparing to unpack .../050-libdeflate-dev_1.23-1_armhf.deb ... 374s Unpacking libdeflate-dev:armhf (1.23-1) ... 374s Selecting previously unselected package libgraphite2-3:armhf. 374s Preparing to unpack .../051-libgraphite2-3_1.3.14-2ubuntu1_armhf.deb ... 374s Unpacking libgraphite2-3:armhf (1.3.14-2ubuntu1) ... 374s Selecting previously unselected package libgslcblas0:armhf. 374s Preparing to unpack .../052-libgslcblas0_2.8+dfsg-5ubuntu1_armhf.deb ... 374s Unpacking libgslcblas0:armhf (2.8+dfsg-5ubuntu1) ... 374s Selecting previously unselected package libgsl28:armhf. 374s Preparing to unpack .../053-libgsl28_2.8+dfsg-5ubuntu1_armhf.deb ... 374s Unpacking libgsl28:armhf (2.8+dfsg-5ubuntu1) ... 374s Selecting previously unselected package libharfbuzz0b:armhf. 374s Preparing to unpack .../054-libharfbuzz0b_10.2.0-1_armhf.deb ... 374s Unpacking libharfbuzz0b:armhf (10.2.0-1) ... 375s Selecting previously unselected package x11-common. 375s Preparing to unpack .../055-x11-common_1%3a7.7+23ubuntu4_all.deb ... 375s Unpacking x11-common (1:7.7+23ubuntu4) ... 375s Selecting previously unselected package libice6:armhf. 375s Preparing to unpack .../056-libice6_2%3a1.1.1-1_armhf.deb ... 375s Unpacking libice6:armhf (2:1.1.1-1) ... 375s Selecting previously unselected package libicu-dev:armhf. 375s Preparing to unpack .../057-libicu-dev_76.1-1ubuntu2_armhf.deb ... 375s Unpacking libicu-dev:armhf (76.1-1ubuntu2) ... 375s Selecting previously unselected package libjpeg-turbo8:armhf. 375s Preparing to unpack .../058-libjpeg-turbo8_2.1.5-3ubuntu2_armhf.deb ... 375s Unpacking libjpeg-turbo8:armhf (2.1.5-3ubuntu2) ... 375s Selecting previously unselected package libjpeg-turbo8-dev:armhf. 375s Preparing to unpack .../059-libjpeg-turbo8-dev_2.1.5-3ubuntu2_armhf.deb ... 375s Unpacking libjpeg-turbo8-dev:armhf (2.1.5-3ubuntu2) ... 375s Selecting previously unselected package libjpeg8:armhf. 375s Preparing to unpack .../060-libjpeg8_8c-2ubuntu11_armhf.deb ... 375s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 375s Selecting previously unselected package libjpeg8-dev:armhf. 375s Preparing to unpack .../061-libjpeg8-dev_8c-2ubuntu11_armhf.deb ... 375s Unpacking libjpeg8-dev:armhf (8c-2ubuntu11) ... 375s Selecting previously unselected package libjpeg-dev:armhf. 375s Preparing to unpack .../062-libjpeg-dev_8c-2ubuntu11_armhf.deb ... 375s Unpacking libjpeg-dev:armhf (8c-2ubuntu11) ... 375s Selecting previously unselected package liblapack3:armhf. 375s Preparing to unpack .../063-liblapack3_3.12.1-2_armhf.deb ... 375s Unpacking liblapack3:armhf (3.12.1-2) ... 375s Selecting previously unselected package liblapack-dev:armhf. 375s Preparing to unpack .../064-liblapack-dev_3.12.1-2_armhf.deb ... 375s Unpacking liblapack-dev:armhf (3.12.1-2) ... 375s Selecting previously unselected package liblerc4:armhf. 375s Preparing to unpack .../065-liblerc4_4.0.0+ds-5ubuntu1_armhf.deb ... 375s Unpacking liblerc4:armhf (4.0.0+ds-5ubuntu1) ... 375s Selecting previously unselected package libncurses-dev:armhf. 375s Preparing to unpack .../066-libncurses-dev_6.5+20250216-2_armhf.deb ... 375s Unpacking libncurses-dev:armhf (6.5+20250216-2) ... 376s Selecting previously unselected package libthai-data. 376s Preparing to unpack .../067-libthai-data_0.1.29-2build1_all.deb ... 376s Unpacking libthai-data (0.1.29-2build1) ... 376s Selecting previously unselected package libthai0:armhf. 376s Preparing to unpack .../068-libthai0_0.1.29-2build1_armhf.deb ... 376s Unpacking libthai0:armhf (0.1.29-2build1) ... 376s Selecting previously unselected package libpango-1.0-0:armhf. 376s Preparing to unpack .../069-libpango-1.0-0_1.56.3-1_armhf.deb ... 376s Unpacking libpango-1.0-0:armhf (1.56.3-1) ... 376s Selecting previously unselected package libpangoft2-1.0-0:armhf. 376s Preparing to unpack .../070-libpangoft2-1.0-0_1.56.3-1_armhf.deb ... 376s Unpacking libpangoft2-1.0-0:armhf (1.56.3-1) ... 376s Selecting previously unselected package libpangocairo-1.0-0:armhf. 376s Preparing to unpack .../071-libpangocairo-1.0-0_1.56.3-1_armhf.deb ... 376s Unpacking libpangocairo-1.0-0:armhf (1.56.3-1) ... 376s Selecting previously unselected package libpaper2:armhf. 376s Preparing to unpack .../072-libpaper2_2.2.5-0.3_armhf.deb ... 376s Unpacking libpaper2:armhf (2.2.5-0.3) ... 376s Selecting previously unselected package libpaper-utils. 376s Preparing to unpack .../073-libpaper-utils_2.2.5-0.3_armhf.deb ... 376s Unpacking libpaper-utils (2.2.5-0.3) ... 376s Selecting previously unselected package libpcre2-16-0:armhf. 376s Preparing to unpack .../074-libpcre2-16-0_10.45-1_armhf.deb ... 376s Unpacking libpcre2-16-0:armhf (10.45-1) ... 376s Selecting previously unselected package libpcre2-32-0:armhf. 376s Preparing to unpack .../075-libpcre2-32-0_10.45-1_armhf.deb ... 376s Unpacking libpcre2-32-0:armhf (10.45-1) ... 376s Selecting previously unselected package libpcre2-posix3:armhf. 376s Preparing to unpack .../076-libpcre2-posix3_10.45-1_armhf.deb ... 376s Unpacking libpcre2-posix3:armhf (10.45-1) ... 376s Selecting previously unselected package libpcre2-dev:armhf. 376s Preparing to unpack .../077-libpcre2-dev_10.45-1_armhf.deb ... 376s Unpacking libpcre2-dev:armhf (10.45-1) ... 376s Selecting previously unselected package libpkgconf3:armhf. 376s Preparing to unpack .../078-libpkgconf3_1.8.1-4_armhf.deb ... 376s Unpacking libpkgconf3:armhf (1.8.1-4) ... 376s Selecting previously unselected package zlib1g-dev:armhf. 376s Preparing to unpack .../079-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_armhf.deb ... 376s Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 376s Selecting previously unselected package libpng-dev:armhf. 376s Preparing to unpack .../080-libpng-dev_1.6.47-1.1_armhf.deb ... 376s Unpacking libpng-dev:armhf (1.6.47-1.1) ... 376s Selecting previously unselected package libreadline-dev:armhf. 376s Preparing to unpack .../081-libreadline-dev_8.2-6_armhf.deb ... 376s Unpacking libreadline-dev:armhf (8.2-6) ... 376s Selecting previously unselected package libsharpyuv0:armhf. 376s Preparing to unpack .../082-libsharpyuv0_1.5.0-0.1_armhf.deb ... 376s Unpacking libsharpyuv0:armhf (1.5.0-0.1) ... 376s Selecting previously unselected package libsm6:armhf. 376s Preparing to unpack .../083-libsm6_2%3a1.2.4-1_armhf.deb ... 376s Unpacking libsm6:armhf (2:1.2.4-1) ... 376s Selecting previously unselected package libtcl8.6:armhf. 376s Preparing to unpack .../084-libtcl8.6_8.6.16+dfsg-1_armhf.deb ... 376s Unpacking libtcl8.6:armhf (8.6.16+dfsg-1) ... 376s Selecting previously unselected package libjbig0:armhf. 376s Preparing to unpack .../085-libjbig0_2.1-6.1ubuntu2_armhf.deb ... 376s Unpacking libjbig0:armhf (2.1-6.1ubuntu2) ... 376s Selecting previously unselected package libwebp7:armhf. 376s Preparing to unpack .../086-libwebp7_1.5.0-0.1_armhf.deb ... 376s Unpacking libwebp7:armhf (1.5.0-0.1) ... 376s Selecting previously unselected package libtiff6:armhf. 376s Preparing to unpack .../087-libtiff6_4.7.0-3ubuntu1_armhf.deb ... 376s Unpacking libtiff6:armhf (4.7.0-3ubuntu1) ... 376s Selecting previously unselected package libxft2:armhf. 376s Preparing to unpack .../088-libxft2_2.3.6-1build1_armhf.deb ... 376s Unpacking libxft2:armhf (2.3.6-1build1) ... 376s Selecting previously unselected package libxss1:armhf. 376s Preparing to unpack .../089-libxss1_1%3a1.2.3-1build3_armhf.deb ... 376s Unpacking libxss1:armhf (1:1.2.3-1build3) ... 376s Selecting previously unselected package libtk8.6:armhf. 376s Preparing to unpack .../090-libtk8.6_8.6.16-1_armhf.deb ... 376s Unpacking libtk8.6:armhf (8.6.16-1) ... 376s Selecting previously unselected package libxt6t64:armhf. 377s Preparing to unpack .../091-libxt6t64_1%3a1.2.1-1.2build1_armhf.deb ... 377s Unpacking libxt6t64:armhf (1:1.2.1-1.2build1) ... 377s Selecting previously unselected package zip. 377s Preparing to unpack .../092-zip_3.0-14ubuntu2_armhf.deb ... 377s Unpacking zip (3.0-14ubuntu2) ... 377s Selecting previously unselected package unzip. 377s Preparing to unpack .../093-unzip_6.0-28ubuntu6_armhf.deb ... 377s Unpacking unzip (6.0-28ubuntu6) ... 377s Selecting previously unselected package xdg-utils. 377s Preparing to unpack .../094-xdg-utils_1.2.1-2ubuntu1_all.deb ... 377s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 377s Selecting previously unselected package r-base-core. 377s Preparing to unpack .../095-r-base-core_4.4.3-1_armhf.deb ... 377s Unpacking r-base-core (4.4.3-1) ... 377s Selecting previously unselected package liblzma-dev:armhf. 377s Preparing to unpack .../096-liblzma-dev_5.6.4-1ubuntu1_armhf.deb ... 377s Unpacking liblzma-dev:armhf (5.6.4-1ubuntu1) ... 377s Selecting previously unselected package pkgconf-bin. 377s Preparing to unpack .../097-pkgconf-bin_1.8.1-4_armhf.deb ... 377s Unpacking pkgconf-bin (1.8.1-4) ... 377s Selecting previously unselected package pkgconf:armhf. 377s Preparing to unpack .../098-pkgconf_1.8.1-4_armhf.deb ... 377s Unpacking pkgconf:armhf (1.8.1-4) ... 377s Selecting previously unselected package libtirpc-dev:armhf. 377s Preparing to unpack .../099-libtirpc-dev_1.3.4+ds-1.3_armhf.deb ... 377s Unpacking libtirpc-dev:armhf (1.3.4+ds-1.3) ... 377s Selecting previously unselected package r-base-dev. 377s Preparing to unpack .../100-r-base-dev_4.4.3-1_all.deb ... 377s Unpacking r-base-dev (4.4.3-1) ... 377s Selecting previously unselected package pkg-r-autopkgtest. 377s Preparing to unpack .../101-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 377s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 377s Selecting previously unselected package r-cran-abind. 377s Preparing to unpack .../102-r-cran-abind_1.4-8-1_all.deb ... 377s Unpacking r-cran-abind (1.4-8-1) ... 377s Selecting previously unselected package r-cran-deldir. 377s Preparing to unpack .../103-r-cran-deldir_2.0-4-1build1_armhf.deb ... 377s Unpacking r-cran-deldir (2.0-4-1build1) ... 377s Selecting previously unselected package r-cran-goftest. 377s Preparing to unpack .../104-r-cran-goftest_1.2-3-1_armhf.deb ... 377s Unpacking r-cran-goftest (1.2-3-1) ... 377s Selecting previously unselected package r-cran-gsl. 377s Preparing to unpack .../105-r-cran-gsl_2.1-8-1build1_armhf.deb ... 377s Unpacking r-cran-gsl (2.1-8-1build1) ... 377s Selecting previously unselected package r-cran-lattice. 377s Preparing to unpack .../106-r-cran-lattice_0.22-6-1_armhf.deb ... 377s Unpacking r-cran-lattice (0.22-6-1) ... 378s Selecting previously unselected package r-cran-matrix. 378s Preparing to unpack .../107-r-cran-matrix_1.7-3-1_armhf.deb ... 378s Unpacking r-cran-matrix (1.7-3-1) ... 378s Selecting previously unselected package r-cran-nlme. 378s Preparing to unpack .../108-r-cran-nlme_3.1.168-1_armhf.deb ... 378s Unpacking r-cran-nlme (3.1.168-1) ... 378s Selecting previously unselected package r-cran-mgcv. 378s Preparing to unpack .../109-r-cran-mgcv_1.9-1-1_armhf.deb ... 378s Unpacking r-cran-mgcv (1.9-1-1) ... 378s Selecting previously unselected package r-cran-polyclip. 378s Preparing to unpack .../110-r-cran-polyclip_1.10-7-1_armhf.deb ... 378s Unpacking r-cran-polyclip (1.10-7-1) ... 378s Selecting previously unselected package r-cran-survival. 378s Preparing to unpack .../111-r-cran-survival_3.8-3-1_armhf.deb ... 378s Unpacking r-cran-survival (3.8-3-1) ... 378s Selecting previously unselected package r-cran-rpart. 378s Preparing to unpack .../112-r-cran-rpart_4.1.24-1_armhf.deb ... 378s Unpacking r-cran-rpart (4.1.24-1) ... 378s Selecting previously unselected package r-cran-sm. 378s Preparing to unpack .../113-r-cran-sm_2.2-6.0-1_armhf.deb ... 378s Unpacking r-cran-sm (2.2-6.0-1) ... 378s Selecting previously unselected package r-cran-spatial. 378s Preparing to unpack .../114-r-cran-spatial_7.3-18-1_armhf.deb ... 378s Unpacking r-cran-spatial (7.3-18-1) ... 378s Selecting previously unselected package r-cran-spatstat.utils. 378s Preparing to unpack .../115-r-cran-spatstat.utils_3.1-3-1_armhf.deb ... 378s Unpacking r-cran-spatstat.utils (3.1-3-1) ... 378s Selecting previously unselected package r-cran-spatstat.data. 378s Preparing to unpack .../116-r-cran-spatstat.data_3.1-6-1_all.deb ... 378s Unpacking r-cran-spatstat.data (3.1-6-1) ... 378s Selecting previously unselected package r-cran-spatstat.univar. 378s Preparing to unpack .../117-r-cran-spatstat.univar_3.1-2-1_armhf.deb ... 378s Unpacking r-cran-spatstat.univar (3.1-2-1) ... 378s Selecting previously unselected package r-cran-spatstat.geom. 378s Preparing to unpack .../118-r-cran-spatstat.geom_3.3-6-1_armhf.deb ... 378s Unpacking r-cran-spatstat.geom (3.3-6-1) ... 378s Selecting previously unselected package r-cran-spatstat.random. 378s Preparing to 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382s Setting up gfortran (4:14.2.0-1ubuntu1) ... 382s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 382s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 382s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 382s 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 382s Setting up r-cran-deldir (2.0-4-1build1) ... 382s Setting up r-cran-goftest (1.2-3-1) ... 382s Setting up r-cran-matrix (1.7-3-1) ... 382s Setting up r-cran-spatstat.sparse (3.1-0-1) ... 382s Setting up r-cran-mgcv (1.9-1-1) ... 382s Setting up r-base-dev (4.4.3-1) ... 382s Setting up r-cran-survival (3.8-3-1) ... 382s Setting up r-cran-spatstat.data (3.1-6-1) ... 382s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 382s Setting up r-cran-spatstat.geom (3.3-6-1) ... 382s Setting up r-cran-rpart (4.1.24-1) ... 382s Setting up r-cran-spatstat.random (3.3-3-1) ... 382s Setting up r-cran-spatstat.explore (3.3-4-1) ... 382s Setting up r-cran-spatstat.model (3.3-4-1) ... 382s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 382s Setting up r-cran-spatstat (3.3-1-1) ... 382s Processing triggers for install-info (7.1.1-1) ... 382s Processing triggers for libc-bin (2.41-6ubuntu1) ... 382s Processing triggers for man-db (2.13.0-1) ... 397s autopkgtest [02:38:00]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 397s autopkgtest [02:38:00]: test pkg-r-autopkgtest: [----------------------- 399s Test: Try to load the R library spatstat.explore 399s 399s R version 4.4.3 (2025-02-28) -- "Trophy Case" 399s Copyright (C) 2025 The R Foundation for Statistical Computing 399s Platform: arm-unknown-linux-gnueabihf (32-bit) 399s 399s R is free software and comes with ABSOLUTELY NO WARRANTY. 399s You are welcome to redistribute it under certain conditions. 399s Type 'license()' or 'licence()' for distribution details. 399s 399s R is a collaborative project with many contributors. 399s Type 'contributors()' for more information and 399s 'citation()' on how to cite R or R packages in publications. 399s 399s Type 'demo()' for some demos, 'help()' for on-line help, or 399s 'help.start()' for an HTML browser interface to help. 399s Type 'q()' to quit R. 399s 399s > library('spatstat.explore') 399s Loading required package: spatstat.data 400s Loading required package: spatstat.univar 400s spatstat.univar 3.1-2 400s Loading required package: spatstat.geom 400s spatstat.geom 3.3-6 400s Loading required package: spatstat.random 400s spatstat.random 3.3-3 400s Loading required package: nlme 400s spatstat.explore 3.3-4 400s > 400s > 400s Other tests are currently unsupported! 400s They will be progressively added. 400s autopkgtest [02:38:03]: test pkg-r-autopkgtest: -----------------------] 404s autopkgtest [02:38:07]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 404s pkg-r-autopkgtest PASS 408s autopkgtest [02:38:11]: @@@@@@@@@@@@@@@@@@@@ summary 408s run-unit-test PASS 408s pkg-r-autopkgtest PASS