0s autopkgtest [18:54:12]: starting date and time: 2025-05-03 18:54:12+0000 0s autopkgtest [18:54:12]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [18:54:12]: host juju-7f2275-prod-proposed-migration-environment-23; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mzpzjhp5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-23@bos03-17.secgroup --name adt-questing-amd64-r-cran-spatstat.explore-20250503-185411-juju-7f2275-prod-proposed-migration-environment-23-68191334-26bb-4788-9a31-31cb2a03847c --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-23 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 42s autopkgtest [18:54:54]: testbed dpkg architecture: amd64 42s autopkgtest [18:54:54]: testbed apt version: 3.0.0 43s autopkgtest [18:54:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 43s autopkgtest [18:54:55]: testbed release detected to be: None 44s autopkgtest [18:54:56]: updating testbed package index (apt update) 44s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 44s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 44s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 44s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 45s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1442 kB] 45s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 45s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 45s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [146 kB] 45s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [203 kB] 45s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [576 kB] 45s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1424 kB] 45s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [48.6 kB] 45s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [23.1 kB] 45s Fetched 4155 kB in 1s (3862 kB/s) 46s Reading package lists... 46s autopkgtest [18:54:58]: upgrading testbed (apt dist-upgrade and autopurge) 46s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 47s Starting 2 pkgProblemResolver with broken count: 0 47s Done 47s Entering ResolveByKeep 48s 48s Calculating upgrade... 48s The following packages will be upgraded: 48s cloud-init cloud-init-base debianutils libmbim-glib4 libmbim-proxy 48s libnftnl11 libqmi-glib5 libqmi-proxy libsepol2 python3-lazr.restfulclient 48s sos 48s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 48s Need to get 2693 kB of archives. 48s After this operation, 104 kB disk space will be freed. 48s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB] 48s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libsepol2 amd64 3.8.1-1 [327 kB] 48s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB] 48s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 48s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B] 48s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB] 48s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B] 48s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB] 49s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB] 49s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 sos all 4.9.1-1 [367 kB] 49s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 49s Preconfiguring packages ... 49s Fetched 2693 kB in 1s (2663 kB/s) 49s (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 ... 80514 files and directories currently installed.) 49s Preparing to unpack .../debianutils_5.22_amd64.deb ... 49s Unpacking debianutils (5.22) over (5.21) ... 49s Setting up debianutils (5.22) ... 49s (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 ... 80514 files and directories currently installed.) 49s Preparing to unpack .../libsepol2_3.8.1-1_amd64.deb ... 49s Unpacking libsepol2:amd64 (3.8.1-1) over (3.7-1) ... 49s Setting up libsepol2:amd64 (3.8.1-1) ... 50s (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 ... 80514 files and directories currently installed.) 50s Preparing to unpack .../0-libnftnl11_1.2.9-1_amd64.deb ... 50s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ... 50s Preparing to unpack .../1-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 50s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 50s Preparing to unpack .../2-libmbim-proxy_1.32.0-1_amd64.deb ... 50s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 50s Preparing to unpack .../3-libmbim-glib4_1.32.0-1_amd64.deb ... 50s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 50s Preparing to unpack .../4-libqmi-proxy_1.36.0-1_amd64.deb ... 50s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 50s Preparing to unpack .../5-libqmi-glib5_1.36.0-1_amd64.deb ... 50s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ... 50s Preparing to unpack .../6-python3-lazr.restfulclient_0.14.6-3_all.deb ... 50s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ... 50s Preparing to unpack .../7-sos_4.9.1-1_all.deb ... 50s Unpacking sos (4.9.1-1) over (4.9.0-6) ... 50s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 50s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 50s Setting up sos (4.9.1-1) ... 51s Setting up libnftnl11:amd64 (1.2.9-1) ... 51s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 52s Setting up python3-lazr.restfulclient (0.14.6-3) ... 52s Setting up libmbim-glib4:amd64 (1.32.0-1) ... 52s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 52s Setting up libmbim-proxy (1.32.0-1) ... 52s Setting up libqmi-glib5:amd64 (1.36.0-1) ... 52s Setting up libqmi-proxy (1.36.0-1) ... 52s Processing triggers for libc-bin (2.41-6ubuntu1) ... 52s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 52s Processing triggers for man-db (2.13.0-1) ... 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 55s Starting pkgProblemResolver with broken count: 0 55s Starting 2 pkgProblemResolver with broken count: 0 55s Done 55s Solving dependencies... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s autopkgtest [18:55:07]: rebooting testbed after setup commands that affected boot 78s autopkgtest [18:55:30]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 81s autopkgtest [18:55:33]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.explore 83s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (dsc) [2563 B] 83s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (tar) [668 kB] 83s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (diff) [3452 B] 83s gpgv: Signature made Fri Jan 31 07:56:43 2025 UTC 83s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 83s gpgv: issuer "plessy@debian.org" 83s gpgv: Can't check signature: No public key 83s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.explore_3.3-4-1.dsc: no acceptable signature found 83s autopkgtest [18:55:35]: testing package r-cran-spatstat.explore version 3.3-4-1 83s autopkgtest [18:55:35]: build not needed 85s autopkgtest [18:55:37]: test run-unit-test: preparing testbed 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Starting pkgProblemResolver with broken count: 0 85s Starting 2 pkgProblemResolver with broken count: 0 85s Done 86s The following NEW packages will be installed: 86s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 86s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 86s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libice6 libjbig0 86s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 86s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 86s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 86s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 86s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 86s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 86s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 86s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 86s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 86s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 86s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 86s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 87.8 MB of archives. 86s After this operation, 147 MB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 86s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 86s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 86s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 86s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 87s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 87s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 87s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 87s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 87s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 87s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 87s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 87s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 87s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 87s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 87s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 87s Get:17 http://ftpmaster.internal/ubuntu questing/universe amd64 libgslcblas0 amd64 2.8+dfsg-5ubuntu1 [113 kB] 87s Get:18 http://ftpmaster.internal/ubuntu questing/universe amd64 libgsl28 amd64 2.8+dfsg-5ubuntu1 [1043 kB] 87s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 87s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 87s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 87s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 87s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 87s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 88s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 88s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 88s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 88s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 88s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 88s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 88s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 88s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 88s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 88s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 88s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 88s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 88s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 88s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 88s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 88s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 88s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 88s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 88s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 88s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 88s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 88s Get:46 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 89s Get:47 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB] 89s Get:48 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-deldir amd64 2.0-4-1build1 [270 kB] 89s Get:49 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-goftest amd64 1.2-3-1 [59.5 kB] 89s Get:50 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-gsl amd64 2.1-8-1build1 [486 kB] 89s Get:51 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 89s Get:52 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-locfit amd64 1.5-9.12-1 [552 kB] 89s Get:53 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 90s Get:54 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 90s Get:55 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 90s Get:56 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-polyclip amd64 1.10-7-1 [116 kB] 90s Get:57 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB] 90s Get:58 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rpart amd64 4.1.24-1 [670 kB] 90s Get:59 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-sm amd64 2.2-6.0-1 [788 kB] 90s Get:60 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatial amd64 7.3-18-1 [137 kB] 90s Get:61 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.utils amd64 3.1-3-1 [387 kB] 90s Get:62 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.data all 3.1-6-1 [4153 kB] 90s Get:63 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.univar amd64 3.1-2-1 [315 kB] 90s Get:64 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.geom amd64 3.3-6-1 [3968 kB] 90s Get:65 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.random amd64 3.3-3-1 [1177 kB] 90s Get:66 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-tensor all 1.5-4 [15.7 kB] 90s Get:67 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.sparse amd64 3.1-0-1 [221 kB] 90s Get:68 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.explore amd64 3.3-4-1 [3347 kB] 91s Get:69 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.model amd64 3.3-4-1 [3397 kB] 91s Get:70 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.linnet amd64 3.2-5-1 [1509 kB] 91s Get:71 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat amd64 3.3-1-1 [4121 kB] 91s Preconfiguring packages ... 91s Fetched 87.8 MB in 5s (16.5 MB/s) 91s Selecting previously unselected package fonts-dejavu-mono. 92s (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 ... 80518 files and directories currently installed.) 92s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-mono (2.37-8) ... 92s Selecting previously unselected package fonts-dejavu-core. 92s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 92s Unpacking fonts-dejavu-core (2.37-8) ... 92s Selecting previously unselected package fontconfig-config. 92s Preparing to unpack .../02-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 92s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 92s Selecting previously unselected package libfontconfig1:amd64. 92s Preparing to unpack .../03-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 92s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 92s Selecting previously unselected package fontconfig. 92s Preparing to unpack .../04-fontconfig_2.15.0-2.2ubuntu1_amd64.deb ... 92s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 92s Selecting previously unselected package libblas3:amd64. 92s Preparing to unpack .../05-libblas3_3.12.1-2_amd64.deb ... 92s Unpacking libblas3:amd64 (3.12.1-2) ... 92s Selecting previously unselected package libpixman-1-0:amd64. 92s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_amd64.deb ... 92s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 92s Selecting previously unselected package libxcb-render0:amd64. 92s Preparing to unpack .../07-libxcb-render0_1.17.0-2_amd64.deb ... 92s Unpacking 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r-cran-spatstat.data (3.1-6-1) ... 98s Setting up r-cran-spatstat.geom (3.3-6-1) ... 98s Setting up r-cran-rpart (4.1.24-1) ... 98s Setting up r-cran-spatstat.random (3.3-3-1) ... 98s Setting up r-cran-spatstat.explore (3.3-4-1) ... 98s Setting up r-cran-spatstat.model (3.3-4-1) ... 98s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 98s Setting up r-cran-spatstat (3.3-1-1) ... 98s Processing triggers for install-info (7.1.1-1) ... 98s Processing triggers for libc-bin (2.41-6ubuntu1) ... 98s Processing triggers for man-db (2.13.0-1) ... 100s autopkgtest [18:55:52]: test run-unit-test: [----------------------- 100s BEGIN TEST testsAtoC.R 100s 100s R version 4.4.3 (2025-02-28) -- "Trophy Case" 100s Copyright (C) 2025 The R Foundation for Statistical Computing 100s Platform: x86_64-pc-linux-gnu 100s 100s R is free software and comes with ABSOLUTELY NO WARRANTY. 100s You are welcome to redistribute it under certain conditions. 100s Type 'license()' or 'licence()' for distribution details. 100s 100s R is a collaborative project with many contributors. 100s Type 'contributors()' for more information and 100s 'citation()' on how to cite R or R packages in publications. 100s 100s Type 'demo()' for some demos, 'help()' for on-line help, or 100s 'help.start()' for an HTML browser interface to help. 100s Type 'q()' to quit R. 100s 100s > #' 100s > #' Header for all (concatenated) test files 100s > #' 100s > #' Require spatstat.explore 100s > #' Obtain environment variable controlling tests. 100s > #' 100s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 100s > 100s > require(spatstat.explore) 100s Loading required package: spatstat.explore 100s Loading required package: spatstat.data 101s Loading required package: spatstat.univar 101s spatstat.univar 3.1-2 101s Loading required package: spatstat.geom 101s spatstat.geom 3.3-6 101s Loading required package: spatstat.random 101s spatstat.random 3.3-3 101s Loading required package: nlme 101s spatstat.explore 3.3-4 101s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 101s > ALWAYS <- TRUE 101s > cat(paste("--------- Executing", 101s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 101s + "test code -----------\n")) 101s --------- Executing **RESTRICTED** subset of test code ----------- 101s > ## tests/cdf.test.R 101s > 101s > 101s > local({ 101s + NSIM <- 9 101s + op <- spatstat.options(ndummy.min=16, npixel=32) 101s + AA <- split(ants, un=FALSE) 101s + AC <- AA[["Cataglyphis"]] 101s + AM <- AA[["Messor"]] 101s + DM <- distmap(AM) 101s + if(ALWAYS) { 101s + ## Check cdf.test with strange data 101s + ## Marked point patterns with some marks not represented 101s + ## should produce a warning, rather than a crash: 101s + cdf.test(AC, DM) 101s + } 101s + if(FULLTEST) { 101s + ## should be OK: 101s + cdf.test(unmark(AC), DM) 101s + cdf.test(unmark(AC), DM, "cvm") 101s + cdf.test(unmark(AC), DM, "ad") 101s + ## other code blocks 101s + cdf.test(finpines, "x") 101s + } 101s + }) 101s > 101s > 101s > #' tests/circular.R 101s > #' 101s > #' Circular data and periodic distributions 101s > #' 101s > #' $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 101s > 101s > 101s > local({ 101s + if(ALWAYS) { 101s + a <- pairorient(redwood, 0.05, 0.15, correction="none") 101s + rose(a) 101s + } 101s + if(FULLTEST) { 101s + b <- pairorient(redwood, 0.05, 0.15, correction="best") 101s + rose(b, start="N", clockwise=TRUE) 101s + } 101s + if(ALWAYS) { 101s + #' arcs on the circle 101s + #' (depends on numerical behaviour) 101s + set.seed(19171025) 101s + aa <- replicate(7, runif(1, 0, 2*pi) + c(0, runif(1, 0, pi)), 101s + simplify=FALSE) 101s + bb <- circunion(aa) 101s + 101s + assertsingle <- function(x, a, id) { 101s + y <- circunion(x) 101s + if(length(y) != 1 || max(abs(y[[1]] - a)) > .Machine$double.eps) 101s + stop(paste("Incorrect result from circunion in case", id), 101s + call.=FALSE) 101s + invisible(NULL) 101s + } 101s + 101s + assertsingle(list(c(pi/3, pi), c(pi/2, 3*pi/2)), 101s + c(pi/3, 3*pi/2), 101s + 1) 101s + assertsingle(list(c(0, pi/2), c(pi/4, pi)), 101s + c(0,pi), 101s + 2) 101s + assertsingle(list(c(-pi/4, pi/2), c(pi/4, pi)), 101s + c((2-1/4)*pi, pi), 101s + 3) 101s + } 101s + }) 101s Warning message: 101s In cdf.test.ppp(AC, DM) : 101s Ignoring marks, because some mark values have zero frequency 101s > 101s > 101s > #' 101s > #' tests/closecore.R 101s > #' 101s > #' check 'closepairs/crosspairs' code 101s > #' invoked in core package 101s > #' 101s > #' $Revision: 1.4 $ $Date: 2021/04/17 04:16:43 $ 101s > #' 101s > #' ------- All this code must be run on every hardware ------- 101s > #' 101s > 101s > local({ 101s + #' weightedclosepairs is in wtdclosepair.R 101s + wi <- weightedclosepairs(redwood, 0.05, "isotropic") 101s + if(FULLTEST) { 101s + wt <- weightedclosepairs(redwood, 0.05, "translate") 101s + wp <- weightedclosepairs(redwood, 0.05, "periodic") 101s + } 101s + #' markmarkscatter uses closepairs.pp3 101s + X <- runifpoint3(100) 101s + marks(X) <- runif(100) 101s + markmarkscatter(X, 0.2) 101s + if(FULLTEST) { 101s + markmarkscatter(X[FALSE], 0.2) 101s + } 101s + }) 101s > 101s > #' 101s > #' contact.R 101s > #' 101s > #' Check machinery for first contact distributions 101s > #' 101s > #' $Revision: 1.8 $ $Date: 2021/04/17 02:25:55 $ 101s > 101s > local({ 101s + if(ALWAYS) { 101s + #' reduce complexity 101s + Y <- as.mask(heather$coarse, dimyx=c(50, 25)) 101s + 101s + X <- runifpoint(100, win = complement.owin(Y)) 101s + if(FULLTEST) G <- Gfox(X, Y) 101s + J <- Jfox(X, Y) 101s + 101s + Y <- as.polygonal(Y) 101s + X <- runifpoint(100, win = complement.owin(Y)) 101s + if(FULLTEST) G <- Gfox(X, Y) 101s + J <- Jfox(X, Y) 101s + 101s + op <- spatstat.options(exactdt.checks.data=TRUE) 101s + U <- exactdt(X) 101s + spatstat.options(op) 101s + } 101s + }) 102s > 102s > reset.spatstat.options() 102s > 102s BEGIN TEST testsD.R 102s 102s R version 4.4.3 (2025-02-28) -- "Trophy Case" 102s Copyright (C) 2025 The R Foundation for Statistical Computing 102s Platform: x86_64-pc-linux-gnu 102s 102s R is free software and comes with ABSOLUTELY NO WARRANTY. 102s You are welcome to redistribute it under certain conditions. 102s Type 'license()' or 'licence()' for distribution details. 102s 102s R is a collaborative project with many contributors. 102s Type 'contributors()' for more information and 102s 'citation()' on how to cite R or R packages in publications. 102s 102s Type 'demo()' for some demos, 'help()' for on-line help, or 102s 'help.start()' for an HTML browser interface to help. 102s Type 'q()' to quit R. 102s 102s > #' 102s > #' Header for all (concatenated) test files 102s > #' 102s > #' Require spatstat.explore 102s > #' Obtain environment variable controlling tests. 102s > #' 102s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 102s > 102s > require(spatstat.explore) 102s Loading required package: spatstat.explore 102s Loading required package: spatstat.data 103s Loading required package: spatstat.univar 103s spatstat.univar 3.1-2 103s Loading required package: spatstat.geom 103s spatstat.geom 3.3-6 103s Loading required package: spatstat.random 103s spatstat.random 3.3-3 103s Loading required package: nlme 103s spatstat.explore 3.3-4 103s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 103s > ALWAYS <- TRUE 103s > cat(paste("--------- Executing", 103s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 103s + "test code -----------\n")) 103s --------- Executing **RESTRICTED** subset of test code ----------- 103s > #' 103s > #' tests/density.R 103s > #' 103s > #' Test behaviour of density() methods, 103s > #' relrisk(), Smooth() 103s > #' and inhomogeneous summary functions 103s > #' and idw, adaptive.density, intensity 103s > #' and SpatialMedian, SpatialQuantile 103s > #' 103s > #' $Revision: 1.67 $ $Date: 2024/01/29 07:07:16 $ 103s > #' 103s > 103s > if(!FULLTEST) 103s + spatstat.options(npixel=32, ndummy.min=16) 103s > 103s > 103s > local({ 103s + 103s + # test all cases of density.ppp and densityfun.ppp 103s + 103s + tryit <- function(..., do.fun=TRUE, badones=FALSE) { 103s + Z <- density(cells, ..., at="pixels") 103s + Z <- density(cells, ..., at="points") 103s + if(do.fun) { 103s + f <- densityfun(cells, ...) 103s + U <- f(0.1, 0.3) 103s + if(badones) { 103s + U2 <- f(1.1, 0.3) 103s + U3 <- f(1.1, 0.3, drop=FALSE) 103s + } 103s + } 103s + return(invisible(NULL)) 103s + } 103s + 103s + if(ALWAYS) { 103s + tryit(0.05) 103s + tryit(0.05, diggle=TRUE) 103s + tryit(0.05, se=TRUE) 103s + tryit(0.05, weights=expression(x)) 103s + tryit(0.07, kernel="epa") 103s + tryit(sigma=Inf) 103s + tryit(0.05, badones=TRUE) 103s + } 103s + if(FULLTEST) { 103s + tryit(0.07, kernel="quartic") 103s + tryit(0.07, kernel="disc") 103s + tryit(0.07, kernel="epa", weights=expression(x)) 103s + tryit(sigma=Inf, weights=expression(x)) 103s + } 103s + 103s + V <- diag(c(0.05^2, 0.07^2)) 103s + 103s + if(ALWAYS) { 103s + tryit(varcov=V) 103s + } 103s + if(FULLTEST) { 103s + tryit(varcov=V, diggle=TRUE) 103s + tryit(varcov=V, weights=expression(x)) 103s + tryit(varcov=V, weights=expression(x), diggle=TRUE) 103s + Z <- distmap(runifpoint(5, Window(cells))) 103s + tryit(0.05, weights=Z) 103s + tryit(0.05, weights=Z, diggle=TRUE) 103s + } 103s + 103s + trymost <- function(...) tryit(..., do.fun=FALSE) 103s + wdf <- data.frame(a=1:42,b=42:1) 103s + if(ALWAYS) { 103s + trymost(0.05, weights=wdf) 103s + trymost(sigma=Inf, weights=wdf) 103s + } 103s + if(FULLTEST) { 103s + trymost(0.05, weights=wdf, diggle=TRUE) 103s + trymost(varcov=V, weights=wdf) 103s + trymost(varcov=V, weights=expression(cbind(x,y))) 103s + } 103s + 103s + ## check conservation of mass 103s + checkconserve <- function(X, xname, sigma, toler=0.01) { 103s + veritas <- npoints(X) 103s + vino <- integral(density(X, sigma, diggle=TRUE)) 103s + relerr <- abs(vino - veritas)/veritas 103s + if(relerr > toler) 103s + stop(paste("density.ppp(diggle=TRUE) fails to conserve mass:", 103s + vino, "!=", veritas, 103s + "for", sQuote(xname)), 103s + call.=FALSE) 103s + return(relerr) 103s + } 103s + if(FULLTEST) { 103s + checkconserve(cells, "cells", 0.15) 103s + } 103s + if(ALWAYS) { 103s + checkconserve(split(chorley)[["lung"]], "lung", 2) 103s + } 103s + 103s + ## run C algorithm 'denspt' 103s + opa <- spatstat.options(densityC=TRUE, densityTransform=FALSE) 103s + if(ALWAYS) { 103s + tryit(varcov=V) 103s + } 103s + if(FULLTEST) { 103s + tryit(varcov=V, weights=expression(x)) 103s + trymost(varcov=V, weights=wdf) 103s + } 103s + spatstat.options(opa) 103s + 103s + crossit <- function(..., sigma=NULL) { 103s + U <- runifpoint(20, Window(cells)) 103s + a <- densitycrossEngine(cells, U, ..., sigma=sigma) 103s + a <- densitycrossEngine(cells, U, ..., sigma=sigma, diggle=TRUE) 103s + invisible(NULL) 103s + } 103s + if(ALWAYS) { 103s + crossit(varcov=V, weights=cells$x) 103s + crossit(sigma=Inf) 103s + } 103s + if(FULLTEST) { 103s + crossit(varcov=V, weights=wdf) 103s + crossit(sigma=0.1, weights=wdf) 103s + crossit(sigma=0.1, kernel="epa", weights=wdf) 103s + } 103s + 103s + ## apply different discretisation rules 103s + if(ALWAYS) { 103s + Z <- density(cells, 0.05, fractional=TRUE) 103s + } 103s + if(FULLTEST) { 103s + Z <- density(cells, 0.05, preserve=TRUE) 103s + Z <- density(cells, 0.05, fractional=TRUE, preserve=TRUE) 103s + } 103s + 103s + ## compare results with different algorithms 103s + crosscheque <- function(expr) { 103s + e <- as.expression(substitute(expr)) 103s + ename <- sQuote(deparse(substitute(expr))) 103s + ## interpreted R 103s + opa <- spatstat.options(densityC=FALSE, densityTransform=FALSE) 103s + val.interpreted <- eval(e) 103s + ## established C algorithm 'denspt' 103s + spatstat.options(densityC=TRUE, densityTransform=FALSE) 103s + val.C <- eval(e) 103s + ## new C algorithm 'Gdenspt' using transformed coordinates 103s + spatstat.options(densityC=TRUE, densityTransform=TRUE) 103s + val.Transform <- eval(e) 103s + spatstat.options(opa) 103s + if(max(abs(val.interpreted - val.C)) > 0.001) 103s + stop(paste("Numerical discrepancy between R and C algorithms in", 103s + ename)) 103s + if(max(abs(val.C - val.Transform)) > 0.001) 103s + stop(paste("Numerical discrepancy between C algorithms", 103s + "using transformed and untransformed coordinates in", 103s + ename)) 103s + invisible(NULL) 103s + } 103s + 103s + ## execute & compare results of density(at="points") with different algorithms 103s + wdfr <- cbind(1:npoints(redwood), 2) 103s + if(ALWAYS) { 103s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE)) 103s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 103s + weights=wdfr[,1])) 103s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 103s + weights=wdfr)) 103s + } 103s + 103s + ## correctness of non-Gaussian kernel calculation 103s + leavein <- function(ker, maxd=0.025) { 103s + ZI <- density(redwood, 0.12, kernel=ker, edge=FALSE, 103s + dimyx=256)[redwood] 103s + ZP <- density(redwood, 0.12, kernel=ker, edge=FALSE, 103s + at="points", leaveoneout=FALSE) 103s + discrep <- max(abs(ZP - ZI))/npoints(redwood) 103s + if(discrep > maxd) 103s + stop(paste("Discrepancy", 103s + signif(discrep, 3), 103s + "in calculation for", ker, "kernel")) 103s + return(invisible(NULL)) 103s + } 103s + if(ALWAYS) { 103s + leavein("epanechnikov", 0.015) 103s + } 103s + if(FULLTEST) { 103s + leavein("quartic", 0.010) 103s + leavein("disc", 0.100) 103s + } 103s + 103s + ## bandwidth selection code blocks 103s + sigvec <- 0.01 * 2:15 103s + sigran <- range(sigvec) 103s + if(ALWAYS) { 103s + bw.ppl(redwood, sigma=sigvec) 103s + bw.CvL(redwood, sigma=sigvec) 103s + } 103s + if(FULLTEST) { 103s + bw.ppl(redwood, srange=sigran, ns=5) 103s + bw.CvL(redwood, srange=sigran, ns=5) 103s + } 103s + ## adaptive bandwidth 103s + if(ALWAYS) { 103s + a <- bw.abram(redwood) 103s + } 103s + if(FULLTEST) { 103s + a <- bw.abram(redwood, pilot=density(redwood, 0.2)) 103s + a <- bw.abram(redwood, smoother="densityVoronoi", at="pixels") 103s + } 103s + 103s + ## Kinhom 103s + if(ALWAYS) { 103s + lam <- density(redwood) 103s + K <- Kinhom(redwood, lam) 103s + 103s + lamX <- density(redwood, at="points") 103s + KX <- Kinhom(redwood, lamX) 103s + } 103s + 103s + ## test all code cases of new 'relrisk.ppp' algorithm 103s + pants <- function(..., X=ants, sigma=100, se=TRUE) { 103s + a <- relrisk(X, sigma=sigma, se=se, ...) 103s + return(TRUE) 103s + } 103s + if(ALWAYS) { 103s + pants() 103s + pants(diggle=TRUE) 103s + pants(edge=FALSE) 103s + pants(at="points") 103s + pants(casecontrol=FALSE) 103s + pants(relative=TRUE) 103s + pants(sigma=Inf) 103s + pants(sigma=NULL, varcov=diag(c(100,100)^2)) 103s + f <- 1/area(Window(ants)) 103s + pants(fudge=f) 103s + } 103s + if(FULLTEST) { 103s + pants(diggle=TRUE, at="points") 103s + pants(edge=FALSE, at="points", fudge=f) 103s + pants(casecontrol=FALSE, relative=TRUE) 103s + pants(casecontrol=FALSE,at="points") 103s + pants(relative=TRUE,at="points", fudge=f) 103s + pants(casecontrol=FALSE, relative=TRUE,at="points") 103s + pants(relative=TRUE, control="Cataglyphis", case="Messor", fudge=f) 103s + pants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 103s + pants(casecontrol=FALSE, case="Messor", se=FALSE) 103s + pants(case=2, at="pixels", relative=TRUE) 103s + pants(case=2, at="points", relative=TRUE) 103s + pants(case=2, at="pixels", relative=FALSE) 103s + pants(case=2, at="points", relative=FALSE) 103s + } 103s + if(ALWAYS) { 103s + ## underflow example from stackoverflow! 103s + funky <- scanpp("funky.tab", owin(c(4, 38), c(0.3, 17))) 103s + P <- relrisk(funky, 0.5) 103s + R <- relrisk(funky, 0.5, relative=TRUE) 103s + } 103s + ## more than 2 types 103s + if(ALWAYS) { 103s + pants(X=sporophores) 103s + pants(X=sporophores, sigma=20, at="points") 103s + pants(X=sporophores, sigma=20, at="points", fudge=f) 103s + bw.relrisk(sporophores, method="leastsquares") 103s + } 103s + if(FULLTEST) { 103s + pants(X=sporophores, sigma=20, relative=TRUE, at="points", fudge=f) 103s + pants(X=sporophores, sigma=20, at="pixels", se=FALSE) 103s + pants(X=sporophores, sigma=20, relative=TRUE, at="pixels", se=FALSE) 103s + bw.relrisk(sporophores, method="weightedleastsquares") 103s + } 103s + 103s + ## execute Smooth.ppp and Smoothfun.ppp in all cases 103s + stroke <- function(..., Y = longleaf, FUN=TRUE) { 103s + Z <- Smooth(Y, ..., at="pixels") 103s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 103s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 103s + if(FUN) { 103s + f <- Smoothfun(Y, ...) 103s + f(120, 80) 103s + f(Y[1:2]) 103s + f(Y[FALSE]) 103s + U <- as.im(f) 103s + } 103s + return(invisible(NULL)) 103s + } 103s + if(ALWAYS) { 103s + stroke() 103s + stroke(5, diggle=TRUE) 103s + stroke(5, geometric=TRUE) 103s + stroke(1e-6) # generates warning about small bandwidth 103s + stroke(5, weights=expression(x)) 103s + stroke(5, kernel="epa") 103s + stroke(sigma=Inf) 103s + stroke(varcov1=diag(c(1,1))) # 'anisotropic' code 103s + } 103s + if(FULLTEST) { 103s + Z <- as.im(function(x,y){abs(x)+1}, Window(longleaf)) 103s + stroke(5, weights=Z) 103s + stroke(5, weights=runif(npoints(longleaf))) 103s + stroke(varcov=diag(c(25, 36))) 103s + stroke(varcov=diag(c(25, 36)), weights=runif(npoints(longleaf))) 103s + stroke(5, Y=longleaf %mark% 1) 103s + stroke(5, Y=cut(longleaf,breaks=3)) 103s + stroke(5, weights=Z, geometric=TRUE) 103s + g <- function(x,y) { dnorm(x, sd=10) * dnorm(y, sd=10) } 103s + stroke(kernel=g, cutoff=30, FUN=FALSE) 103s + stroke(kernel=g, cutoff=30, scalekernel=TRUE, sigma=1, FUN=FALSE) 103s + } 103s + if(FULLTEST) { 103s + ## standard errors - single column of marks 103s + stroke(sigma=5, se=TRUE) 103s + stroke(sigma=5, se=TRUE, loctype="f") 103s + w <- runif(npoints(longleaf)) 103s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="i") 103s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="m") 103s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="i") 103s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="m") 103s + } 103s + 103s + niets <- markmean(longleaf, 9) 103s + 103s + strike <- function(..., Y=finpines) { 103s + Z <- Smooth(Y, ..., at="pixels") 103s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 103s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 103s + f <- Smoothfun(Y, ...) 103s + f(4, 1) 103s + f(Y[1:2]) 103s + f(Y[FALSE]) 103s + U <- as.im(f) 103s + return(invisible(NULL)) 103s + } 103s + if(ALWAYS) { 103s + strike() 103s + strike(sigma=1.5, kernel="epa") 103s + strike(varcov=diag(c(1.2, 2.1))) 103s + strike(sigma=1e-6) 103s + strike(sigma=Inf) 103s + } 103s + if(FULLTEST) { 103s + strike(sigma=1e-6, kernel="epa") 103s + strike(1.5, weights=runif(npoints(finpines))) 103s + strike(1.5, weights=expression(y)) 103s + strike(1.5, geometric=TRUE) 103s + strike(1.5, Y=finpines[FALSE]) 103s + flatfin <- finpines %mark% data.frame(a=rep(1, npoints(finpines)), b=2) 103s + strike(1.5, Y=flatfin) 103s + strike(1.5, Y=flatfin, geometric=TRUE) 103s + } 103s + if(FULLTEST) { 103s + ## standard errors - multivariate marks 103s + strike(sigma=1.5, se=TRUE) 103s + strike(sigma=1.5, se=TRUE, loctype="f") 103s + w <- runif(npoints(finpines)) 103s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="i") 103s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="m") 103s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="i") 103s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="m") 103s + } 103s + opx <- spatstat.options(densityTransform=FALSE) 103s + if(ALWAYS) { 103s + stroke(5, Y=longleaf[order(longleaf$x)], sorted=TRUE) 103s + } 103s + if(FULLTEST) { 103s + strike(1.5, Y=finpines[order(finpines$x)], sorted=TRUE) 103s + } 103s + spatstat.options(opx) 103s + 103s + ## detect special cases 103s + if(ALWAYS) { 103s + Smooth(longleaf[FALSE]) 103s + Smooth(longleaf, minnndist(longleaf)) 103s + Xconst <- cells %mark% 1 103s + Smooth(Xconst, 0.1) 103s + Smooth(Xconst, 0.1, at="points") 103s + Smooth(cells %mark% runif(42), sigma=Inf) 103s + Smooth(cells %mark% runif(42), sigma=Inf, at="points") 103s + Smooth(cells %mark% runif(42), sigma=Inf, at="points", leaveoneout=FALSE) 103s + Smooth(cut(longleaf, breaks=4)) 103s + } 103s + 103s + ## code not otherwise reached 103s + if(ALWAYS) { 103s + smoothpointsEngine(cells, values=rep(1, npoints(cells)), sigma=0.2) 103s + } 103s + if(FULLTEST) { 103s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=Inf) 103s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=1e-16) 103s + } 103s + 103s + ## validity of Smooth.ppp(at='points') 103s + Y <- longleaf %mark% runif(npoints(longleaf), min=41, max=43) 103s + Z <- Smooth(Y, 5, at="points", leaveoneout=TRUE) 103s + rZ <- range(Z) 103s + if(rZ[1] < 40 || rZ[2] > 44) 103s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=TRUE)") 103s + 103s + Z <- Smooth(Y, 5, at="points", leaveoneout=FALSE) 103s + rZ <- range(Z) 103s + if(rZ[1] < 40 || rZ[2] > 44) 103s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=FALSE)") 103s + 103s + ## compare Smooth.ppp results with different algorithms 103s + if(ALWAYS) { 103s + crosscheque(Smooth(longleaf, at="points", sigma=6)) 103s + wt <- runif(npoints(longleaf)) 103s + crosscheque(Smooth(longleaf, at="points", sigma=6, weights=wt)) 103s + } 103s + if(FULLTEST) { 103s + vc <- diag(c(25,36)) 103s + crosscheque(Smooth(longleaf, at="points", varcov=vc)) 103s + crosscheque(Smooth(longleaf, at="points", varcov=vc, weights=wt)) 103s + } 103s + ## drop-dimension coding errors 103s + if(FULLTEST) { 103s + X <- longleaf 103s + marks(X) <- cbind(marks(X), 1) 103s + Z <- Smooth(X, 5) 103s + 103s + ZZ <- bw.smoothppp(finpines, hmin=0.01, hmax=0.012, nh=2) # reshaping problem 103s + } 103s + 103s + ## geometric-mean smoothing 103s + if(ALWAYS) { 103s + U <- Smooth(longleaf, 5, geometric=TRUE) 103s + } 103s + if(FULLTEST) { 103s + UU <- Smooth(X, 5, geometric=TRUE) 103s + V <- Smooth(longleaf, 5, geometric=TRUE, at="points") 103s + VV <- Smooth(X, 5, geometric=TRUE, at="points") 103s + } 103s + 103s + if(FULLTEST) { 103s + ## isotropic and anisotropic cases of bw.smoothppp 103s + bi <- bw.smoothppp(longleaf) 103s + ba <- bw.smoothppp(longleaf, varcov1=diag(c(1,1))) 103s + ## should be equal 103s + if(abs(bi-ba) > 0.001) 103s + stop(paste("Inconsistency in bw.smoothppp: isotropic =", bi, 103s + "!=", ba, "= anisotropic")) 103s + } 103s + }) 105s > 105s > reset.spatstat.options() 105s > 105s > local({ 105s + if(ALWAYS) { 105s + #' Kmeasure, second.moment.engine 105s + #' Expansion of window 105s + Zno <- Kmeasure(redwood, sigma=0.2, expand=FALSE) 105s + Zyes <- Kmeasure(redwood, sigma=0.2, expand=TRUE) 105s + #' All code blocks 105s + sigmadouble <- rep(0.1, 2) 105s + diagmat <- diag(sigmadouble^2) 105s + generalmat <- matrix(c(1, 0.5, 0.5, 1)/100, 2, 2) 105s + Z <- Kmeasure(redwood, sigma=sigmadouble) 105s + Z <- Kmeasure(redwood, varcov=diagmat) 105s + Z <- Kmeasure(redwood, varcov=generalmat) 105s + A <- second.moment.calc(redwood, 0.1, what="all", debug=TRUE) 105s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 105s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 105s + D <- second.moment.calc(redwood, varcov=generalmat, what="all") 105s + PR <- pixellate(redwood) 105s + There were 22 warnings (use warnings() to see them) 105s DRno <- second.moment.calc(PR, 0.2, debug=TRUE, expand=FALSE, 105s + npts=npoints(redwood), obswin=Window(redwood)) 105s + DRyes <- second.moment.calc(PR, 0.2, debug=TRUE, expand=TRUE, 105s + npts=npoints(redwood), obswin=Window(redwood)) 105s + DR2 <- second.moment.calc(solist(PR, PR), 0.2, debug=TRUE, expand=TRUE, 105s + npts=npoints(redwood), obswin=Window(redwood)) 105s + Gmat <- generalmat * 100 105s + isoGauss <- function(x,y) {dnorm(x) * dnorm(y)} 105s + ee <- evaluate2Dkernel(isoGauss, runif(10), runif(10), 105s + varcov=Gmat, scalekernel=TRUE) 105s + isoGaussIm <- as.im(isoGauss, square(c(-3,3))) 105s + gg <- evaluate2Dkernel(isoGaussIm, runif(10), runif(10), 105s + varcov=Gmat, scalekernel=TRUE) 105s + ## experimental code 105s + op <- spatstat.options(developer=TRUE) 105s + DR <- density(redwood, 0.1) 105s + spatstat.options(op) 105s + } 105s + }) 106s smooth: maximum imaginary part= 4.97e-18 106s smooth: mass error= 0 106s 2nd moment measure: maximum imaginary part= 1.22e-16 106s 2nd moment measure: mass error= 0 106s smooth: maximum imaginary part= 2.39e-18 106s smooth: mass error= 0 106s 2nd moment measure: maximum imaginary part= 9.09e-17 106s 2nd moment measure: mass error= 0 106s smooth: maximum imaginary part= 6.82e-18 106s smooth: mass error= -2.13e-14 106s 2nd moment measure: maximum imaginary part= 4.07e-16 106s 2nd moment measure: mass error= 1.82e-12 106s smooth component 1 : maximum imaginary part= 6.82e-18 106s smooth component 1 : mass error= -2.13e-14 106s smooth component 2 : maximum imaginary part= 6.82e-18 106s smooth component 2 : mass error= -2.13e-14 106s 2nd moment measure: maximum imaginary part= 4.07e-16 106s 2nd moment measure: mass error= 1.82e-12 106s 2nd moment measure: maximum imaginary part= 4.07e-16 106s 2nd moment measure: mass error= 1.82e-12 106s > 106s > local({ 106s + if(FULLTEST) { 106s + #' bandwidth selection 106s + op <- spatstat.options(n.bandwidth=8) 106s + bw.diggle(cells) 106s + bw.diggle(cells, method="interpreted") # undocumented test 106s + ## bw.relrisk(urkiola, hmax=20) is tested in man/bw.relrisk.Rd 106s + bw.relrisk(urkiola, hmax=20, method="leastsquares") 106s + bw.relrisk(urkiola, hmax=20, method="weightedleastsquares") 106s + ZX <- density(swedishpines, at="points") 106s + bw.pcf(swedishpines, lambda=ZX) 106s + bw.pcf(swedishpines, lambda=ZX, 106s + bias.correct=FALSE, simple=FALSE, cv.method="leastSQ") 106s + spatstat.options(op) 106s + } 106s + }) 106s > 106s > local({ 106s + if(FULLTEST) { 106s + ## idw 106s + Z <- idw(longleaf, power=4) 106s + Z <- idw(longleaf, power=4, se=TRUE) 106s + ZX <- idw(longleaf, power=4, at="points") 106s + ZX <- idw(longleaf, power=4, at="points", se=TRUE) 106s + } 106s + if(ALWAYS) { 106s + ## former bug in densityVoronoi.ppp 106s + X <- redwood[1:2] 106s + A <- densityVoronoi(X, f=0.51, counting=FALSE, fixed=FALSE, nrep=50, verbose=FALSE) 106s + ## dodgy code blocks in densityVoronoi.R 106s + A <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE) 106s + B <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE, fixed=TRUE) 106s + D <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE) 106s + E <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE, fixed=TRUE) 106s + } 106s + if(FULLTEST) { 106s + #' adaptive kernel estimation 106s + d10 <- nndist(nztrees, k=10) 106s + d10fun <- distfun(nztrees, k=10) 106s + d10im <- as.im(d10fun) 106s + uN <- 2 * runif(npoints(nztrees)) 106s + AA <- densityAdaptiveKernel(nztrees, bw=d10) 106s + BB <- densityAdaptiveKernel(nztrees, bw=d10, weights=uN) 106s + DD <- densityAdaptiveKernel(nztrees, bw=d10fun, weights=uN) 106s + EE <- densityAdaptiveKernel(nztrees, bw=d10im, weights=uN) 106s + } 106s + }) 106s Computing 2 intensity estimates...1, 106s 2. 106s Done. 106s Computing 2 intensity estimates...1, 106s 2. 106s Done. 106s Computing 2 intensity estimates...1, 106s 2. 106s Done. 106s Computing 2 intensity estimates...1, 106s 2. 106s Done. 106s > 106s > local({ 106s + if(FULLTEST) { 106s + ## cases of 'intensity' etc 106s + a <- intensity(amacrine, weights=expression(x)) 106s + SA <- split(amacrine) 106s + a <- intensity(SA, weights=expression(x)) 106s + a <- intensity(SA, weights=amacrine$x) 106s + 106s + ## check infrastructure for 'densityfun' 106s + f <- densityfun(cells, 0.05) 106s + Z <- as.im(f) 106s + Z <- as.im(f, W=square(0.5)) 106s + } 106s + }) 106s > 106s > local({ 106s + if(FULLTEST) { 106s + ## other cases of SpatialQuantile.ppp 106s + X <- longleaf 106s + marks(X) <- round(marks(X), -1) 106s + Z <- SpatialMedian(X, 30, type=4) 106s + ZX <- SpatialMedian(X, 30, type=4, at="points") 106s + ZXP <- SpatialMedian(X, 30, at="points", leaveoneout=FALSE) 106s + } 106s + }) 106s > 106s > 106s > 106s > reset.spatstat.options() 106s > 106s > 106s BEGIN TEST testsEtoF.R 107s 107s R version 4.4.3 (2025-02-28) -- "Trophy Case" 107s Copyright (C) 2025 The R Foundation for Statistical Computing 107s Platform: x86_64-pc-linux-gnu 107s 107s R is free software and comes with ABSOLUTELY NO WARRANTY. 107s You are welcome to redistribute it under certain conditions. 107s Type 'license()' or 'licence()' for distribution details. 107s 107s R is a collaborative project with many contributors. 107s Type 'contributors()' for more information and 107s 'citation()' on how to cite R or R packages in publications. 107s 107s Type 'demo()' for some demos, 'help()' for on-line help, or 107s 'help.start()' for an HTML browser interface to help. 107s Type 'q()' to quit R. 107s 107s > #' 107s > #' Header for all (concatenated) test files 107s > #' 107s > #' Require spatstat.explore 107s > #' Obtain environment variable controlling tests. 107s > #' 107s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 107s > 107s > require(spatstat.explore) 107s Loading required package: spatstat.explore 107s Loading required package: spatstat.data 107s Loading required package: spatstat.univar 107s spatstat.univar 3.1-2 107s Loading required package: spatstat.geom 107s spatstat.geom 3.3-6 107s Loading required package: spatstat.random 107s spatstat.random 3.3-3 107s Loading required package: nlme 107s spatstat.explore 3.3-4 107s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 107s > ALWAYS <- TRUE 107s > cat(paste("--------- Executing", 107s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 107s + "test code -----------\n")) 107s --------- Executing **RESTRICTED** subset of test code ----------- 107s > # 107s > # tests/envelopes.R 107s > # 107s > # Test validity of envelope data 107s > # 107s > # $Revision: 1.29 $ $Date: 2024/01/10 13:45:29 $ 107s > # 107s > 107s > local({ 107s + 107s + 107s + 107s + ## check envelope calls from 'alltypes' 107s + if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE) 107s + if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE) 107s + ## check 'transform' idioms 107s + if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x)) 107s + if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x)) 107s + 107s + 107s + # check conditional simulation 107s + if(FULLTEST) { 107s + e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE) 107s + e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE) 107s + e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE) 107s + e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks 107s + e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE) 107s + } 107s + 107s + 107s + ## check pooling of envelopes in global case 107s + E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE) 107s + E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE) 107s + p12 <- pool(E1, E2) 107s + p12 <- pool(E1, E2, savefuns=TRUE) 107s + if(FULLTEST) { 107s + F1 <- envelope(cells, Kest, nsim=5, 107s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 107s + F2 <- envelope(cells, Kest, nsim=12, 107s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 107s + p12 <- pool(F1, F2) 107s + p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE) 107s + E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE, 107s + ginterval=c(0.05, 0.15)) 107s + E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE, 107s + ginterval=c(0.05, 0.15)) 107s + p12r <- pool(E1r, E2r) 107s + } 107s + 107s + if(FULLTEST) { 107s + #' as.data.frame.envelope 107s + Nsim <- 5 107s + E <- envelope(cells, nsim=Nsim, savefuns=TRUE) 107s + A <- as.data.frame(E) 107s + B <- as.data.frame(E, simfuns=TRUE) 107s + stopifnot(ncol(B) - ncol(A) == Nsim) 107s + } 107s + 107s + if(FULLTEST) { 107s + #' cases not covered elsewhere 107s + A <- envelope(cells, nsim=5, alternative="less", 107s + do.pwrong=TRUE, use.theory=FALSE, 107s + savepatterns=TRUE, savefuns=TRUE) 107s + print(A) 107s + B <- envelope(A, nsim=5, savefuns=TRUE) 107s + D <- envelope(cells, "Lest", nsim=5) 107s + 107s + UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE) 107s + 107s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE) 107s + AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE) 107s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 107s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 107s + 107s + #' spotted by Art Stock - bugs in ratfv class support 107s + BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="border") 107s + CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border") 107s + DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="trans") 107s + EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans") 107s + 107s + #' envelopes based on sample variance 107s + E <- envelope(cells, nsim=8, VARIANCE=TRUE) 107s + G <- envelope(cells, nsim=8, VARIANCE=TRUE, 107s + use.theory=FALSE, do.pwrong=TRUE) 107s + print(G) 107s + #' summary method 107s + summary(E) 107s + summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42)))) 107s + #' weights argument 107s + H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 107s + H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 107s + J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 107s + J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 107s + #' pooling with weights 107s + H <- pool(H1, H2) 107s + J <- pool(J1, J2) 107s + #' pooling envelopes with non-identical attributes 107s + H0 <- envelope(cells, nsim=4, savefuns=TRUE) 107s + HH <- pool(H0, H1) 107s + #' malformed argument 'simulate' 107s + A <- replicate(3, list(list(runifpoint(ex=cells)))) # list(list(ppp), list(ppp), list(ppp)) 107s + E <- envelope(cells, simulate=A, nsim=3) 107s + #' undocumented/secret 107s + K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE) 107s + #' so secret I've even forgotten how to do it 107s + M <- envelope(cells, nsim=4, internal=list(eject="patterns")) 107s + } 107s + 107s + 107s + if(ALWAYS) { 107s + #' Test robustness of envelope() sorting procedure when NA's are present 107s + #' Fails with spatstat.utils 1.12-0 107s + set.seed(42) 107s + EP <- envelope(longleaf, pcf, nsim=10, nrank=2) 107s + 107s + #' Test case when the maximum permitted number of failures is exceeded 107s + X <- amacrine[1:153] # contains exactly one point with mark='off' 107s + #' High probability of generating a pattern with no marks = 'off' 107s + E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn") 107s + A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2) 107s + } 107s + 107s + if(ALWAYS) { 107s + #' Internals: envelope.matrix 107s + Y <- matrix(rnorm(200), 10, 20) 107s + rr <- 1:10 107s + oo <- rnorm(10) 107s + zz <- numeric(10) 107s + E <- envelope(Y, rvals=rr, observed=oo, nsim=10) 107s + E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10) 107s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 107s + type="global", use.theory=TRUE) 107s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 107s + type="global", use.theory=TRUE, nsim=10) 107s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 107s + type="global", use.theory=FALSE, nsim=10) 107s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 107s + nsim=10, nsim2=10) 107s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 107s + jsim=1:10, jsim.mean=11:20) 107s + if(FULLTEST) print(E) 107s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 107s + nsim=10, jsim.mean=11:20) 107s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 107s + jsim=1:10, nsim2=10) 107s + } 107s + 107s + if(ALWAYS) { 107s + #' quirk with handmade summary functions ('conserve' attribute) 107s + Kdif <- function(X, r=NULL) { # note no ellipsis 107s + Y <- split(X) 107s + K1 <- Kest(Y[[1]], r=r) 107s + K2 <- Kest(Y[[2]], r=r) 107s + D <- eval.fv(K1-K2) 107s + return(D) 107s + } 107s + envelope(amacrine, Kdif, nsim=3) 107s + } 107s + 107s + 107s + ## close 'local' 107s + }) 108s Generating 4 simulations of CSR ... 108s 1, 2, 3, 108s 4. 108s 108s Done. 108s Generating 5 simulations of CSR ... 108s 1, 2, 3, 4, 108s 5. 108s 108s Done. 108s Generating 12 simulations of CSR ... 108s 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 108s 12. 108s 108s Done. 108s Generating 10 simulations of CSR ... 108s 1, 2, 3, 4, 5, 6, 7, 8, 9, 108s 10. 108s 108s Done. 108s Generating 39 simulations of CSR ... 108s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 108s No points have mark i = off 108s [retrying] 108s 1, 2, 3, 4, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 108s No points have mark i = off 108s [retrying] 108s 5, 6, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 108s No points have mark i = off 108s 108s Done. 108s Generating 3 simulations of CSR ... 108s 1, 2, 108s 3. 108s 108s Done. 108s Pointwise critical envelopes for K1(r)-K2(r) 108s and observed value for ‘amacrine’ 108s Edge correction: “iso” 108s Obtained from 3 simulations of CSR 108s Alternative: two.sided 108s Significance level of pointwise Monte Carlo test: 2/4 = 0.5 108s ................................................................................ 108s Math.label 108s r r 108s obs hat((K1-K2))[obs](r) 108s theo (K1-K2)[theo](r) 108s lo hat((K1-K2))[lo](r) 108s hi hat((K1-K2))[hi](r) 108s Description 108s r distance argument r 108s obs observed value of K1(r)-K2(r) for data pattern 108s theo theoretical value of K1(r)-K2(r) for CSR 108s lo lower pointwise envelope of K1(r)-K2(r) from simulations 108s hi upper pointwise envelope of K1(r)-K2(r) from simulations 108s ................................................................................ 108s Default plot formula: .~r 108s where “.” stands for ‘obs’, ‘theo’, ‘hi’, ‘lo’ 108s Columns ‘lo’ and ‘hi’ will be plotted as shading (by default) 108s Recommended range of argument r: [0, 0.25] 108s Available range of argument r: [0, 0.25] 108s Unit of length: 662 microns 108s > # 108s > # tests/fastK.R 108s > # 108s > # check fast and slow code for Kest 108s > # and options not tested elsewhere 108s > # 108s > # $Revision: 1.5 $ $Date: 2020/04/28 12:58:26 $ 108s > # 108s > if(ALWAYS) { 108s + local({ 108s + ## fast code 108s + Kb <- Kest(cells, nlarge=0) 108s + Ku <- Kest(cells, correction="none") 108s + Kbu <- Kest(cells, correction=c("none", "border")) 108s + ## slow code, full set of corrections, sqrt transformation, ratios 108s + Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE) 108s + ## Lotwick-Silverman var approx (rectangular window) 108s + Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE) 108s + ## Code for large dataset 108s + nbig <- .Machine$integer.max 108s + if(!is.null(nbig)) { 108s + nn <- ceiling(sqrt(nbig)) 108s + if(nn < 1e6) Kbig <- Kest(runifpoint(nn), 108s + correction=c("border", "bord.modif", "none"), 108s + ratio=TRUE) 108s + } 108s + 108s + ## Kinhom 108s + lam <- density(cells, at="points", leaveoneout=TRUE) 108s + ## fast code 108s + Kib <- Kinhom(cells, lam, nlarge=0) 108s + Kiu <- Kest(cells, lam, correction="none") 108s + Kibu <- Kest(cells, lam, correction=c("none", "border")) 108s + ## slow code 108s + Lidd <- Linhom(unmark(demopat), sigma=bw.scott) 108s + }) 108s + 108s + } 108s Warning messages: 108s 1: Exceeded maximum permissible number of (maxnerr = 2) when evaluating summary function for simulated point patterns 108s 2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) : 108s 3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns 108s number of data points exceeds 0 - computing border correction estimate only 111s number of data points exceeds 0 - computing border correction estimate only 111s Warning message: 111s Periodic correction is not defined for non-rectangular windows 111s > ## 111s > ## tests/fvproblems.R 111s > ## 111s > ## problems with fv, ratfv and fasp code 111s > ## 111s > ## $Revision: 1.15 $ $Date: 2020/04/28 12:58:26 $ 111s > 111s > #' This appears in the workshop notes 111s > #' Problem detected by Martin Bratschi 111s > 111s > if(FULLTEST) { 111s + local({ 111s + Jdif <- function(X, ..., i) { 111s + Jidot <- Jdot(X, ..., i=i) 111s + J <- Jest(X, ...) 111s + dif <- eval.fv(Jidot - J) 111s + return(dif) 111s + } 111s + Z <- Jdif(amacrine, i="on") 111s + }) 111s + } 111s > #' 111s > #' Test mathlegend code 111s > #' 111s > local({ 111s + K <- Kest(cells) 111s + if(FULLTEST) { 111s + plot(K) 111s + plot(K, . ~ r) 111s + plot(K, . - theo ~ r) 111s + } 111s + if(ALWAYS) { 111s + plot(K, sqrt(./pi) ~ r) 111s + } 111s + if(FULLTEST) { 111s + plot(K, cbind(iso, theo) ~ r) 111s + plot(K, cbind(iso, theo) - theo ~ r) 111s + plot(K, sqrt(cbind(iso, theo)/pi) ~ r) 111s + plot(K, cbind(iso/2, -theo) ~ r) 111s + plot(K, cbind(iso/2, trans/2) - theo ~ r) 111s + } 111s + if(FULLTEST) { 111s + ## test expansion of .x and .y 111s + plot(K, . ~ .x) 111s + plot(K, . - theo ~ .x) 111s + plot(K, .y - theo ~ .x) 111s + } 111s + if(ALWAYS) { 111s + plot(K, sqrt(.y) - sqrt(theo) ~ .x) 111s + } 111s + 111s + # problems with parsing weird strings in levels(marks(X)) 111s + # noted by Ulf Mehlig 111s + if(ALWAYS) { 111s + levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis") 111s + plot(Kcross(amacrine)) 111s + plot(alltypes(amacrine, "K")) 111s + } 111s + if(FULLTEST) { 111s + plot(alltypes(amacrine, "J")) 111s + plot(alltypes(amacrine, pcfcross)) 111s + } 111s + }) 111s > 111s > #' 111s > #' Test quirks related to 'alim' attribute 111s > 111s > if(FULLTEST) { 111s + local({ 111s + K <- Kest(cells) 111s + attr(K, "alim") <- NULL 111s + plot(K) 111s + attr(K, "alim") <- c(0, 0.1) 111s + plot(tail(K)) 111s + }) 111s + } 111s > 111s > #' 111s > #' Check that default 'r' vector passes the test for fine spacing 111s > 111s > if(ALWAYS) { 111s + local({ 111s + a <- Fest(cells) 111s + A <- Fest(cells, r=a$r) 111s + b <- Hest(heather$coarse) 111s + B <- Hest(heather$coarse, r=b$r) 111s + # from Cenk Icos 111s + X <- runifpoint(100, owin(c(0,3), c(0,10))) 111s + FX <- Fest(X) 111s + FXr <- Fest(X, r=FX$r) 111s + JX <- Jest(X) 111s + }) 111s + } 111s > 111s > ##' various functionality in fv.R 111s > 111s > if(ALWAYS) { 111s + local({ 111s + M <- cbind(1:20, matrix(runif(100), 20, 5)) 111s + A <- as.fv(M) 111s + fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)") 111s + A <- rename.fv(A, "M", quote(M(r))) 111s + A <- tweak.fv.entry(A, "V1", new.tag="r") 111s + A[,3] <- NULL 111s + A$hogwash <- runif(nrow(A)) 111s + fvnames(A, ".") <- NULL 111s + #' bind.fv with qualitatively different functions 111s + GK <- harmonise(G=Gest(cells), K=Kest(cells)) 111s + G <- GK$G 111s + K <- GK$K 111s + ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10)) 111s + U <- bind.fv(G, K[ss, ], clip=TRUE) 111s + #' 111s + H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2) 111s + H <- rebadge.as.dotfun(K, "H", "inhom", 3) 111s + #' text layout 111s + op <- options(width=27) 111s + print(K) 111s + options(width=18) 111s + print(K) 111s + options(op) 111s + #' collapse.fv 111s + Kb <- Kest(cells, correction="border") 111s + Ki <- Kest(cells, correction="isotropic") 111s + collapse.fv(Kb, Ki, same="theo") 111s + collapse.fv(anylist(B=Kb, I=Ki), same="theo") 111s + collapse.fv(anylist(B=Kb), I=Ki, same="theo") 111s + Xlist <- replicate(3, runifpoint(30), simplify=FALSE) 111s + Klist <- anylapply(Xlist, Kest) 111s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 111s + names(Klist) <- LETTERS[24:26] 111s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 111s + }) 111s + } 111s Function value object 111s (class ‘fv’) 111s for the function r -> K(r) 111s ........................... 111s Math.label 111s r r 111s theo K[pois](r) 111s border hat(K)[bord](r) 111s trans hat(K)[trans](r) 111s iso hat(K)[iso](r) 111s Description 111s r distance argument r 111s theo theoretical [..] 111s border [..] 111s trans [..] 111s iso [..] 111s ........................... 111s Default plot formula: .~r 111s where “.” stands for 111s ‘iso’, ‘trans’, 111s ‘border’, ‘theo’ 111s Recommended range of 111s argument r: [0, 0.25] 111s Available range of 111s argument r: [0, 0.25] 111s Function value 111s object (class 111s ‘fv’) 111s for the function 111s r -> K(r) 111s .................. 111s Math.label 111s r r 111s theo K[pois](r) 111s border hat(K)[bord](r) 111s trans hat(K)[trans](r) 111s iso hat(K)[iso](r) 111s Description 111s r [..] 111s theo [..] 111s border [..] 111s trans [..] 111s iso [..] 111s .................. 111s Default plot 111s formula: .~r 111s where “.” 111s stands for 111s ‘iso’, 111s ‘trans’, 111s ‘border’, 111s ‘theo’ 111s Recommended range 111s of argument r: 111s [0, 0.25] 111s Available range 111s of argument r: 111s [0, 0.25] 111s Function value object (class ‘fv’) 111s for the function r -> K(r) 111s ................................................................ 111s Math.label Description 111s r r distance argument r 111s theo K[pois](r) theoretical Poisson K(r) 111s Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r) 111s Xiso X~hat(K)[iso](r) X isotropic-corrected estimate of K(r) 111s Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r) 111s Yiso Y~hat(K)[iso](r) Y isotropic-corrected estimate of K(r) 111s Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r) 111s Ziso Z~hat(K)[iso](r) Z isotropic-corrected estimate of K(r) 111s ................................................................ 111s Default plot formula: .~.x 111s where “.” stands for ‘theo’, ‘Xborder’, ‘Xiso’, ‘Yborder’, 111s ‘Yiso’, ‘Zborder’, ‘Ziso’ 111s Recommended range of argument r: [0, 0.25] 111s Available range of argument r: [0, 0.25] 111s > 111s > if(FULLTEST) { 111s + local({ 111s + ## rat 111s + K <- Kest(cells, ratio=TRUE) 111s + G <- Gest(cells, ratio=TRUE) 111s + print(K) 111s + compatible(K, K) 111s + compatible(K, G) 111s + H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE) 111s + }) 111s + } 111s > 111s > if(FULLTEST) { 111s + local({ 111s + ## bug in Jmulti.R colliding with breakpts.R 111s + B <- owin(c(0,3), c(0,10)) 111s + Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B)) 111s + JDX <- Jdot(Y) 111s + JCX <- Jcross(Y) 111s + Jdif <- function(X, ..., i) { 111s + Jidot <- Jdot(X, ..., i=i) 111s + J <- Jest(X, ...) 111s + dif <- eval.fv(Jidot - J) 111s + return(dif) 111s + } 111s + E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y))) 111s + }) 111s + } 111s > 111s > if(FULLTEST) { 111s + local({ 111s + #' fasp axes, title, dimnames 111s + a <- alltypes(amacrine) 111s + a$title <- NULL 111s + plot(a, samex=TRUE, samey=TRUE) 111s + dimnames(a) <- lapply(dimnames(a), toupper) 111s + 111s + b <- as.fv(a) 111s + }) 111s + } 111s > 111s > if(FULLTEST) { 111s + local({ 111s + ## plot.anylist (fv) 111s + b <- anylist(A=Kcross(amacrine), B=Kest(amacrine)) 111s + plot(b, equal.scales=TRUE, main=expression(sqrt(pi))) 111s + plot(b, arrange=FALSE) 111s + }) 111s + } 111s > 111s Warning message: 111s In bind.fv(G, K[ss, ], clip = TRUE) : 111s The column name ‘theo’ was duplicated. Unique names were generated 111s BEGIN TEST testsGtoJ.R 111s 111s R version 4.4.3 (2025-02-28) -- "Trophy Case" 111s Copyright (C) 2025 The R Foundation for Statistical Computing 111s Platform: x86_64-pc-linux-gnu 111s 111s R is free software and comes with ABSOLUTELY NO WARRANTY. 111s You are welcome to redistribute it under certain conditions. 111s Type 'license()' or 'licence()' for distribution details. 111s 111s R is a collaborative project with many contributors. 111s Type 'contributors()' for more information and 111s 'citation()' on how to cite R or R packages in publications. 111s 111s Type 'demo()' for some demos, 'help()' for on-line help, or 111s 'help.start()' for an HTML browser interface to help. 111s Type 'q()' to quit R. 111s 111s > #' 111s > #' Header for all (concatenated) test files 111s > #' 111s > #' Require spatstat.explore 111s > #' Obtain environment variable controlling tests. 111s > #' 111s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 111s > 111s > require(spatstat.explore) 111s Loading required package: spatstat.explore 111s Loading required package: spatstat.data 112s Loading required package: spatstat.univar 112s spatstat.univar 3.1-2 112s Loading required package: spatstat.geom 112s spatstat.geom 3.3-6 112s Loading required package: spatstat.random 112s spatstat.random 3.3-3 112s Loading required package: nlme 112s spatstat.explore 3.3-4 112s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 112s > ALWAYS <- TRUE 112s > cat(paste("--------- Executing", 112s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 112s + "test code -----------\n")) 112s --------- Executing **RESTRICTED** subset of test code ----------- 112s > ## 112s > ## tests/gcc323.R 112s > ## 112s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 112s > ## 112s > if(ALWAYS) { # depends on hardware 112s + local({ 112s + # critical R values that provoke GCC bug #323 112s + a <- marktable(lansing, R=0.25) 112s + a <- marktable(lansing, R=0.21) 112s + a <- marktable(lansing, R=0.20) 112s + a <- marktable(lansing, R=0.10) 112s + }) 112s + } 113s > #' tests/hypotests.R 113s > #' Hypothesis tests 113s > #' 113s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 113s > 113s > if(FULLTEST) { 113s + local({ 113s + 113s + hopskel.test(redwood, method="MonteCarlo", nsim=5) 113s + 113s + #' quadrat test - spatial methods 113s + a <- quadrat.test(redwood, 3) 113s + domain(a) 113s + shift(a, c(1,1)) 113s + 113s + #' quadrat test - correctness of mapping from table to quadrats 113s + Q2 <- quadratcount(humberside, 2, 3) 113s + T2 <- suppressWarnings(quadrat.test(Q2)) 113s + R2 <- cbind(as.numeric(t(Q2)), round(10 * residuals(T2))) 113s + R2correct <- cbind(c(2, 20, 13, 11, 34, 123), 113s + c(-46, -12, -62, -41, 50, 134)) 113s + if(!all(R2 == R2correct)) 113s + stop("Incorrect count-residual map for quadrat.test(2,3)") 113s + 113s + Q5 <- quadratcount(humberside, 5, 3) 113s + T5 <- suppressWarnings(quadrat.test(Q5)) 113s + R5 <- cbind(as.numeric(t(Q5)), round(10 * residuals(T5))) 113s + R5correct <- cbind( 113s + c( 0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3), 113s + c(-19, -33, -42, 16, -37, -49, -28, -35, -5, -21, 295, 40, -32)) 113s + if(!all(R5 == R5correct)) 113s + stop("Incorrect count-residual map for quadrat.test(5,3)") 113s + 113s + #' cases of studpermu.test 113s + #' X is a hyperframe 113s + b <- studpermu.test(pyramidal, nperm=9) 113s + b <- studpermu.test(pyramidal, nperm=9, use.Tbar=TRUE) 113s + #' X is a list of lists of ppp 113s + ZZ <- split(pyramidal$Neurons, pyramidal$group) 113s + bb <- studpermu.test(ZZ, nperm=9) 113s + 113s + #' Issue #115 113s + X <- runifpoint(50, nsim = 3) 113s + Y <- runifpoint(3000, nsim = 3) 113s + h <- hyperframe(ppp = c(X, Y), group = rep(1:2, 3)) 113s + studpermu.test(h, ppp ~ group) 113s + 113s + #' scan test 113s + Z <- scanmeasure(cells, 0.1, method="fft") 113s + rr <- c(0.05, 1) 113s + scan.test(amacrine, rr, nsim=5, 113s + method="binomial", alternative="less") 113s + }) 113s + } 113s > # 113s > # tests/imageops.R 113s > # 113s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 113s > # 113s > 113s > 113s > if(FULLTEST) { 113s + local({ 113s + #' case of "[.im" and "[<-.im" where index is an ssf 113s + d <- distmap(cells, dimyx=32) 113s + Empty <- cells[FALSE] 113s + EmptyFun <- ssf(Empty, numeric(0)) 113s + ff <- d[EmptyFun] 113s + d[EmptyFun] <- 42 113s + 113s + #' Smooth.im -> blur.im with sigma=NULL 113s + Z <- as.im(function(x,y) { x - y }, letterR, dimyx=32) 113s + ZS <- Smooth(Z) 113s + 113s + #' deprecated -> im.apply(DA, which.max) 113s + Z <- which.max.im(bei.extra) 113s + 113s + #' rotmean 113s + U <- rotmean(Z, origin="midpoint", result="im", padzero=FALSE) 113s + 113s + #' cases of distcdf 113s + distcdf(cells[1:5]) 113s + distcdf(W=cells[1:5], dW=1:5) 113s + distcdf(W=Window(cells), V=cells[1:5]) 113s + distcdf(W=Window(cells), V=cells[1:5], dV=1:5) 113s + }) 113s + } 113s > 113s > 113s BEGIN TEST testsK.R 113s 113s R version 4.4.3 (2025-02-28) -- "Trophy Case" 113s Copyright (C) 2025 The R Foundation for Statistical Computing 113s Platform: x86_64-pc-linux-gnu 113s 113s R is free software and comes with ABSOLUTELY NO WARRANTY. 113s You are welcome to redistribute it under certain conditions. 113s Type 'license()' or 'licence()' for distribution details. 113s 113s R is a collaborative project with many contributors. 113s Type 'contributors()' for more information and 113s 'citation()' on how to cite R or R packages in publications. 113s 113s Type 'demo()' for some demos, 'help()' for on-line help, or 113s 'help.start()' for an HTML browser interface to help. 113s Type 'q()' to quit R. 113s 113s > #' 113s > #' Header for all (concatenated) test files 113s > #' 113s > #' Require spatstat.explore 113s > #' Obtain environment variable controlling tests. 113s > #' 113s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 113s > 113s > require(spatstat.explore) 113s Loading required package: spatstat.explore 113s Loading required package: spatstat.data 114s Loading required package: spatstat.univar 114s spatstat.univar 3.1-2 114s Loading required package: spatstat.geom 114s spatstat.geom 3.3-6 114s Loading required package: spatstat.random 114s spatstat.random 3.3-3 114s Loading required package: nlme 114s spatstat.explore 3.3-4 114s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 114s > ALWAYS <- TRUE 114s > cat(paste("--------- Executing", 114s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 114s + "test code -----------\n")) 114s --------- Executing **RESTRICTED** subset of test code ----------- 114s > #' 114s > #' tests/kernelstuff.R 114s > #' 114s > #' $Revision: 1.2 $ $Date: 2023/11/05 01:49:45 $ 114s > 114s > local({ 114s + if(FULLTEST) { 114s + #' test all cases in kernels.R 114s + kernames <- c("gaussian", "rectangular", "triangular", 114s + "epanechnikov", "biweight", "cosine", "optcosine") 114s + X <- rnorm(20) 114s + U <- runif(20) 114s + for(ker in kernames) { 114s + dX <- dkernel(X, ker) 114s + fX <- pkernel(X, ker) 114s + qU <- qkernel(U, ker) 114s + m0 <- kernel.moment(0, 0, ker) 114s + m1 <- kernel.moment(1, 0, ker) 114s + m2 <- kernel.moment(2, 0, ker) 114s + m3 <- kernel.moment(3, 0, ker) 114s + } 114s + } 114s + }) 114s > 114s > #' 114s > #' tests/Kfuns.R 114s > #' 114s > #' Various K and L functions and pcf 114s > #' 114s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 114s > #' 114s > #' Assumes 'EveryStart.R' was run 114s > 114s > if(FULLTEST) { 114s + Cells <- cells 114s + Amacrine <- amacrine 114s + Redwood <- redwood 114s + } else { 114s + ## reduce numbers of data + dummy points 114s + spatstat.options(npixel=32, ndummy.min=16) 114s + Cells <- cells[c(FALSE, TRUE)] 114s + Amacrine <- amacrine[c(FALSE, TRUE)] 114s + Redwood <- redwood[c(FALSE, TRUE)] 114s + } 114s > 114s > 114s > myfun <- function(x,y){(x+1) * y } # must be outside 114s > 114s > local({ 114s + if(FULLTEST) { 114s + #' supporting code 114s + rmax.rule("Kscaled", owin(), 42) 114s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 114s + "polygonal", TRUE) 114s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 114s + "mask", TRUE) 114s + implemented.for.K(c("border", "isotropic"), "mask", TRUE) 114s + implemented.for.K(c("border", "isotropic"), "mask", FALSE) 114s + #' shortcuts 114s + D <- density(Cells) 114s + K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 114s + K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 114s + allcor <- c("none", "border", "bord.modif","isotropic", "translate") 114s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor) 114s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 114s + weights=D) 114s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 114s + use.integers=FALSE) 114s + #' Kest special code blocks 114s + K <- Kest(Cells, var.approx=TRUE, ratio=FALSE) 114s + Z <- distmap(Cells) + 1 114s + Kb <- Kest(Cells, correction=c("border","bord.modif"), 114s + weights=Z, ratio=TRUE) 114s + Kn <- Kest(Cells, correction="none", 114s + weights=Z, ratio=TRUE) 114s + Knb <- Kest(Cells, correction=c("border","bord.modif","none"), 114s + weights=Z, ratio=TRUE) 114s + } 114s + if(ALWAYS) { 114s + bigint <- 50000 # This is only "big" on a 32-bit system where 114s + # sqrt(.Machine$integer.max) = 46340.9 114s + X <- runifpoint(bigint) 114s + Z <- as.im(1/bigint, owin()) 114s + Kb <- Kest(X, correction=c("border","bord.modif"), 114s + rmax=0.02, weights=Z, ratio=TRUE) 114s + } 114s + if(FULLTEST) { 114s + Kn <- Kest(X, correction="none", 114s + rmax=0.02, weights=Z, ratio=TRUE) 114s + Knb <- Kest(X, correction=c("border","bord.modif","none"), 114s + rmax=0.02, weights=Z, ratio=TRUE) 114s + #' pcf.ppp special code blocks 114s + pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE) 114s + pc <- pcf(Cells, domain=square(0.5)) 114s + pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE) 114s + pw <- pcf(Redwood, correction="none") 114s + pwr <- pcf(Redwood, correction="none", ratio=TRUE) 114s + pv <- pcf(Redwood, kernel="rectangular") 114s + p1 <- pcf(Redwood[1]) 114s + #' pcf.fv 114s + K <- Kest(Redwood) 114s + g <- pcf(K, method="a") 114s + g <- pcf(K, method="c") 114s + g <- pcf(K, method="d") 114s + #' Kinhom code blocks 114s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 114s + lambda <- 100 * X$x 114s + Kin <- Kinhom(X, lambda, correction=c("none", "border")) 114s + lambda2 <- outer(lambda, lambda, "*") 114s + Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE, 114s + correction=c("translate", "isotropic")) 114s + } 114s + if(ALWAYS) { 114s + #' edge corrections 114s + rr <- rep(0.1, npoints(Cells)) 114s + eC <- edge.Ripley(Cells, rr) 114s + eI <- edge.Ripley(Cells, rr, method="interpreted") 114s + if(max(abs(eC-eI)) > 0.1) 114s + stop("Ripley edge correction results do not match") 114s + } 114s + if(FULLTEST) { 114s + a <- rmax.Ripley(square(1)) 114s + a <- rmax.Rigid(square(1)) 114s + a <- rmax.Ripley(as.polygonal(square(1))) 114s + a <- rmax.Rigid(as.polygonal(square(1))) 114s + a <- rmax.Ripley(letterR) 114s + a <- rmax.Rigid(letterR) 114s + } 114s + if(ALWAYS) { 114s + #' run slow code for edge correction and compare results 114s + op <- spatstat.options(npixel=128) 114s + X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)] 114s + Window(X) <- as.polygonal(Window(X)) 114s + Eapprox <- edge.Trans(X) 114s + Eexact <- edge.Trans(X, exact=TRUE) 114s + maxrelerr <- max(abs(1 - range(Eapprox/Eexact))) 114s + if(maxrelerr > 0.1) 114s + stop(paste("Exact and approximate algorithms for edge.Trans disagree by", 114s + paste0(round(100*maxrelerr), "%")), 114s + call.=FALSE) 114s + spatstat.options(op) 114s + } 114s + }) 115s > 115s > local({ 115s + if(FULLTEST) { 115s + #' ---- multitype ------ 115s + K <- Kcross(Amacrine, correction=c("none", "bord.modif")) 115s + K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"), 115s + ratio=TRUE) 115s + #' inhomogeneous multitype 115s + K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine)) 115s + K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points")) 115s + K5 <- Kcross.inhom(Amacrine, correction="bord.modif") 115s + #' markconnect, markcorr 115s + M <- markconnect(Amacrine, "on", "off", normalise=TRUE) 115s + M <- markcorr(longleaf, normalise=TRUE, 115s + correction=c("isotropic", "translate", "border", "none")) 115s + M <- markcorr(longleaf, normalise=TRUE, fargs=list()) 115s + #' Kmark (=markcorrint) 115s + X <- runifpoint(100) %mark% runif(100) 115s + km <- Kmark(X, f=atan2) 115s + km <- Kmark(X, f1=sin) 115s + km <- Kmark(X, f="myfun") 115s + aa <- Kmark(X, normalise=FALSE, returnL=FALSE) 115s + aa <- Kmark(X, normalise=FALSE, returnL=TRUE) 115s + aa <- Kmark(X, normalise=TRUE, returnL=FALSE) 115s + aa <- Kmark(X, normalise=TRUE, returnL=TRUE) 115s + } 115s + }) 115s > 115s > local({ 115s + if(FULLTEST) { 115s + #' various modified K functions 115s + #' 115s + #' directional K functions 115s + #' 115s + a <- Ksector(swedishpines, 115s + -pi/2, pi/2, units="radians", 115s + correction=c("none", "border", "bord.modif", 115s + "Ripley", "translate"), 115s + ratio=TRUE) 115s + plot(a) 115s + #' 115s + #' local K functions 115s + #' 115s + Z <- as.im(intensity(swedishpines), W=Window(swedishpines)) 115s + ZX <- Z[swedishpines] 115s + a <- localLinhom(swedishpines, lambda=Z) 115s + a <- localLinhom(swedishpines, lambda=ZX) 115s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 115s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 115s + a <- localLcross(Amacrine) 115s + a <- localLcross(Amacrine, from="off", to="off") 115s + a <- localKdot(Amacrine) 115s + a <- localLdot(Amacrine) 115s + a <- localKcross.inhom(Amacrine) 115s + a <- localLcross.inhom(Amacrine) 115s + Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine)) 115s + Lum <- evaluateCovariateAtPoints(Zed, Amacrine) 115s + moff <- (marks(Amacrine) == "off") 115s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 115s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 115s + a <- localLcross.inhom(Amacrine, from="off", to="on", 115s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 115s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 115s + correction="none") 115s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 115s + correction="translate") 115s + #' 115s + #' cases of resolve.lambdacross 115s + #' 115s + h <- resolve.lambdacross(Amacrine, moff, !moff) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, 115s + lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, 115s + lambdaI=Lum[moff], lambdaJ=Lum[!moff]) 115s + d <- densityfun(unmark(Amacrine), sigma=0.1) 115s + dm <- lapply(split(Amacrine), densityfun, sigma=0.1) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=d) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, 115s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 115s + h <- resolve.lambdacross(Amacrine, moff, !moff, 115s + lambdaX=function(x,y,m){ d(x,y) }) 115s + #' 115s + #' multitype inhomogeneous pcf 115s + #' 115s + g <- pcfcross.inhom(Amacrine, 115s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 115s + 115s + #' 115s + #' lohboot code blocks 115s + #' 115s + Ared <- lohboot(Redwood, fun="Kest", block=TRUE, 115s + Vcorrection=TRUE, global=FALSE, correction="none") 115s + Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE) 115s + Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE, 115s + correction="translate") 115s + Dred <- lohboot(Redwood, Lest) 115s + Kred <- lohboot(Redwood, Kinhom) 115s + Lred <- lohboot(Redwood, Linhom) 115s + gred <- lohboot(Redwood, pcfinhom, sigma=0.1) 115s + #' 115s + X <- runifpoint(100, letterR) 115s + AX <- lohboot(X, block=TRUE, nx=7, ny=10) 115s + #' multitype 115s + b <- lohboot(Amacrine, Kcross) 115s + b <- lohboot(Amacrine, Lcross) 115s + b <- lohboot(Amacrine, Kdot) 115s + b <- lohboot(Amacrine, Ldot) 115s + b <- lohboot(Amacrine, Kcross.inhom) 115s + b <- lohboot(Amacrine, Lcross.inhom) 115s + 115s + ## Kscaled 115s + A <- Lscaled(japanesepines, renormalise=TRUE, correction="all") 115s + } 115s + }) 115s > 115s > local({ 115s + if(ALWAYS) { 115s + #' From Ege, in response to a stackoverflow question. 115s + #' The following example has two points separated by r = 1 with 1/4 of the 115s + #' circumference outside the 10x10 window (i.e. area 100). 115s + discrepancy in isotropic edge correction at interior point of rectangle is 2.22e-16, within tolerance of 1e-06 115s discrepancy in isotropic edge correction near corner of rectangle is 8.882e-16, within tolerance of 1e-06 115s discrepancy in isotropic edge correction at interior point of polygon (debug on) is 7.55e-15, within tolerance of 1e-06 115s discrepancy in isotropic edge correction at interior point of polygon (debug off) is 7.55e-15, within tolerance of 1e-06 115s #' Thus the value of K^(r) should jump from 0 to 115s + #' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333. 115s + x <- c(4.5,5.5) 115s + y <- c(10,10)-sqrt(2)/2 115s + W <- square(10) 115s + X <- ppp(x, y, W) 115s + compere <- function(a, b, where, tol=1e-6) { 115s + descrip <- paste("discrepancy in isotropic edge correction", where) 115s + err <- as.numeric(a) - as.numeric(b) 115s + maxerr <- max(abs(err)) 115s + blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","), 115s + if(maxerr > tol) "exceeding" else "within", 115s + "tolerance of", tol) 115s + message(blurb) 115s + if(maxerr > tol) { 115s + message(paste("Discrepancies:", paste(err, collapse=", "))) 115s + stop(paste("excessive", descrip), call.=FALSE) 115s + } 115s + invisible(TRUE) 115s + } 115s + ## Testing: 115s + eX <- edge.Ripley(X, c(1,1)) 115s + compere(eX, c(4/3,4/3), "at interior point of rectangle") 115s + ## Corner case: 115s + Y <- X 115s + Y$x <- X$x-4.5+sqrt(2)/2 115s + eY <- edge.Ripley(Y, c(1,1)) 115s + compere(eY, c(2,4/3), "near corner of rectangle") 115s + ## Invoke polygonal code 115s + Z <- rotate(Y, pi/4) 115s + eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE)) 115s + compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)") 115s + ## test validity without debugger,in case of quirks of compiler optimisation 115s + eZ <- edge.Ripley(Z, c(1,1)) 115s + compere(eZ, c(2,4/3), "at interior point of polygon (debug off)") 115s + } 115s + }) 115s /// Debug level 3 /// 115s ------- centre[0] = (-6.071068, 7.071068) ------ 115s boundary distance 0.707107 115s radius[0] = 1.000000 115s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 115s Left: det = -35.857864 115s Right: det = -171.715729 115s Top: det = -34143.145751 115s Finished cutting; ncut = 0 115s contrib = -0.000000 115s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 115s Left: det = -171.715729 115s Right: det = -35.857864 115s Top: det = -34143.145751 115s Finished cutting; ncut = 0 115s contrib = 0.000000 115s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 115s Left: det = -35.857864 115s Right: det = 0.000000 115s det = 0 115s Top: det = 200.000000 115s det > 0 115s hits + segment: t = 1.000000, theta = 3.141593 115s hits - segment: t = 0.858579, theta = 1.570796 115s Finished cutting; ncut = 2 115s theta[0] = 1.570796 115s theta[1] = 3.141593 115s Interval 0, width 1.570796:inside 115s Interval 1, width 1.570796:outside 115s Interval 2, width 3.141593:inside 115s contrib = 4.712389 115s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 115s Left: det = 0.000000 115s det = 0 115s Right: det = -35.857864 115s Top: det = 200.000000 115s det > 0 115s hits + segment: t = 0.141421, theta = -1.570796 115s hits - segment: t = 0.000000, theta = 3.141593 115s Finished cutting; ncut = 2 115s theta[0] = 3.141593 115s theta[1] = 4.712389 115s Interval 0, width 3.141593:outside 115s Interval 1, width 1.570796:inside 115s Interval 2, width 1.570796:outside 115s contrib = -1.570796 115s 115s Total = 3.141593 = 0.500000 * (2 * pi) 115s ------- centre[1] = (-5.363961, 7.778175) ------ 115s boundary distance 0.707107 115s radius[0] = 1.000000 115s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 115s Left: det = -27.772078 115s Right: det = -153.629942 115s Top: det = -34143.145751 115s Finished cutting; ncut = 0 115s contrib = -0.000000 115s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 115s Left: det = -153.629942 115s Right: det = -27.772078 115s Top: det = -27108.831175 115s Finished cutting; ncut = 0 115s contrib = 0.000000 115s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 115s Left: det = -27.772078 115s Right: det = -1.914214 115s Top: det = 200.000000 115s det > 0 115s hits + segment: t = 0.900000, theta = 3.141593 115s hits - segment: t = 0.758579, theta = 1.570796 115s Finished cutting; ncut = 2 115s theta[0] = 1.570796 115s theta[1] = 3.141593 115s Interval 0, width 1.570796:inside 115s Interval 1, width 1.570796:outside 115s Interval 2, width 3.141593:inside 115s contrib = 4.712389 115s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 115s Left: det = -1.914214 115s Right: det = -27.772078 115s Top: det = -765.685425 115s Finished cutting; ncut = 0 115s contrib = -0.000000 115s 115s Total = 4.712389 = 0.750000 * (2 * pi) 115s > 115s > 115s > 115s > reset.spatstat.options() 115s > 115s BEGIN TEST testsL.R 115s 115s R version 4.4.3 (2025-02-28) -- "Trophy Case" 115s Copyright (C) 2025 The R Foundation for Statistical Computing 115s Platform: x86_64-pc-linux-gnu 115s 115s R is free software and comes with ABSOLUTELY NO WARRANTY. 115s You are welcome to redistribute it under certain conditions. 115s Type 'license()' or 'licence()' for distribution details. 115s 115s R is a collaborative project with many contributors. 115s Type 'contributors()' for more information and 115s 'citation()' on how to cite R or R packages in publications. 115s 115s Type 'demo()' for some demos, 'help()' for on-line help, or 115s 'help.start()' for an HTML browser interface to help. 115s Type 'q()' to quit R. 115s 115s > #' 115s > #' Header for all (concatenated) test files 115s > #' 115s > #' Require spatstat.explore 115s > #' Obtain environment variable controlling tests. 115s > #' 115s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 115s > 115s > require(spatstat.explore) 115s Loading required package: spatstat.explore 115s Loading required package: spatstat.data 115s Loading required package: spatstat.univar 115s spatstat.univar 3.1-2 115s Loading required package: spatstat.geom 115s spatstat.geom 3.3-6 115s Loading required package: spatstat.random 115s spatstat.random 3.3-3 115s Loading required package: nlme 115s spatstat.explore 3.3-4 115s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 115s > ALWAYS <- TRUE 115s > cat(paste("--------- Executing", 115s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 115s + "test code -----------\n")) 115s --------- Executing **RESTRICTED** subset of test code ----------- 115s > ## 115s > ## tests/localpcf.R 115s > ## 115s > ## temporary test file for localpcfmatrix 115s > ## $Revision: 1.2 $ $Date: 2015/12/29 08:54:49 $ 115s > 115s > local({ 116s + a <- localpcfmatrix(redwood) 116s + if(FULLTEST) { 116s + a 116s + plot(a) 116s + a[, 3:5] 116s + } 116s + }) 116s > 116s BEGIN TEST testsM.R 116s 116s R version 4.4.3 (2025-02-28) -- "Trophy Case" 116s Copyright (C) 2025 The R Foundation for Statistical Computing 116s Platform: x86_64-pc-linux-gnu 116s 116s R is free software and comes with ABSOLUTELY NO WARRANTY. 116s You are welcome to redistribute it under certain conditions. 116s Type 'license()' or 'licence()' for distribution details. 116s 116s R is a collaborative project with many contributors. 116s Type 'contributors()' for more information and 116s 'citation()' on how to cite R or R packages in publications. 116s 116s Type 'demo()' for some demos, 'help()' for on-line help, or 116s 'help.start()' for an HTML browser interface to help. 116s Type 'q()' to quit R. 116s 116s > #' 116s > #' Header for all (concatenated) test files 116s > #' 116s > #' Require spatstat.explore 116s > #' Obtain environment variable controlling tests. 116s > #' 116s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 116s > 116s > require(spatstat.explore) 116s Loading required package: spatstat.explore 116s Loading required package: spatstat.data 116s Loading required package: spatstat.univar 116s spatstat.univar 3.1-2 116s Loading required package: spatstat.geom 116s spatstat.geom 3.3-6 116s Loading required package: spatstat.random 116s spatstat.random 3.3-3 116s Loading required package: nlme 116s spatstat.explore 3.3-4 116s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 116s > ALWAYS <- TRUE 116s > cat(paste("--------- Executing", 116s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 116s + "test code -----------\n")) 116s --------- Executing **RESTRICTED** subset of test code ----------- 116s > ## 116s > ## tests/markcor.R 116s > ## 116s > ## Tests of mark correlation code (etc) 116s > ## 116s > ## $Revision: 1.7 $ $Date: 2020/11/25 01:23:32 $ 116s > 116s > local({ 116s + if(ALWAYS) { 116s + ## check.testfun checks equality of functions 116s + ## and is liable to break if the behaviour of all.equal is changed 116s + fe <- function(m1, m2) {m1 == m2} 116s + fm <- function(m1, m2) {m1 * m2} 116s + fs <- function(m1, m2) {sqrt(m1)} 116s + if(check.testfun(fe, X=amacrine)$ftype != "equ") 116s + warning("check.testfun fails to recognise mark equality function") 116s + if(check.testfun(fm, X=longleaf)$ftype != "mul") 116s + warning("check.testfun fails to recognise mark product function") 116s + check.testfun(fs, X=longleaf) 116s + check.testfun("mul") 116s + check.testfun("equ") 116s + } 116s + 116s + if(FULLTEST) { 116s + ## test all is well in Kmark -> Kinhom 116s + MA <- Kmark(amacrine,function(m1,m2){m1==m2}) 116s + set.seed(42) 116s + AR <- rlabel(amacrine) 116s + MR <- Kmark(AR,function(m1,m2){m1==m2}) 116s + if(isTRUE(all.equal(MA,MR))) 116s + stop("Kmark unexpectedly ignores marks") 116s + 116s + ## cover code blocks in markcorr() 116s + X <- runifpoint(100) %mark% runif(100) 116s + Y <- X %mark% data.frame(u=runif(100), v=runif(100)) 116s + ww <- runif(100) 116s + fone <- function(x) { x/2 } 116s + ffff <- function(x,y) { fone(x) * fone(y) } 116s + aa <- markcorr(Y) 116s Warning messages: 116s 1: In eval(quote({ : 116s check.testfun fails to recognise mark equality function 116s 2: In eval(quote({ : 116s check.testfun fails to recognise mark product function 116s + bb <- markcorr(Y, ffff, weights=ww, normalise=TRUE) 116s + bb <- markcorr(Y, ffff, weights=ww, normalise=FALSE) 116s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=TRUE) 116s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=FALSE) 116s + 116s + ## markcrosscorr 116s + a <- markcrosscorr(betacells, normalise=FALSE) 116s + if(require(sm)) { 116s + b <- markcrosscorr(betacells, method="sm") 116s + } 116s + 116s + ## Vmark with normalisation 116s + v <- Vmark(spruces, normalise=TRUE) 116s + v <- Vmark(finpines, normalise=TRUE) 116s + } 116s + }) 116s > #' tests/mctests.R 116s > #' Monte Carlo tests 116s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 116s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 116s > 116s > local({ 116s + if(FULLTEST) { 116s + envelopeTest(cells, Lest, exponent=1, nsim=9, savepatterns=TRUE) 116s + (a3 <- envelopeTest(cells, Lest, exponent=3, nsim=9, savepatterns=TRUE)) 116s + 116s + envelopeTest(a3, Lest, exponent=3, nsim=9, alternative="less") 116s + 116s + envelopeTest(redwood, Lest, exponent=1, nsim=19, 116s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 116s + envelopeTest(redwood, pcf, exponent=Inf, nsim=19, 116s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 116s + } 116s + }) 116s > 116s > 116s > 116s BEGIN TEST testsNtoO.R 116s 116s R version 4.4.3 (2025-02-28) -- "Trophy Case" 116s Copyright (C) 2025 The R Foundation for Statistical Computing 116s Platform: x86_64-pc-linux-gnu 116s 116s R is free software and comes with ABSOLUTELY NO WARRANTY. 116s You are welcome to redistribute it under certain conditions. 116s Type 'license()' or 'licence()' for distribution details. 116s 116s R is a collaborative project with many contributors. 116s Type 'contributors()' for more information and 116s 'citation()' on how to cite R or R packages in publications. 116s 116s Type 'demo()' for some demos, 'help()' for on-line help, or 116s 'help.start()' for an HTML browser interface to help. 116s Type 'q()' to quit R. 116s 117s > #' 117s > #' Header for all (concatenated) test files 117s > #' 117s > #' Require spatstat.explore 117s > #' Obtain environment variable controlling tests. 117s > #' 117s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 117s > 117s > require(spatstat.explore) 117s Loading required package: spatstat.explore 117s Loading required package: spatstat.data 117s Loading required package: spatstat.univar 117s spatstat.univar 3.1-2 117s Loading required package: spatstat.geom 117s spatstat.geom 3.3-6 117s Loading required package: spatstat.random 117s spatstat.random 3.3-3 117s Loading required package: nlme 117s spatstat.explore 3.3-4 117s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 117s > ALWAYS <- TRUE 117s > cat(paste("--------- Executing", 117s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 117s + "test code -----------\n")) 117s --------- Executing **RESTRICTED** subset of test code ----------- 117s > # 117s > # tests/nnstat.R 117s > # 117s > # Check code that uses nndist/nnwhich 117s > # 117s > # nnorient() 117s > # stienen() 117s > # 117s > # $Revision: 1.1 $ $Date: 2020/12/04 03:45:44 $ 117s > # 117s > 117s > 117s > local({ 117s + if(FULLTEST) { 117s + #' test nnorient 117s + nnorient(cells, domain=erosion(Window(cells), 0.1)) 117s + #' degenerate case 117s + X <- cells[nndist(cells) > bdist.points(cells)] 117s + f <- nnorient(X) 117s + #' nnclean 117s + A <- nnclean(shapley, k=17, edge.correct=TRUE) 117s + B <- nnclean(runifpoint3(300), 3) 117s + #' stienen set 117s + #' bug when disc radius is zero 117s + Y <- unmark(humberside)[40:100] # contains duplicated points 117s + stienen(Y) 117s + Z <- stienenSet(Y) 117s + #' other cases 117s + U <- stienen(cells[1]) 117s + V <- stienenSet(cells, edge=FALSE) 117s + } 117s + }) 117s > 117s > 117s > 117s > 117s BEGIN TEST testsP1.R 117s 117s R version 4.4.3 (2025-02-28) -- "Trophy Case" 117s Copyright (C) 2025 The R Foundation for Statistical Computing 117s Platform: x86_64-pc-linux-gnu 117s 117s R is free software and comes with ABSOLUTELY NO WARRANTY. 117s You are welcome to redistribute it under certain conditions. 117s Type 'license()' or 'licence()' for distribution details. 117s 117s R is a collaborative project with many contributors. 117s Type 'contributors()' for more information and 117s 'citation()' on how to cite R or R packages in publications. 117s 117s Type 'demo()' for some demos, 'help()' for on-line help, or 117s 'help.start()' for an HTML browser interface to help. 117s Type 'q()' to quit R. 117s 117s > #' 117s > #' Header for all (concatenated) test files 117s > #' 117s > #' Require spatstat.explore 117s > #' Obtain environment variable controlling tests. 117s > #' 117s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 117s > 117s > require(spatstat.explore) 117s Loading required package: spatstat.explore 117s Loading required package: spatstat.data 118s Loading required package: spatstat.univar 118s spatstat.univar 3.1-2 118s Loading required package: spatstat.geom 118s spatstat.geom 3.3-6 118s Loading required package: spatstat.random 118s spatstat.random 3.3-3 118s Loading required package: nlme 118s spatstat.explore 3.3-4 118s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 118s > ALWAYS <- TRUE 118s > cat(paste("--------- Executing", 118s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 118s + "test code -----------\n")) 118s --------- Executing **RESTRICTED** subset of test code ----------- 118s > ## 118s > ## tests/pixelgripes.R 118s > ## Problems related to pixellation of windows 118s > ## 118s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 118s > 118s > if(FULLTEST) { 118s + local({ 118s + 118s + 118s + }) 118s + } 118s > 118s BEGIN TEST testsP2.R 118s 118s R version 4.4.3 (2025-02-28) -- "Trophy Case" 118s Copyright (C) 2025 The R Foundation for Statistical Computing 118s Platform: x86_64-pc-linux-gnu 118s 118s R is free software and comes with ABSOLUTELY NO WARRANTY. 118s You are welcome to redistribute it under certain conditions. 118s Type 'license()' or 'licence()' for distribution details. 118s 118s R is a collaborative project with many contributors. 118s Type 'contributors()' for more information and 118s 'citation()' on how to cite R or R packages in publications. 118s 118s Type 'demo()' for some demos, 'help()' for on-line help, or 118s 'help.start()' for an HTML browser interface to help. 118s Type 'q()' to quit R. 118s 118s > #' 118s > #' Header for all (concatenated) test files 118s > #' 118s > #' Require spatstat.explore 118s > #' Obtain environment variable controlling tests. 118s > #' 118s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 118s > 118s > require(spatstat.explore) 118s Loading required package: spatstat.explore 118s Loading required package: spatstat.data 119s Loading required package: spatstat.univar 119s spatstat.univar 3.1-2 119s Loading required package: spatstat.geom 119s spatstat.geom 3.3-6 119s Loading required package: spatstat.random 119s spatstat.random 3.3-3 119s Loading required package: nlme 119s spatstat.explore 3.3-4 119s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 119s > ALWAYS <- TRUE 119s > cat(paste("--------- Executing", 119s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 119s + "test code -----------\n")) 119s --------- Executing **RESTRICTED** subset of test code ----------- 119s > 119s BEGIN TEST testsQ.R 119s 119s R version 4.4.3 (2025-02-28) -- "Trophy Case" 119s Copyright (C) 2025 The R Foundation for Statistical Computing 119s Platform: x86_64-pc-linux-gnu 119s 119s R is free software and comes with ABSOLUTELY NO WARRANTY. 119s You are welcome to redistribute it under certain conditions. 119s Type 'license()' or 'licence()' for distribution details. 119s 119s R is a collaborative project with many contributors. 119s Type 'contributors()' for more information and 119s 'citation()' on how to cite R or R packages in publications. 119s 119s Type 'demo()' for some demos, 'help()' for on-line help, or 119s 'help.start()' for an HTML browser interface to help. 119s Type 'q()' to quit R. 119s 119s > #' 119s > #' Header for all (concatenated) test files 119s > #' 119s > #' Require spatstat.explore 119s > #' Obtain environment variable controlling tests. 119s > #' 119s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 119s > 119s > require(spatstat.explore) 119s Loading required package: spatstat.explore 119s Loading required package: spatstat.data 120s Loading required package: spatstat.univar 120s spatstat.univar 3.1-2 120s Loading required package: spatstat.geom 120s spatstat.geom 3.3-6 120s Loading required package: spatstat.random 120s spatstat.random 3.3-3 120s Loading required package: nlme 120s spatstat.explore 3.3-4 120s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 120s > ALWAYS <- TRUE 120s > cat(paste("--------- Executing", 120s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 120s + "test code -----------\n")) 120s --------- Executing **RESTRICTED** subset of test code ----------- 120s > 120s BEGIN TEST testsR1.R 120s 120s R version 4.4.3 (2025-02-28) -- "Trophy Case" 120s Copyright (C) 2025 The R Foundation for Statistical Computing 120s Platform: x86_64-pc-linux-gnu 120s 120s R is free software and comes with ABSOLUTELY NO WARRANTY. 120s You are welcome to redistribute it under certain conditions. 120s Type 'license()' or 'licence()' for distribution details. 120s 120s R is a collaborative project with many contributors. 120s Type 'contributors()' for more information and 120s 'citation()' on how to cite R or R packages in publications. 120s 120s Type 'demo()' for some demos, 'help()' for on-line help, or 120s 'help.start()' for an HTML browser interface to help. 120s Type 'q()' to quit R. 120s 120s > #' 120s > #' Header for all (concatenated) test files 120s > #' 120s > #' Require spatstat.explore 120s > #' Obtain environment variable controlling tests. 120s > #' 120s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 120s > 120s > require(spatstat.explore) 120s Loading required package: spatstat.explore 120s Loading required package: spatstat.data 121s Loading required package: spatstat.univar 121s spatstat.univar 3.1-2 121s Loading required package: spatstat.geom 121s spatstat.geom 3.3-6 121s Loading required package: spatstat.random 121s spatstat.random 3.3-3 121s Loading required package: nlme 121s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 121s > ALWAYS <- TRUE 121s > cat(paste("--------- Executing", 121s spatstat.explore 3.3-4 121s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 121s + "test code -----------\n")) 121s --------- Executing **RESTRICTED** subset of test code ----------- 121s > ## 121s > ## tests/rhohat.R 121s > ## 121s > ## Test all combinations of options for rhohatCalc 121s > ## 121s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 121s > 121s > local({ 121s + if(FULLTEST) { 121s + X <- rpoispp(function(x,y){exp(3+3*x)}) 121s + Z <- as.im(function(x,y) { x }, Window(X)) 121s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 121s + 121s + ## rhohat.ppp 121s + ## done in example(rhohat): 121s + ## rhoA <- rhohat(X, "x") 121s + ## rhoB <- rhohat(X, "x", method="reweight") 121s + ## rhoC <- rhohat(X, "x", method="transform") 121s + ## alternative smoother (if package locfit available) 121s + rhoA <- rhohat(X, "x", smoother="local") 121s + rhoB <- rhohat(X, "x", smoother="local", method="reweight") 121s + rhoC <- rhohat(X, "x", smoother="local", method="transform") 121s + 121s + #' code blocks 121s + rhoD <- rhohat(X, "y", positiveCI=TRUE) 121s + rhoE <- rhohat(X, Z, positiveCI=TRUE) 121s + #' weights 121s + rhoF <- rhohat(X, Z, weights=f(X)) 121s + rhoG <- rhohat(X, Z, weights=f) 121s + rhoH <- rhohat(X, Z, weights=as.im(f)) 121s + 121s + lam <- as.im(function(x,y) {exp(3+2*x)}, W=Window(Z)) 121s + 121s + ## Baseline 121s + rhoAb <- rhohat(X, "x", baseline=lam) 121s + rhoBb <- rhohat(X, "x", method="reweight", baseline=lam) 121s + rhoCb <- rhohat(X, "x", method="transform", baseline=lam) 121s + 121s + ## Horvitz-Thompson 121s + rhoAH <- rhohat(X, "x", horvitz=TRUE) 121s + rhoBH <- rhohat(X, "x", method="reweight", horvitz=TRUE) 121s + rhoCH <- rhohat(X, "x", method="transform", horvitz=TRUE) 121s + 121s + ## class support 121s + plot(rhoA) 121s + plot(rhoA, rho ~ x, shade=NULL) 121s + plot(rhoA, log(rho) ~ x, shade=NULL) 121s + plot(rhoA, log(.) ~ x) 121s + 121s + ## rho2hat 121s + r2xy <- rho2hat(X, "x", "y") 121s + r2xyw <- rho2hat(X, "x", "y", method="reweight") 121s + print(r2xyw) 121s + plot(r2xy, do.points=TRUE) 121s + xcoord <- function(x,y) x 121s + ycoord <- function(x,y) y 121s + xim <- as.im(xcoord, W=Window(X)) 121s + r2fi <- rho2hat(X, ycoord, xim) 121s + r2if <- rho2hat(X, xim, ycoord) 121s + } 121s + }) 121s > 121s BEGIN TEST testsR2.R 121s 121s R version 4.4.3 (2025-02-28) -- "Trophy Case" 121s Copyright (C) 2025 The R Foundation for Statistical Computing 121s Platform: x86_64-pc-linux-gnu 121s 121s R is free software and comes with ABSOLUTELY NO WARRANTY. 121s You are welcome to redistribute it under certain conditions. 121s Type 'license()' or 'licence()' for distribution details. 121s 121s R is a collaborative project with many contributors. 121s Type 'contributors()' for more information and 121s 'citation()' on how to cite R or R packages in publications. 121s 121s Type 'demo()' for some demos, 'help()' for on-line help, or 121s 'help.start()' for an HTML browser interface to help. 121s Type 'q()' to quit R. 121s 121s > #' 121s > #' Header for all (concatenated) test files 121s > #' 121s > #' Require spatstat.explore 121s > #' Obtain environment variable controlling tests. 121s > #' 121s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 121s > 121s > require(spatstat.explore) 121s Loading required package: spatstat.explore 121s Loading required package: spatstat.data 122s Loading required package: spatstat.univar 122s spatstat.univar 3.1-2 122s Loading required package: spatstat.geom 122s spatstat.geom 3.3-6 122s Loading required package: spatstat.random 122s spatstat.random 3.3-3 122s Loading required package: nlme 122s spatstat.explore 3.3-4 122s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 122s > ALWAYS <- TRUE 122s > cat(paste("--------- Executing", 122s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 122s + "test code -----------\n")) 122s --------- Executing **RESTRICTED** subset of test code ----------- 122s > 122s BEGIN TEST testsS.R 122s 122s R version 4.4.3 (2025-02-28) -- "Trophy Case" 122s Copyright (C) 2025 The R Foundation for Statistical Computing 122s Platform: x86_64-pc-linux-gnu 122s 122s R is free software and comes with ABSOLUTELY NO WARRANTY. 122s You are welcome to redistribute it under certain conditions. 122s Type 'license()' or 'licence()' for distribution details. 122s 122s R is a collaborative project with many contributors. 122s Type 'contributors()' for more information and 122s 'citation()' on how to cite R or R packages in publications. 122s 122s Type 'demo()' for some demos, 'help()' for on-line help, or 122s 'help.start()' for an HTML browser interface to help. 122s Type 'q()' to quit R. 122s 122s > Loading required package: spatstat.explore 122s #' 122s > #' Header for all (concatenated) test files 122s > #' 122s > #' Require spatstat.explore 122s > #' Obtain environment variable controlling tests. 122s > #' 122s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 122s > 122s > require(spatstat.explore) 122s Loading required package: spatstat.data 123s Loading required package: spatstat.univar 123s spatstat.univar 3.1-2 123s Loading required package: spatstat.geom 123s spatstat.geom 3.3-6 123s Loading required package: spatstat.random 123s spatstat.random 3.3-3 123s Loading required package: nlme 123s spatstat.explore 3.3-4 123s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 123s > ALWAYS <- TRUE 123s > cat(paste("--------- Executing", 123s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 123s + "test code -----------\n")) 123s --------- Executing **RESTRICTED** subset of test code ----------- 123s > #' tests/sdr.R 123s > #' 123s > #' $Revision: 1.2 $ $Date: 2020/05/01 09:59:59 $ 123s > 123s > if(FULLTEST) { 123s + local({ 123s + AN <- sdr(bei, bei.extra, method="NNIR") 123s + AV <- sdr(bei, bei.extra, method="SAVE") 123s + AI <- sdr(bei, bei.extra, method="SIR") 123s + AT <- sdr(bei, bei.extra, method="TSE") 123s + subspaceDistance(AN$B, AV$B) 123s + dimhat(AN$M) 123s + }) 123s + } 123s > ## 123s > ## tests/segments.R 123s > ## Tests of psp class and related code 123s > ## [SEE ALSO: tests/xysegment.R] 123s > ## 123s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 123s > 123s > 123s > local({ 123s + if(ALWAYS) { # C code 123s + #' tests of density.psp 123s + Y <- edges(letterR) 123s + Window(Y) <- grow.rectangle(Frame(Y), 0.4) 123s + YC <- density(Y, 0.2, method="C", edge=FALSE, dimyx=64) 123s + YI <- density(Y, 0.2, method="interpreted", edge=FALSE, dimyx=64) 123s + YF <- density(Y, 0.2, method="FFT", edge=FALSE, dimyx=64) 123s + xCI <- max(abs(YC/YI - 1)) 123s + xFI <- max(abs(YF/YI - 1)) 123s + cat(paste("xCI =", xCI, "\txFI =", signif(xFI, 5)), fill=TRUE) 123s + if(xCI > 0.01) stop(paste("density.psp C algorithm relative error =", xCI)) 123s + if(xFI > 0.1) stop(paste("density.psp FFT algorithm relative error =", xFI)) 123s + 123s + B <- square(0.3) 123s + density(Y, 0.2, at=B) 123s + density(Y, 0.2, at=B, edge=TRUE, method="C") 123s + Z <- runifrect(3, B) 123s + density(Y, 0.2, at=Z) 123s + density(Y, 0.2, at=Z, edge=TRUE, method="C") 123s + } 123s + 123s + if(FULLTEST) { 123s + #' segment clipping in window (bug found by Rolf) 123s + set.seed(42) 123s + X <- runifpoint(50, letterR) 123s + SP <- dirichletEdges(X) #' clip to polygonal window 123s + Window(X) <- as.mask(Window(X)) 123s + SM <- dirichletEdges(X) #' clip to mask window 123s + } 123s + 123s + if(FULLTEST) { 123s + #' test rshift.psp and append.psp with marks (Ute Hahn) 123s + m <- data.frame(A=1:10, B=letters[1:10]) 123s + g <- gl(3, 3, length=10) 123s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 123s + Y <- rshift(X, radius = 0.1) 123s + Y <- rshift(X, radius = 0.1, group=g) 123s + #' mark management 123s + b <- data.frame(A=1:10) 123s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=b) 123s + stopifnot(is.data.frame(marks(X))) 123s + Y <- rshift(X, radius = 0.1) 123s + Y <- rshift(X, radius = 0.1, group=g) 123s + } 123s + 123s + }) 123s xCI = 0 xFI = 0.073128 125s > 125s > 125s > Warning message: 125s the images ‘dens’ and ‘edg’ were not compatible 125s 125s > # 125s > ## tests/sigtraceprogress.R 125s > # 125s > ## Tests of *.sigtrace and *.progress 125s > # 125s > ## $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 125s > 125s > if(FULLTEST) { 125s + local({ 125s + plot(dclf.sigtrace(redwood, nsim=19, alternative="greater", rmin=0.02, 125s + verbose=FALSE)) 125s + plot(dclf.progress(redwood, nsim=19, alternative="greater", rmin=0.02, 125s + verbose=FALSE)) 125s + plot(dg.sigtrace(redwood, nsim=5, alternative="greater", rmin=0.02, 125s + verbose=FALSE)) 125s + plot(dg.progress(redwood, nsim=5, alternative="greater", rmin=0.02, 125s + verbose=FALSE)) 125s + ## test 'leave-two-out' algorithm 125s + a <- dclf.sigtrace(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 125s + verbose=FALSE) 125s + aa <- dclf.progress(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 125s + verbose=FALSE) 125s + b <- dg.sigtrace(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2) 125s + bb <- dg.progress(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2, 125s + verbose=FALSE) 125s + ## other code blocks 125s + e <- mad.progress(redwood, nsim=5) 125s + e <- mad.progress(redwood, nsim=19, alpha=0.05) 125s + f <- dclf.progress(redwood, nsim=5, scale=function(x) x^2) 125s + f <- dclf.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 125s + g <- dg.progress(redwood, nsim=5, scale=function(x) x^2) 125s + g <- dg.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 125s + }) 125s + } 125s > #' 125s > #' tests/ssf.R 125s > #' 125s > #' Tests of 'ssf' class 125s > #' 125s > #' $Revision: 1.5 $ $Date: 2020/12/04 08:02:25 $ 125s > #' 125s > 125s > if(FULLTEST) { 125s + local({ 125s + Y <- cells[1:5] 125s + X <- rsyst(Window(Y), 5) 125s + Z <- runifpoint(3, Window(Y)) 125s + f1 <- ssf(X, nncross(X,Y,what="dist")) 125s + f2 <- ssf(X, nncross(X,Y,what="dist", k=1:2)) 125s + image(f1) 125s + g1 <- as.function(f1) 125s + g1(Z) 125s + g2 <- as.function(f2) 125s + g2(Z) 125s + plot(f1, style="contour") 125s + plot(f1, style="imagecontour") 125s + contour(f1) 125s + apply.ssf(f2, 1, sum) 125s + range(f1) 125s + min(f1) 125s + max(f1) 125s + integral(f1, weights=tile.areas(dirichlet(X))) 125s + }) 125s + } 125s > #' 125s > #' tests/sumfun.R 125s > #' 125s > #' Tests of code for summary functions 125s > #' 125s > #' $Revision: 1.9 $ $Date: 2022/05/22 08:45:23 $ 125s > 125s > if(ALWAYS) { # involves C code 125s + local({ 125s + W <- owin(c(0,1), c(-1/2, 0)) 125s + Gr <- Gest(redwood, correction="all",domain=W) 125s + Fr <- Fest(redwood, correction="all",domain=W) 125s + Jr <- Jest(redwood, correction="all",domain=W) 125s + 125s + F0 <- Fest(redwood[FALSE], correction="all") 125s + Fh <- Fest(humberside, domain=erosion(Window(humberside), 100)) 125s + 125s + FIr <- Finhom(redwood, savelambda=TRUE, ratio=TRUE) 125s + JIr <- Jinhom(redwood, savelambda=TRUE, ratio=TRUE) 125s + 125s + Ga <- Gcross(amacrine, correction="all") 125s + Ia <- Iest(amacrine, correction="all") 125s + lam <- intensity(amacrine) 125s + lmin <- 0.9 * min(lam) 125s + nJ <- sum(marks(amacrine) == "off") 125s + FM <- FmultiInhom(amacrine, marks(amacrine) == "off", 125s + lambdaJ=rep(lam["off"], nJ), 125s + lambdamin = lmin) 125s + GM <- GmultiInhom(amacrine, marks(amacrine) == "on", 125s + marks(amacrine) == "off", 125s + lambda=lam[marks(amacrine)], 125s + lambdamin=lmin, 125s + ReferenceMeasureMarkSetI=42) 125s + 125s + a <- compileCDF(D=nndist(redwood), 125s + B=bdist.points(redwood), 125s + r=seq(0, 1, length=256)) 125s + 125s + #' Tstat (triplet) function, all code blocks 125s + a <- Tstat(redwood, ratio=TRUE, 125s + correction=c("none", "border", "bord.modif", "translate")) 125s + 125s + ## distance argument spacing and breakpoints 125s + e <- check.finespacing(c(0,1,2), eps=0.1, action="silent") 125s + b <- as.breakpts(pi, 20) 125s + b <- as.breakpts(42, max=pi, npos=20) 125s + b <- even.breaks.owin(letterR) 125s + }) 125s + } 126s Searching 59340 potential triangles; estimated time 0.000426 sec 127s > 127s BEGIN TEST testsT.R 127s 127s R version 4.4.3 (2025-02-28) -- "Trophy Case" 127s Copyright (C) 2025 The R Foundation for Statistical Computing 127s Platform: x86_64-pc-linux-gnu 127s 127s R is free software and comes with ABSOLUTELY NO WARRANTY. 127s You are welcome to redistribute it under certain conditions. 127s Type 'license()' or 'licence()' for distribution details. 127s 127s R is a collaborative project with many contributors. 127s Type 'contributors()' for more information and 127s 'citation()' on how to cite R or R packages in publications. 127s 127s Type 'demo()' for some demos, 'help()' for on-line help, or 127s 'help.start()' for an HTML browser interface to help. 127s Type 'q()' to quit R. 127s 127s > Loading required package: spatstat.explore 127s #' 127s > #' Header for all (concatenated) test files 127s > #' 127s > #' Require spatstat.explore 127s > #' Obtain environment variable controlling tests. 127s > #' 127s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 127s > 127s > require(spatstat.explore) 127s Loading required package: spatstat.data 127s Loading required package: spatstat.univar 127s spatstat.univar 3.1-2 127s Loading required package: spatstat.geom 127s spatstat.geom 3.3-6 127s Loading required package: spatstat.random 127s spatstat.random 3.3-3 127s Loading required package: nlme 128s spatstat.explore 3.3-4 128s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 128s > ALWAYS <- TRUE 128s > cat(paste("--------- Executing", 128s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 128s + "test code -----------\n")) 128s --------- Executing **RESTRICTED** subset of test code ----------- 128s > #' 128s > #' tests/threedee.R 128s > #' 128s > #' Tests of 3D code 128s > #' 128s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 128s > #' 128s > 128s > local({ 128s + X <- runifpoint3(30) 128s + Y <- runifpoint3(20) 128s + if(FULLTEST) { 128s + A <- runifpoint3(10, nsim=2) 128s + Z <- ppsubset(X, 2:4) 128s + } 128s + ## 128s + if(ALWAYS) { # includes C code 128s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 128s + d <- crossdist(X, Y, squared=TRUE) 128s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 128s + #' 128s + h <- has.close(X, 0.2) 128s + h <- has.close(X, 0.2, periodic=TRUE) 128s + h <- has.close(X, 0.2, Y=Y) 128s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 128s + #' code blocks not otherwise reached 128s + rmax <- 0.6 * max(nndist(X)) 128s + g <- G3est(X, rmax=rmax, correction="rs") 128s + g <- G3est(X, rmax=rmax, correction="km") 128s + g <- G3est(X, rmax=rmax, correction="Hanisch") 128s + g <- G3est(X, rmax=rmax, sphere="ideal") 128s + g <- G3est(X, rmax=rmax, sphere="digital") 128s + v <- sphere.volume() 128s + v <- digital.volume() 128s + #' older code 128s + co <- coords(X) 128s + xx <- co$x 128s + yy <- co$y 128s + zz <- co$z 128s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 128s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 128s + ff1 <- f3engine(xx, yy, zz, correction="no") 128s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 128s + } 128s + ## 128s + if(ALWAYS) { 128s + #'class support 128s + X <- runifpoint3(10) 128s + print(X) 128s + print(X %mark% runif(10)) 128s + print(X %mark% factor(letters[c(1:5,5:1)])) 128s + print(X %mark% data.frame(a=1:10, b=runif(10))) 128s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 128s + print(X %mark% da) 128s + print(X %mark% data.frame(a=1:10, b=da)) 128s + } 128s + }) 128s Three-dimensional point pattern: 10 points 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s Marked three-dimensional point pattern: 10 points 128s marks are numeric, of storage type ‘double’ 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s Marked three-dimensional point pattern: 10 points 128s Multitype, with levels = a, b, c, d, e 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s Marked three-dimensional point pattern: 10 points 128s Mark variables: a, b 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s Marked three-dimensional point pattern: 10 points 128s marks are dates, of class ‘Date’ 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s Marked three-dimensional point pattern: 10 points 128s Mark variables: a, b 128s Box: [0, 1] x [0, 1] x [0, 1] units 128s > 128s Warning messages: 128s 1: In G3est: unrecognised argument ‘sphere’ was ignored 128s 2: In G3est: unrecognised argument ‘sphere’ was ignored 128s BEGIN TEST testsUtoZ.R 128s 128s R version 4.4.3 (2025-02-28) -- "Trophy Case" 128s Copyright (C) 2025 The R Foundation for Statistical Computing 128s Platform: x86_64-pc-linux-gnu 128s 128s R is free software and comes with ABSOLUTELY NO WARRANTY. 128s You are welcome to redistribute it under certain conditions. 128s Type 'license()' or 'licence()' for distribution details. 128s 128s R is a collaborative project with many contributors. 128s Type 'contributors()' for more information and 128s 'citation()' on how to cite R or R packages in publications. 128s 128s Type 'demo()' for some demos, 'help()' for on-line help, or 128s 'help.start()' for an HTML browser interface to help. 128s Type 'q()' to quit R. 128s 128s Loading required package: spatstat.explore 128s > #' 128s > #' Header for all (concatenated) test files 128s > #' 128s > #' Require spatstat.explore 128s > #' Obtain environment variable controlling tests. 128s > #' 128s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 128s > 128s > require(spatstat.explore) 128s Loading required package: spatstat.data 128s Loading required package: spatstat.univar 128s spatstat.univar 3.1-2 128s Loading required package: spatstat.geom 128s spatstat.geom 3.3-6 128s Loading required package: spatstat.random 128s spatstat.random 3.3-3 128s Loading required package: nlme 129s spatstat.explore 3.3-4 129s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 129s > ALWAYS <- TRUE 129s > cat(paste("--------- Executing", 129s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 129s + "test code -----------\n")) 129s --------- Executing **RESTRICTED** subset of test code ----------- 129s > 129s autopkgtest [18:56:21]: test run-unit-test: -----------------------] 130s run-unit-test PASS 130s autopkgtest [18:56:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 130s autopkgtest [18:56:22]: test pkg-r-autopkgtest: preparing testbed 176s autopkgtest [18:57:08]: testbed dpkg architecture: amd64 176s autopkgtest [18:57:08]: testbed apt version: 3.0.0 176s autopkgtest [18:57:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 176s autopkgtest [18:57:08]: testbed release detected to be: questing 177s autopkgtest [18:57:09]: updating testbed package index (apt update) 177s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 178s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 178s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 178s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 178s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [149 kB] 178s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.7 kB] 178s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1442 kB] 178s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [203 kB] 178s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [146 kB] 178s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1424 kB] 178s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [576 kB] 178s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [23.1 kB] 178s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [48.6 kB] 178s Fetched 4155 kB in 1s (3811 kB/s) 179s Reading package lists... 180s autopkgtest [18:57:12]: upgrading testbed (apt dist-upgrade and autopurge) 180s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s Entering ResolveByKeep 181s 181s Calculating upgrade... 181s The following packages will be upgraded: 181s cloud-init cloud-init-base debianutils libmbim-glib4 libmbim-proxy 181s libnftnl11 libqmi-glib5 libqmi-proxy libsepol2 python3-lazr.restfulclient 181s sos 181s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 2693 kB of archives. 181s After this operation, 104 kB disk space will be freed. 181s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 debianutils amd64 5.22 [93.0 kB] 182s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libsepol2 amd64 3.8.1-1 [327 kB] 182s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libnftnl11 amd64 1.2.9-1 [69.1 kB] 182s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init-base all 25.2~1g7a0265d3-0ubuntu1 [619 kB] 182s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-proxy amd64 1.32.0-1 [6276 B] 182s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 libmbim-glib4 amd64 1.32.0-1 [233 kB] 182s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-proxy amd64 1.36.0-1 [6220 B] 182s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libqmi-glib5 amd64 1.36.0-1 [920 kB] 182s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 python3-lazr.restfulclient all 0.14.6-3 [51.0 kB] 182s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 sos all 4.9.1-1 [367 kB] 182s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 cloud-init all 25.2~1g7a0265d3-0ubuntu1 [2106 B] 182s Preconfiguring packages ... 182s Fetched 2693 kB in 1s (4352 kB/s) 182s (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 ... 80514 files and directories currently installed.) 182s Preparing to unpack .../debianutils_5.22_amd64.deb ... 182s Unpacking debianutils (5.22) over (5.21) ... 182s Setting up debianutils (5.22) ... 183s (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 ... 80514 files and directories currently installed.) 183s Preparing to unpack .../libsepol2_3.8.1-1_amd64.deb ... 183s Unpacking libsepol2:amd64 (3.8.1-1) over (3.7-1) ... 183s Setting up libsepol2:amd64 (3.8.1-1) ... 183s (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 ... 80514 files and directories currently installed.) 183s Preparing to unpack .../0-libnftnl11_1.2.9-1_amd64.deb ... 183s Unpacking libnftnl11:amd64 (1.2.9-1) over (1.2.8-1) ... 183s Preparing to unpack .../1-cloud-init-base_25.2~1g7a0265d3-0ubuntu1_all.deb ... 183s Unpacking cloud-init-base (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 183s Preparing to unpack .../2-libmbim-proxy_1.32.0-1_amd64.deb ... 183s Unpacking libmbim-proxy (1.32.0-1) over (1.31.2-0ubuntu4) ... 183s Preparing to unpack .../3-libmbim-glib4_1.32.0-1_amd64.deb ... 183s Unpacking libmbim-glib4:amd64 (1.32.0-1) over (1.31.2-0ubuntu4) ... 183s Preparing to unpack .../4-libqmi-proxy_1.36.0-1_amd64.deb ... 183s Unpacking libqmi-proxy (1.36.0-1) over (1.35.6-1) ... 183s Preparing to unpack .../5-libqmi-glib5_1.36.0-1_amd64.deb ... 183s Unpacking libqmi-glib5:amd64 (1.36.0-1) over (1.35.6-1) ... 183s Preparing to unpack .../6-python3-lazr.restfulclient_0.14.6-3_all.deb ... 183s Unpacking python3-lazr.restfulclient (0.14.6-3) over (0.14.6-2) ... 183s Preparing to unpack .../7-sos_4.9.1-1_all.deb ... 183s Unpacking sos (4.9.1-1) over (4.9.0-6) ... 184s Preparing to unpack .../8-cloud-init_25.2~1g7a0265d3-0ubuntu1_all.deb ... 184s Unpacking cloud-init (25.2~1g7a0265d3-0ubuntu1) over (25.1.1-0ubuntu2) ... 184s Setting up sos (4.9.1-1) ... 184s Setting up libnftnl11:amd64 (1.2.9-1) ... 184s Setting up cloud-init-base (25.2~1g7a0265d3-0ubuntu1) ... 185s Setting up python3-lazr.restfulclient (0.14.6-3) ... 185s Setting up libmbim-glib4:amd64 (1.32.0-1) ... 185s Setting up cloud-init (25.2~1g7a0265d3-0ubuntu1) ... 185s Setting up libmbim-proxy (1.32.0-1) ... 185s Setting up libqmi-glib5:amd64 (1.36.0-1) ... 185s Setting up libqmi-proxy (1.36.0-1) ... 185s Processing triggers for libc-bin (2.41-6ubuntu1) ... 185s Processing triggers for rsyslog (8.2412.0-2ubuntu2) ... 186s Processing triggers for man-db (2.13.0-1) ... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Starting pkgProblemResolver with broken count: 0 188s Starting 2 pkgProblemResolver with broken count: 0 188s Done 188s Solving dependencies... 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 188s autopkgtest [18:57:20]: rebooting testbed after setup commands that affected boot 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s Starting pkgProblemResolver with broken count: 0 215s Starting 2 pkgProblemResolver with broken count: 0 215s Done 215s The following NEW packages will be installed: 215s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 215s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 215s g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14 215s gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 215s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 215s libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 libdeflate-dev 215s libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev libgfortran5 215s libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libhwasan0 215s libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 215s libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblerc4 215s liblsan0 liblzma-dev libmpc3 libncurses-dev libpango-1.0-0 215s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 215s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 215s libpng-dev libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev 215s libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 215s libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 215s libxt6t64 pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 215s r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl r-cran-lattice 215s r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-polyclip r-cran-rpart r-cran-sm 215s r-cran-spatial r-cran-spatstat r-cran-spatstat.data r-cran-spatstat.explore 215s r-cran-spatstat.geom r-cran-spatstat.linnet r-cran-spatstat.model 215s r-cran-spatstat.random r-cran-spatstat.sparse r-cran-spatstat.univar 215s r-cran-spatstat.utils r-cran-survival r-cran-tensor unzip x11-common 215s xdg-utils zip zlib1g-dev 215s 0 upgraded, 125 newly installed, 0 to remove and 0 not upgraded. 215s Need to get 190 MB of archives. 215s After this operation, 509 MB of additional disk space will be used. 215s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 libisl23 amd64 0.27-1 [685 kB] 216s Get:2 http://ftpmaster.internal/ubuntu questing/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 216s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [11.9 MB] 216s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-14 amd64 14.2.0-19ubuntu2 [1030 B] 216s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 216s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 216s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libcc1-0 amd64 15-20250404-0ubuntu1 [47.1 kB] 216s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 216s Get:9 http://ftpmaster.internal/ubuntu questing/main amd64 libitm1 amd64 15-20250404-0ubuntu1 [29.5 kB] 216s Get:10 http://ftpmaster.internal/ubuntu questing/main amd64 libasan8 amd64 15-20250404-0ubuntu1 [3076 kB] 216s Get:11 http://ftpmaster.internal/ubuntu questing/main amd64 liblsan0 amd64 15-20250404-0ubuntu1 [1362 kB] 216s Get:12 http://ftpmaster.internal/ubuntu questing/main amd64 libtsan2 amd64 15-20250404-0ubuntu1 [2760 kB] 216s Get:13 http://ftpmaster.internal/ubuntu questing/main amd64 libubsan1 amd64 15-20250404-0ubuntu1 [1211 kB] 216s Get:14 http://ftpmaster.internal/ubuntu questing/main amd64 libhwasan0 amd64 15-20250404-0ubuntu1 [1687 kB] 216s Get:15 http://ftpmaster.internal/ubuntu questing/main amd64 libquadmath0 amd64 15-20250404-0ubuntu1 [153 kB] 216s Get:16 http://ftpmaster.internal/ubuntu questing/main amd64 libgcc-14-dev amd64 14.2.0-19ubuntu2 [2815 kB] 216s Get:17 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [23.3 MB] 217s Get:18 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-14 amd64 14.2.0-19ubuntu2 [540 kB] 217s Get:19 http://ftpmaster.internal/ubuntu questing/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 217s Get:20 http://ftpmaster.internal/ubuntu questing/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 217s Get:21 http://ftpmaster.internal/ubuntu questing/main amd64 libstdc++-14-dev amd64 14.2.0-19ubuntu2 [2510 kB] 217s Get:22 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [13.4 MB] 218s Get:23 http://ftpmaster.internal/ubuntu questing/main amd64 g++-14 amd64 14.2.0-19ubuntu2 [23.0 kB] 218s Get:24 http://ftpmaster.internal/ubuntu questing/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 218s Get:25 http://ftpmaster.internal/ubuntu questing/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 218s Get:26 http://ftpmaster.internal/ubuntu questing/main amd64 build-essential amd64 12.12ubuntu1 [5080 B] 218s Get:27 http://ftpmaster.internal/ubuntu questing/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 218s Get:28 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 218s Get:29 http://ftpmaster.internal/ubuntu questing/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 218s Get:30 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig-config amd64 2.15.0-2.2ubuntu1 [37.8 kB] 218s Get:31 http://ftpmaster.internal/ubuntu questing/main amd64 libfontconfig1 amd64 2.15.0-2.2ubuntu1 [164 kB] 218s Get:32 http://ftpmaster.internal/ubuntu questing/main amd64 fontconfig amd64 2.15.0-2.2ubuntu1 [180 kB] 218s Get:33 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran5 amd64 15-20250404-0ubuntu1 [926 kB] 218s Get:34 http://ftpmaster.internal/ubuntu questing/main amd64 libgfortran-14-dev amd64 14.2.0-19ubuntu2 [967 kB] 218s Get:35 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19ubuntu2 [12.5 MB] 218s Get:36 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-14 amd64 14.2.0-19ubuntu2 [14.2 kB] 218s Get:37 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 218s Get:38 http://ftpmaster.internal/ubuntu questing/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 218s Get:39 http://ftpmaster.internal/ubuntu questing/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 218s Get:40 http://ftpmaster.internal/ubuntu questing/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 218s Get:41 http://ftpmaster.internal/ubuntu questing/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 218s Get:42 http://ftpmaster.internal/ubuntu questing/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 218s Get:43 http://ftpmaster.internal/ubuntu questing/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 218s Get:44 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 218s Get:45 http://ftpmaster.internal/ubuntu questing/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 219s Get:46 http://ftpmaster.internal/ubuntu questing/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 219s Get:47 http://ftpmaster.internal/ubuntu questing/main amd64 libcairo2 amd64 1.18.4-1 [662 kB] 219s Get:48 http://ftpmaster.internal/ubuntu questing/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 219s Get:49 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 219s Get:50 http://ftpmaster.internal/ubuntu questing/main amd64 libdeflate-dev amd64 1.23-2 [56.8 kB] 219s Get:51 http://ftpmaster.internal/ubuntu questing/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 219s Get:52 http://ftpmaster.internal/ubuntu questing/universe amd64 libgslcblas0 amd64 2.8+dfsg-5ubuntu1 [113 kB] 219s Get:53 http://ftpmaster.internal/ubuntu questing/universe amd64 libgsl28 amd64 2.8+dfsg-5ubuntu1 [1043 kB] 219s Get:54 http://ftpmaster.internal/ubuntu questing/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 219s Get:55 http://ftpmaster.internal/ubuntu questing/main amd64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 219s Get:56 http://ftpmaster.internal/ubuntu questing/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 219s Get:57 http://ftpmaster.internal/ubuntu questing/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 219s Get:58 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 219s Get:59 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 219s Get:60 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 219s Get:61 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 219s Get:62 http://ftpmaster.internal/ubuntu questing/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 219s Get:63 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 219s Get:64 http://ftpmaster.internal/ubuntu questing/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 219s Get:65 http://ftpmaster.internal/ubuntu questing/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 219s Get:66 http://ftpmaster.internal/ubuntu questing/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 219s Get:67 http://ftpmaster.internal/ubuntu questing/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 219s Get:68 http://ftpmaster.internal/ubuntu questing/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 219s Get:69 http://ftpmaster.internal/ubuntu questing/main amd64 libpango-1.0-0 amd64 1.56.3-1 [256 kB] 219s Get:70 http://ftpmaster.internal/ubuntu questing/main amd64 libpangoft2-1.0-0 amd64 1.56.3-1 [52.9 kB] 219s Get:71 http://ftpmaster.internal/ubuntu questing/main amd64 libpangocairo-1.0-0 amd64 1.56.3-1 [29.1 kB] 219s Get:72 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 219s Get:73 http://ftpmaster.internal/ubuntu questing/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 220s Get:74 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 220s Get:75 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 220s Get:76 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 220s Get:77 http://ftpmaster.internal/ubuntu questing/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 220s Get:78 http://ftpmaster.internal/ubuntu questing/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 220s Get:79 http://ftpmaster.internal/ubuntu questing/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 220s Get:80 http://ftpmaster.internal/ubuntu questing/main amd64 libpng-dev amd64 1.6.47-1.1 [298 kB] 220s Get:81 http://ftpmaster.internal/ubuntu questing/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 220s Get:82 http://ftpmaster.internal/ubuntu questing/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 220s Get:83 http://ftpmaster.internal/ubuntu questing/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 220s Get:84 http://ftpmaster.internal/ubuntu questing/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 220s Get:85 http://ftpmaster.internal/ubuntu questing/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 220s Get:86 http://ftpmaster.internal/ubuntu questing/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 220s Get:87 http://ftpmaster.internal/ubuntu questing/main amd64 libtiff6 amd64 4.7.0-3ubuntu1 [204 kB] 220s Get:88 http://ftpmaster.internal/ubuntu questing/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 220s Get:89 http://ftpmaster.internal/ubuntu questing/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 220s Get:90 http://ftpmaster.internal/ubuntu questing/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 220s Get:91 http://ftpmaster.internal/ubuntu questing/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 220s Get:92 http://ftpmaster.internal/ubuntu questing/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 220s Get:93 http://ftpmaster.internal/ubuntu questing/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 220s Get:94 http://ftpmaster.internal/ubuntu questing/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 220s Get:95 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 221s Get:96 http://ftpmaster.internal/ubuntu questing/main amd64 liblzma-dev amd64 5.6.4-1ubuntu1 [189 kB] 221s Get:97 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 221s Get:98 http://ftpmaster.internal/ubuntu questing/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 221s Get:99 http://ftpmaster.internal/ubuntu questing/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 221s Get:100 http://ftpmaster.internal/ubuntu questing/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 221s Get:101 http://ftpmaster.internal/ubuntu questing/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 221s Get:102 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB] 221s Get:103 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-deldir amd64 2.0-4-1build1 [270 kB] 221s Get:104 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-goftest amd64 1.2-3-1 [59.5 kB] 221s Get:105 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-gsl amd64 2.1-8-1build1 [486 kB] 221s Get:106 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 221s Get:107 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 222s Get:108 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 222s Get:109 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 222s Get:110 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-polyclip amd64 1.10-7-1 [116 kB] 222s Get:111 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB] 222s Get:112 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-rpart amd64 4.1.24-1 [670 kB] 222s Get:113 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-sm amd64 2.2-6.0-1 [788 kB] 222s Get:114 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatial amd64 7.3-18-1 [137 kB] 222s Get:115 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.utils amd64 3.1-3-1 [387 kB] 222s Get:116 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.data all 3.1-6-1 [4153 kB] 222s Get:117 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.univar amd64 3.1-2-1 [315 kB] 222s Get:118 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.geom amd64 3.3-6-1 [3968 kB] 222s Get:119 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.random amd64 3.3-3-1 [1177 kB] 222s Get:120 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-tensor all 1.5-4 [15.7 kB] 222s Get:121 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.sparse amd64 3.1-0-1 [221 kB] 222s Get:122 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.explore amd64 3.3-4-1 [3347 kB] 223s Get:123 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.model amd64 3.3-4-1 [3397 kB] 223s Get:124 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat.linnet amd64 3.2-5-1 [1509 kB] 223s Get:125 http://ftpmaster.internal/ubuntu questing/universe amd64 r-cran-spatstat amd64 3.3-1-1 [4121 kB] 223s Preconfiguring packages ... 223s Fetched 190 MB in 8s (24.8 MB/s) 223s Selecting previously unselected package libisl23:amd64. 223s (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 ... 80518 files and directories currently installed.) 223s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ... 223s Unpacking libisl23:amd64 (0.27-1) ... 223s Selecting previously unselected package libmpc3:amd64. 223s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ... 223s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 224s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 224s Preparing to unpack .../002-cpp-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 224s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 224s Selecting previously unselected package cpp-14. 224s Preparing to unpack .../003-cpp-14_14.2.0-19ubuntu2_amd64.deb ... 224s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 224s Selecting previously unselected package cpp-x86-64-linux-gnu. 224s Preparing to unpack .../004-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 224s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 224s Selecting previously unselected package cpp. 224s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 224s Unpacking cpp (4:14.2.0-1ubuntu1) ... 224s Selecting previously unselected package libcc1-0:amd64. 224s Preparing to unpack .../006-libcc1-0_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libcc1-0:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libgomp1:amd64. 224s Preparing to unpack .../007-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libitm1:amd64. 224s Preparing to unpack .../008-libitm1_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libitm1:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libasan8:amd64. 224s Preparing to unpack .../009-libasan8_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libasan8:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package liblsan0:amd64. 224s Preparing to unpack .../010-liblsan0_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking liblsan0:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libtsan2:amd64. 224s Preparing to unpack .../011-libtsan2_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libtsan2:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libubsan1:amd64. 224s Preparing to unpack .../012-libubsan1_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libubsan1:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libhwasan0:amd64. 224s Preparing to unpack .../013-libhwasan0_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libhwasan0:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libquadmath0:amd64. 224s Preparing to unpack .../014-libquadmath0_15-20250404-0ubuntu1_amd64.deb ... 224s Unpacking libquadmath0:amd64 (15-20250404-0ubuntu1) ... 224s Selecting previously unselected package libgcc-14-dev:amd64. 224s Preparing to unpack .../015-libgcc-14-dev_14.2.0-19ubuntu2_amd64.deb ... 224s Unpacking libgcc-14-dev:amd64 (14.2.0-19ubuntu2) ... 224s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 224s Preparing to unpack .../016-gcc-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 224s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 225s Selecting previously unselected package gcc-14. 225s Preparing to unpack .../017-gcc-14_14.2.0-19ubuntu2_amd64.deb ... 225s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 225s Selecting previously unselected package gcc-x86-64-linux-gnu. 225s Preparing to unpack .../018-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 225s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 225s Selecting previously unselected package gcc. 225s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 225s Unpacking gcc (4:14.2.0-1ubuntu1) ... 225s Selecting previously unselected package libstdc++-14-dev:amd64. 225s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-19ubuntu2_amd64.deb ... 225s Unpacking libstdc++-14-dev:amd64 (14.2.0-19ubuntu2) ... 225s Selecting previously unselected package g++-14-x86-64-linux-gnu. 225s Preparing to unpack .../021-g++-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 225s Unpacking g++-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 225s Selecting previously unselected package g++-14. 225s Preparing to unpack .../022-g++-14_14.2.0-19ubuntu2_amd64.deb ... 225s Unpacking g++-14 (14.2.0-19ubuntu2) ... 225s Selecting previously unselected package g++-x86-64-linux-gnu. 225s Preparing to unpack .../023-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 225s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 225s Selecting previously unselected package g++. 225s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 225s Unpacking g++ (4:14.2.0-1ubuntu1) ... 225s Selecting previously unselected package build-essential. 225s Preparing to unpack .../025-build-essential_12.12ubuntu1_amd64.deb ... 225s Unpacking build-essential (12.12ubuntu1) ... 225s Selecting previously unselected package dctrl-tools. 225s Preparing to unpack .../026-dctrl-tools_2.24-3build3_amd64.deb ... 225s Unpacking dctrl-tools (2.24-3build3) ... 225s Selecting previously unselected package fonts-dejavu-mono. 225s Preparing to unpack .../027-fonts-dejavu-mono_2.37-8_all.deb ... 225s Unpacking fonts-dejavu-mono (2.37-8) ... 225s Selecting previously unselected package fonts-dejavu-core. 225s Preparing to unpack .../028-fonts-dejavu-core_2.37-8_all.deb ... 225s Unpacking fonts-dejavu-core (2.37-8) ... 225s Selecting previously unselected package fontconfig-config. 225s Preparing to unpack .../029-fontconfig-config_2.15.0-2.2ubuntu1_amd64.deb ... 225s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 225s Selecting previously unselected package libfontconfig1:amd64. 225s Preparing to unpack .../030-libfontconfig1_2.15.0-2.2ubuntu1_amd64.deb ... 225s Unpacking libfontconfig1:amd64 (2.15.0-2.2ubuntu1) ... 225s Selecting previously unselected package fontconfig. 225s Preparing to unpack .../031-fontconfig_2.15.0-2.2ubuntu1_amd64.deb ... 225s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 225s Selecting previously unselected package libgfortran5:amd64. 225s Preparing to unpack .../032-libgfortran5_15-20250404-0ubuntu1_amd64.deb ... 225s Unpacking libgfortran5:amd64 (15-20250404-0ubuntu1) ... 226s Selecting previously unselected package libgfortran-14-dev:amd64. 226s Preparing to unpack .../033-libgfortran-14-dev_14.2.0-19ubuntu2_amd64.deb ... 226s Unpacking libgfortran-14-dev:amd64 (14.2.0-19ubuntu2) ... 226s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 226s Preparing to unpack .../034-gfortran-14-x86-64-linux-gnu_14.2.0-19ubuntu2_amd64.deb ... 226s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-19ubuntu2) ... 226s Selecting previously unselected package gfortran-14. 226s Preparing to unpack .../035-gfortran-14_14.2.0-19ubuntu2_amd64.deb ... 226s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 226s Selecting previously unselected package gfortran-x86-64-linux-gnu. 226s Preparing to unpack .../036-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 226s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 226s Selecting previously unselected package gfortran. 226s Preparing to unpack .../037-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 226s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 226s Selecting previously unselected package icu-devtools. 226s Preparing to unpack .../038-icu-devtools_76.1-1ubuntu2_amd64.deb ... 226s Unpacking icu-devtools (76.1-1ubuntu2) ... 226s Selecting previously unselected package libblas3:amd64. 226s Preparing to unpack .../039-libblas3_3.12.1-2_amd64.deb ... 226s Unpacking libblas3:amd64 (3.12.1-2) ... 226s Selecting previously unselected package libblas-dev:amd64. 226s Preparing to unpack .../040-libblas-dev_3.12.1-2_amd64.deb ... 226s Unpacking libblas-dev:amd64 (3.12.1-2) ... 226s Selecting previously unselected package libbz2-dev:amd64. 226s Preparing to unpack .../041-libbz2-dev_1.0.8-6_amd64.deb ... 226s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 226s Selecting previously unselected package libpixman-1-0:amd64. 226s Preparing to unpack .../042-libpixman-1-0_0.44.0-3_amd64.deb ... 226s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 226s Selecting previously unselected package libxcb-render0:amd64. 226s Preparing to unpack .../043-libxcb-render0_1.17.0-2_amd64.deb ... 226s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 226s Selecting previously unselected package libxcb-shm0:amd64. 226s Preparing to unpack .../044-libxcb-shm0_1.17.0-2_amd64.deb ... 226s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 226s Selecting previously unselected package libxrender1:amd64. 226s Preparing to unpack .../045-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 226s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 226s Selecting previously unselected package libcairo2:amd64. 226s Preparing to unpack .../046-libcairo2_1.18.4-1_amd64.deb ... 226s Unpacking libcairo2:amd64 (1.18.4-1) ... 226s Selecting previously unselected package libdatrie1:amd64. 226s Preparing to unpack .../047-libdatrie1_0.2.13-3build1_amd64.deb ... 226s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 226s Selecting previously unselected package libdeflate0:amd64. 226s Preparing to unpack .../048-libdeflate0_1.23-2_amd64.deb ... 226s Unpacking libdeflate0:amd64 (1.23-2) ... 226s Selecting previously unselected package libdeflate-dev:amd64. 226s Preparing to unpack .../049-libdeflate-dev_1.23-2_amd64.deb ... 226s Unpacking libdeflate-dev:amd64 (1.23-2) ... 226s Selecting previously unselected package libgraphite2-3:amd64. 226s Preparing to unpack .../050-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 226s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 226s Selecting previously unselected package libgslcblas0:amd64. 226s Preparing to unpack .../051-libgslcblas0_2.8+dfsg-5ubuntu1_amd64.deb ... 226s Unpacking libgslcblas0:amd64 (2.8+dfsg-5ubuntu1) ... 226s Selecting previously unselected package libgsl28:amd64. 226s Preparing to unpack .../052-libgsl28_2.8+dfsg-5ubuntu1_amd64.deb ... 226s Unpacking libgsl28:amd64 (2.8+dfsg-5ubuntu1) ... 226s Selecting previously unselected package libharfbuzz0b:amd64. 226s Preparing to unpack .../053-libharfbuzz0b_10.2.0-1_amd64.deb ... 226s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 226s Selecting previously unselected package x11-common. 226s Preparing to unpack .../054-x11-common_1%3a7.7+23ubuntu4_all.deb ... 226s Unpacking x11-common (1:7.7+23ubuntu4) ... 226s Selecting previously unselected package libice6:amd64. 226s Preparing to unpack .../055-libice6_2%3a1.1.1-1_amd64.deb ... 226s Unpacking libice6:amd64 (2:1.1.1-1) ... 226s Selecting previously unselected package libicu-dev:amd64. 226s Preparing to unpack .../056-libicu-dev_76.1-1ubuntu2_amd64.deb ... 226s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 227s Selecting previously unselected package libjpeg-turbo8:amd64. 227s Preparing to unpack .../057-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 227s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 227s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 227s Preparing to unpack .../058-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 227s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 227s Selecting previously unselected package libjpeg8:amd64. 227s Preparing to unpack .../059-libjpeg8_8c-2ubuntu11_amd64.deb ... 227s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 227s Selecting previously unselected package libjpeg8-dev:amd64. 227s Preparing to unpack .../060-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 227s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 227s Selecting previously unselected package libjpeg-dev:amd64. 227s Preparing to unpack .../061-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 227s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 227s Selecting previously unselected package liblapack3:amd64. 227s Preparing to unpack .../062-liblapack3_3.12.1-2_amd64.deb ... 227s Unpacking liblapack3:amd64 (3.12.1-2) ... 227s Selecting previously unselected package liblapack-dev:amd64. 227s Preparing to unpack .../063-liblapack-dev_3.12.1-2_amd64.deb ... 227s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 227s Selecting previously unselected package liblerc4:amd64. 227s Preparing to unpack .../064-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 227s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 227s Selecting previously unselected package libncurses-dev:amd64. 227s Preparing to unpack .../065-libncurses-dev_6.5+20250216-2_amd64.deb ... 227s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ... 227s Selecting previously unselected package libthai-data. 227s Preparing to unpack .../066-libthai-data_0.1.29-2build1_all.deb ... 227s Unpacking libthai-data (0.1.29-2build1) ... 227s Selecting previously unselected package libthai0:amd64. 227s Preparing to unpack .../067-libthai0_0.1.29-2build1_amd64.deb ... 227s Unpacking libthai0:amd64 (0.1.29-2build1) ... 227s Selecting previously unselected package libpango-1.0-0:amd64. 227s Preparing to unpack .../068-libpango-1.0-0_1.56.3-1_amd64.deb ... 227s Unpacking libpango-1.0-0:amd64 (1.56.3-1) ... 227s Selecting previously unselected package libpangoft2-1.0-0:amd64. 227s Preparing to unpack .../069-libpangoft2-1.0-0_1.56.3-1_amd64.deb ... 227s Unpacking libpangoft2-1.0-0:amd64 (1.56.3-1) ... 227s Selecting previously unselected package libpangocairo-1.0-0:amd64. 227s Preparing to unpack .../070-libpangocairo-1.0-0_1.56.3-1_amd64.deb ... 227s Unpacking libpangocairo-1.0-0:amd64 (1.56.3-1) ... 227s Selecting previously unselected package libpaper2:amd64. 227s Preparing to unpack .../071-libpaper2_2.2.5-0.3_amd64.deb ... 227s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 227s Selecting previously unselected package libpaper-utils. 227s Preparing to unpack .../072-libpaper-utils_2.2.5-0.3_amd64.deb ... 227s Unpacking libpaper-utils (2.2.5-0.3) ... 227s Selecting previously unselected package libpcre2-16-0:amd64. 227s Preparing to unpack .../073-libpcre2-16-0_10.45-1_amd64.deb ... 227s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 227s Selecting previously unselected package libpcre2-32-0:amd64. 227s Preparing to unpack .../074-libpcre2-32-0_10.45-1_amd64.deb ... 227s Unpacking 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Setting up r-cran-survival (3.8-3-1) ... 232s Setting up gfortran (4:14.2.0-1ubuntu1) ... 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 232s 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 232s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 232s 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 232s Setting up r-cran-spatstat.data (3.1-6-1) ... 232s Setting up r-cran-spatstat.geom (3.3-6-1) ... 232s Setting up r-base-dev (4.4.3-1) ... 232s Setting up r-cran-rpart (4.1.24-1) ... 232s Setting up r-cran-spatstat.random (3.3-3-1) ... 232s Setting up r-cran-spatstat.explore (3.3-4-1) ... 232s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 232s Setting up r-cran-spatstat.model (3.3-4-1) ... 232s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 232s Setting up r-cran-spatstat (3.3-1-1) ... 232s Processing triggers for install-info (7.1.1-1) ... 232s Processing triggers for libc-bin (2.41-6ubuntu1) ... 232s Processing triggers for man-db (2.13.0-1) ... 236s autopkgtest [18:58:08]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 236s autopkgtest [18:58:08]: test pkg-r-autopkgtest: [----------------------- 237s Test: Try to load the R library spatstat.explore 237s 237s R version 4.4.3 (2025-02-28) -- "Trophy Case" 237s Copyright (C) 2025 The R Foundation for Statistical Computing 237s Platform: x86_64-pc-linux-gnu 237s 237s R is free software and comes with ABSOLUTELY NO WARRANTY. 237s You are welcome to redistribute it under certain conditions. 237s Type 'license()' or 'licence()' for distribution details. 237s 237s R is a collaborative project with many contributors. 237s Type 'contributors()' for more information and 237s 'citation()' on how to cite R or R packages in publications. 237s 237s Type 'demo()' for some demos, 'help()' for on-line help, or 237s 'help.start()' for an HTML browser interface to help. 237s Type 'q()' to quit R. 237s 237s > library('spatstat.explore') 237s Loading required package: spatstat.data 237s Loading required package: spatstat.univar 237s spatstat.univar 3.1-2 237s Loading required package: spatstat.geom 237s spatstat.geom 3.3-6 237s Loading required package: spatstat.random 238s spatstat.random 3.3-3 238s Loading required package: nlme 238s spatstat.explore 3.3-4 238s > 238s > 238s Other tests are currently unsupported! 238s They will be progressively added. 238s autopkgtest [18:58:10]: test pkg-r-autopkgtest: -----------------------] 238s pkg-r-autopkgtest PASS 238s autopkgtest [18:58:10]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 239s autopkgtest [18:58:11]: @@@@@@@@@@@@@@@@@@@@ summary 239s run-unit-test PASS 239s pkg-r-autopkgtest PASS 255s nova [W] Skipping flock for amd64 255s Creating nova instance adt-questing-amd64-r-cran-spatstat.explore-20250503-185411-juju-7f2275-prod-proposed-migration-environment-23-68191334-26bb-4788-9a31-31cb2a03847c from image adt/ubuntu-questing-amd64-server-20250503.img (UUID 57b7c1b6-ad80-4bdb-b031-36f045f7f3b3)... 255s nova [W] Timed out waiting for 4d8e461b-166d-4982-8a52-0f0851f9d79d to get deleted. 255s nova [W] Skipping flock for amd64 255s Creating nova instance adt-questing-amd64-r-cran-spatstat.explore-20250503-185411-juju-7f2275-prod-proposed-migration-environment-23-68191334-26bb-4788-9a31-31cb2a03847c from image adt/ubuntu-questing-amd64-server-20250503.img (UUID 57b7c1b6-ad80-4bdb-b031-36f045f7f3b3)... 255s nova [W] Timed out waiting for e8fe0e99-fd37-4b2b-a4c5-2ef203392f5a to get deleted.