0s autopkgtest [10:49:02]: starting date and time: 2025-05-02 10:49:02+0000 0s autopkgtest [10:49:02]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [10:49:02]: host juju-7f2275-prod-proposed-migration-environment-23; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sal3x2jg/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-23@bos03-arm64-2.secgroup --name adt-questing-arm64-r-cran-spatstat.explore-20250502-104902-juju-7f2275-prod-proposed-migration-environment-23-91a488c2-ddb4-4d55-ac1d-1054177d0d9f --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-23 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 83s autopkgtest [10:50:25]: testbed dpkg architecture: arm64 84s autopkgtest [10:50:26]: testbed apt version: 3.0.0 84s autopkgtest [10:50:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s autopkgtest [10:50:26]: testbed release detected to be: None 85s autopkgtest [10:50:27]: updating testbed package index (apt update) 85s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 86s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 86s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [44.4 kB] 86s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [175 kB] 86s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2076 kB] 86s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [219 kB] 86s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1509 kB] 86s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [15.4 kB] 87s Fetched 4149 kB in 1s (3369 kB/s) 88s Reading package lists... 88s autopkgtest [10:50:30]: upgrading testbed (apt dist-upgrade and autopurge) 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 90s Starting 2 pkgProblemResolver with broken count: 0 90s Done 91s Entering ResolveByKeep 91s 91s Calculating upgrade... 92s The following packages will be upgraded: 92s htop mtd-utils nano 92s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 936 kB of archives. 92s After this operation, 727 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 nano arm64 8.4-1 [290 kB] 92s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 htop arm64 3.4.1-4 [177 kB] 93s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 mtd-utils arm64 1:2.3.0-1ubuntu1 [469 kB] 93s Fetched 936 kB in 1s (1194 kB/s) 94s (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 ... 117820 files and directories currently installed.) 94s Preparing to unpack .../archives/nano_8.4-1_arm64.deb ... 94s Unpacking nano (8.4-1) over (8.3-1) ... 94s Preparing to unpack .../htop_3.4.1-4_arm64.deb ... 94s Unpacking htop (3.4.1-4) over (3.4.0-2) ... 94s Preparing to unpack .../mtd-utils_1%3a2.3.0-1ubuntu1_arm64.deb ... 94s Unpacking mtd-utils (1:2.3.0-1ubuntu1) over (1:2.2.0-2ubuntu2) ... 94s Setting up htop (3.4.1-4) ... 94s Setting up mtd-utils (1:2.3.0-1ubuntu1) ... 94s Setting up nano (8.4-1) ... 94s Installing new version of config file /etc/nanorc ... 94s Processing triggers for man-db (2.13.0-1) ... 95s Processing triggers for install-info (7.1.1-1) ... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 97s Solving dependencies... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [10:50:42]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 101s autopkgtest [10:50:43]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-spatstat.explore 103s Get:1 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (dsc) [2563 B] 103s Get:2 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (tar) [668 kB] 103s Get:3 http://ftpmaster.internal/ubuntu questing/universe r-cran-spatstat.explore 3.3-4-1 (diff) [3452 B] 103s gpgv: Signature made Fri Jan 31 07:56:43 2025 UTC 103s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 103s gpgv: issuer "plessy@debian.org" 103s gpgv: Can't check signature: No public key 103s dpkg-source: warning: cannot verify inline signature for ./r-cran-spatstat.explore_3.3-4-1.dsc: no acceptable signature found 103s autopkgtest [10:50:45]: testing package r-cran-spatstat.explore version 3.3-4-1 104s autopkgtest [10:50:46]: build not needed 105s autopkgtest [10:50:47]: test run-unit-test: preparing testbed 105s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Starting pkgProblemResolver with broken count: 0 107s Starting 2 pkgProblemResolver with broken count: 0 107s Done 108s The following NEW packages will be installed: 108s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libblas3 108s libcairo2 libdatrie1 libdeflate0 libfontconfig1 libgfortran5 libgomp1 108s libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b libice6 libjbig0 108s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libpango-1.0-0 108s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 108s libsharpyuv0 libsm6 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 108s libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 108s r-base-core r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 108s r-cran-lattice r-cran-locfit r-cran-matrix r-cran-mgcv r-cran-nlme 108s r-cran-polyclip r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat 108s r-cran-spatstat.data r-cran-spatstat.explore r-cran-spatstat.geom 108s r-cran-spatstat.linnet r-cran-spatstat.model r-cran-spatstat.random 108s r-cran-spatstat.sparse r-cran-spatstat.univar r-cran-spatstat.utils 108s r-cran-survival r-cran-tensor unzip x11-common xdg-utils zip 108s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 84.2 MB of archives. 108s After this operation, 140 MB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 108s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 109s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 109s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 109s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig arm64 2.15.0-2.2ubuntu1 [191 kB] 109s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 109s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 109s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 109s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 109s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 109s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 109s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 109s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 109s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 109s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 109s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 109s Get:17 http://ftpmaster.internal/ubuntu questing/universe arm64 libgslcblas0 arm64 2.8+dfsg-5ubuntu1 [87.4 kB] 109s Get:18 http://ftpmaster.internal/ubuntu questing/universe arm64 libgsl28 arm64 2.8+dfsg-5ubuntu1 [982 kB] 109s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 109s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 109s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 109s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 109s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 109s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 110s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 110s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 110s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 110s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 110s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 110s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 110s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 110s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 110s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 110s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 110s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 110s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 110s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 110s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 110s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 110s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 110s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 110s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 110s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 110s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 110s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 110s Get:46 http://ftpmaster.internal/ubuntu questing/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 112s Get:47 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 112s Get:48 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 112s Get:49 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 112s Get:50 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-gsl arm64 2.1-8-1build1 [485 kB] 112s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 112s Get:52 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-locfit arm64 1.5-9.12-1 [514 kB] 112s Get:53 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 112s Get:54 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 112s Get:55 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 112s Get:56 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 112s Get:57 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 112s Get:58 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 112s Get:59 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 112s Get:60 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 112s Get:61 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.utils arm64 3.1-3-1 [386 kB] 112s Get:62 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.data all 3.1-6-1 [4153 kB] 112s Get:63 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.univar arm64 3.1-2-1 [314 kB] 112s Get:64 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.geom arm64 3.3-6-1 [3941 kB] 113s Get:65 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.random arm64 3.3-3-1 [1163 kB] 113s Get:66 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 113s Get:67 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 113s Get:68 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 113s Get:69 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 113s Get:70 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 113s Get:71 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 113s Preconfiguring packages ... 113s Fetched 84.2 MB in 5s (16.2 MB/s) 113s Selecting previously unselected package fonts-dejavu-mono. 114s (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 ... 117821 files and directories currently installed.) 114s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-mono (2.37-8) ... 114s Selecting previously unselected package fonts-dejavu-core. 114s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 114s Unpacking fonts-dejavu-core (2.37-8) ... 114s Selecting previously unselected package fontconfig-config. 114s Preparing to unpack .../02-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 114s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 114s Selecting previously unselected package libfontconfig1:arm64. 114s Preparing to unpack .../03-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 114s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 114s Selecting previously unselected package fontconfig. 114s Preparing to unpack .../04-fontconfig_2.15.0-2.2ubuntu1_arm64.deb ... 114s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 114s Selecting previously unselected package libblas3:arm64. 114s Preparing to unpack .../05-libblas3_3.12.1-2_arm64.deb ... 114s Unpacking libblas3:arm64 (3.12.1-2) ... 114s Selecting previously unselected package libpixman-1-0:arm64. 114s Preparing to unpack .../06-libpixman-1-0_0.44.0-3_arm64.deb ... 114s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 114s Selecting previously unselected package libxcb-render0:arm64. 114s Preparing to unpack .../07-libxcb-render0_1.17.0-2_arm64.deb ... 114s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 114s Selecting previously unselected package libxcb-shm0:arm64. 114s Preparing to unpack .../08-libxcb-shm0_1.17.0-2_arm64.deb ... 114s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 114s Selecting previously unselected package libxrender1:arm64. 114s Preparing to unpack .../09-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 114s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 114s Selecting previously unselected package libcairo2:arm64. 114s Preparing to unpack .../10-libcairo2_1.18.4-1_arm64.deb ... 114s Unpacking libcairo2:arm64 (1.18.4-1) ... 115s Selecting previously unselected package libdatrie1:arm64. 115s Preparing to unpack .../11-libdatrie1_0.2.13-3build1_arm64.deb ... 115s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 115s Selecting previously unselected package libdeflate0:arm64. 115s Preparing to unpack .../12-libdeflate0_1.23-1_arm64.deb ... 115s Unpacking libdeflate0:arm64 (1.23-1) ... 115s Selecting previously unselected package libgfortran5:arm64. 115s Preparing to unpack .../13-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 115s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 115s Selecting previously unselected package libgomp1:arm64. 115s Preparing to unpack .../14-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 115s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 115s Selecting previously unselected package libgraphite2-3:arm64. 115s Preparing to unpack .../15-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 115s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 115s Selecting previously unselected package libgslcblas0:arm64. 115s Preparing to unpack .../16-libgslcblas0_2.8+dfsg-5ubuntu1_arm64.deb ... 115s Unpacking libgslcblas0:arm64 (2.8+dfsg-5ubuntu1) ... 115s Selecting previously unselected package libgsl28:arm64. 115s Preparing to unpack .../17-libgsl28_2.8+dfsg-5ubuntu1_arm64.deb ... 115s Unpacking libgsl28:arm64 (2.8+dfsg-5ubuntu1) ... 115s Selecting previously unselected package libharfbuzz0b:arm64. 115s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_arm64.deb ... 115s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 115s Selecting previously unselected package x11-common. 115s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu4_all.deb ... 115s Unpacking x11-common (1:7.7+23ubuntu4) ... 115s Selecting previously unselected package libice6:arm64. 115s Preparing to unpack .../20-libice6_2%3a1.1.1-1_arm64.deb ... 115s Unpacking libice6:arm64 (2:1.1.1-1) ... 115s Selecting previously unselected package libjpeg-turbo8:arm64. 115s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 115s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 115s Selecting previously unselected package libjpeg8:arm64. 115s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_arm64.deb ... 115s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 115s Selecting previously unselected package liblapack3:arm64. 115s Preparing to unpack .../23-liblapack3_3.12.1-2_arm64.deb ... 115s Unpacking liblapack3:arm64 (3.12.1-2) ... 115s Selecting previously unselected package liblerc4:arm64. 115s Preparing to unpack .../24-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 115s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 115s Selecting previously unselected package libthai-data. 115s Preparing to unpack .../25-libthai-data_0.1.29-2build1_all.deb ... 115s Unpacking libthai-data (0.1.29-2build1) ... 115s Selecting previously unselected package libthai0:arm64. 115s Preparing to unpack .../26-libthai0_0.1.29-2build1_arm64.deb ... 115s Unpacking libthai0:arm64 (0.1.29-2build1) ... 116s Selecting previously unselected package libpango-1.0-0:arm64. 116s Preparing to unpack .../27-libpango-1.0-0_1.56.3-1_arm64.deb ... 116s Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... 116s Selecting previously unselected package libpangoft2-1.0-0:arm64. 116s Preparing to unpack .../28-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... 116s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... 116s Selecting 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(2025-02-28) -- "Trophy Case" 124s Copyright (C) 2025 The R Foundation for Statistical Computing 124s Platform: aarch64-unknown-linux-gnu 124s 124s R is free software and comes with ABSOLUTELY NO WARRANTY. 124s You are welcome to redistribute it under certain conditions. 124s Type 'license()' or 'licence()' for distribution details. 124s 124s R is a collaborative project with many contributors. 124s Type 'contributors()' for more information and 124s 'citation()' on how to cite R or R packages in publications. 124s 124s Type 'demo()' for some demos, 'help()' for on-line help, or 124s 'help.start()' for an HTML browser interface to help. 124s Type 'q()' to quit R. 124s 124s > #' 124s > #' Header for all (concatenated) test files 124s > #' 124s > #' Require spatstat.explore 124s > #' Obtain environment variable controlling tests. 124s > #' 124s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 124s > 124s > require(spatstat.explore) 124s Loading required package: spatstat.explore 124s Loading required package: spatstat.data 125s Loading required package: spatstat.univar 125s spatstat.univar 3.1-2 125s Loading required package: spatstat.geom 125s spatstat.geom 3.3-6 125s Loading required package: spatstat.random 125s spatstat.random 3.3-3 125s Loading required package: nlme 125s spatstat.explore 3.3-4 125s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 125s > ALWAYS <- TRUE 125s > cat(paste("--------- Executing", 125s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 125s + "test code -----------\n")) 125s --------- Executing **RESTRICTED** subset of test code ----------- 125s > ## tests/cdf.test.R 125s > 125s > 125s > local({ 125s + NSIM <- 9 125s + op <- spatstat.options(ndummy.min=16, npixel=32) 125s + AA <- split(ants, un=FALSE) 125s + AC <- AA[["Cataglyphis"]] 125s + AM <- AA[["Messor"]] 125s + DM <- distmap(AM) 125s + if(ALWAYS) { 125s + ## Check cdf.test with strange data 125s + ## Marked point patterns with some marks not represented 125s + ## should produce a warning, rather than a crash: 125s + cdf.test(AC, DM) 125s + } 125s + if(FULLTEST) { 125s + ## should be OK: 125s + cdf.test(unmark(AC), DM) 125s + cdf.test(unmark(AC), DM, "cvm") 125s + cdf.test(unmark(AC), DM, "ad") 125s + ## other code blocks 125s + cdf.test(finpines, "x") 125s + } 125s + }) 125s > 125s > 125s > #' tests/circular.R 125s > #' 125s > #' Circular data and periodic distributions 125s > #' 125s > #' $Revision: 1.4 $ $Date: 2020/04/28 12:58:26 $ 125s > 125s > 125s > local({ 125s + if(ALWAYS) { 125s + a <- pairorient(redwood, 0.05, 0.15, correction="none") 125s + rose(a) 125s + Warning message: 125s In cdf.test.ppp(AC, DM) : 125s Ignoring marks, because some mark values have zero frequency 125s } 125s + if(FULLTEST) { 125s + b <- pairorient(redwood, 0.05, 0.15, correction="best") 125s + rose(b, start="N", clockwise=TRUE) 125s + } 125s + if(ALWAYS) { 125s + #' arcs on the circle 125s + #' (depends on numerical behaviour) 125s + set.seed(19171025) 125s + aa <- replicate(7, runif(1, 0, 2*pi) + c(0, runif(1, 0, pi)), 125s + simplify=FALSE) 125s + bb <- circunion(aa) 125s + 125s + assertsingle <- function(x, a, id) { 125s + y <- circunion(x) 125s + if(length(y) != 1 || max(abs(y[[1]] - a)) > .Machine$double.eps) 125s + stop(paste("Incorrect result from circunion in case", id), 125s + call.=FALSE) 125s + invisible(NULL) 125s + } 125s + 125s + assertsingle(list(c(pi/3, pi), c(pi/2, 3*pi/2)), 125s + c(pi/3, 3*pi/2), 125s + 1) 125s + assertsingle(list(c(0, pi/2), c(pi/4, pi)), 125s + c(0,pi), 125s + 2) 125s + assertsingle(list(c(-pi/4, pi/2), c(pi/4, pi)), 126s + c((2-1/4)*pi, pi), 126s + 3) 126s + } 126s + }) 126s > 126s > 126s > #' 126s > #' tests/closecore.R 126s > #' 126s > #' check 'closepairs/crosspairs' code 126s > #' invoked in core package 126s > #' 126s > #' $Revision: 1.4 $ $Date: 2021/04/17 04:16:43 $ 126s > #' 126s > #' ------- All this code must be run on every hardware ------- 126s > #' 126s > 126s > local({ 126s + #' weightedclosepairs is in wtdclosepair.R 126s + wi <- weightedclosepairs(redwood, 0.05, "isotropic") 126s + if(FULLTEST) { 126s + wt <- weightedclosepairs(redwood, 0.05, "translate") 126s + wp <- weightedclosepairs(redwood, 0.05, "periodic") 126s + } 126s + #' markmarkscatter uses closepairs.pp3 126s + X <- runifpoint3(100) 126s + marks(X) <- runif(100) 126s + markmarkscatter(X, 0.2) 126s + if(FULLTEST) { 126s + markmarkscatter(X[FALSE], 0.2) 126s + } 126s + }) 126s > 126s > #' 126s > #' contact.R 126s > #' 126s > #' Check machinery for first contact distributions 126s > #' 126s > #' $Revision: 1.8 $ $Date: 2021/04/17 02:25:55 $ 126s > 126s > local({ 126s + if(ALWAYS) { 126s + #' reduce complexity 126s + Y <- as.mask(heather$coarse, dimyx=c(50, 25)) 126s + 126s + X <- runifpoint(100, win = complement.owin(Y)) 126s + if(FULLTEST) G <- Gfox(X, Y) 126s + J <- Jfox(X, Y) 126s + 126s + Y <- as.polygonal(Y) 126s + X <- runifpoint(100, win = complement.owin(Y)) 126s + if(FULLTEST) G <- Gfox(X, Y) 126s + J <- Jfox(X, Y) 126s + 126s + op <- spatstat.options(exactdt.checks.data=TRUE) 126s + U <- exactdt(X) 126s + spatstat.options(op) 126s + } 126s + }) 126s > 126s > reset.spatstat.options() 126s > 126s BEGIN TEST testsD.R 126s 126s R version 4.4.3 (2025-02-28) -- "Trophy Case" 126s Copyright (C) 2025 The R Foundation for Statistical Computing 126s Platform: aarch64-unknown-linux-gnu 126s 126s R is free software and comes with ABSOLUTELY NO WARRANTY. 126s You are welcome to redistribute it under certain conditions. 126s Type 'license()' or 'licence()' for distribution details. 126s 126s R is a collaborative project with many contributors. 126s Type 'contributors()' for more information and 126s 'citation()' on how to cite R or R packages in publications. 126s 126s Type 'demo()' for some demos, 'help()' for on-line help, or 126s 'help.start()' for an HTML browser interface to help. 126s Type 'q()' to quit R. 126s 126s > #' 126s > #' Header for all (concatenated) test files 126s > #' 126s > #' Require spatstat.explore 126s > #' Obtain environment variable controlling tests. 126s > #' 126s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 126s > 126s > require(spatstat.explore) 126s Loading required package: spatstat.explore 126s 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 128s Loading required package: spatstat.random 128s spatstat.random 3.3-3 128s 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/density.R 128s > #' 128s > #' Test behaviour of density() methods, 128s > #' relrisk(), Smooth() 128s > #' and inhomogeneous summary functions 128s > #' and idw, adaptive.density, intensity 128s > #' and SpatialMedian, SpatialQuantile 128s > #' 128s > #' $Revision: 1.67 $ $Date: 2024/01/29 07:07:16 $ 128s > #' 128s > 128s > if(!FULLTEST) 128s + spatstat.options(npixel=32, ndummy.min=16) 128s > 128s > 128s > local({ 128s + 128s + # test all cases of density.ppp and densityfun.ppp 128s + 128s + tryit <- function(..., do.fun=TRUE, badones=FALSE) { 128s + Z <- density(cells, ..., at="pixels") 128s + Z <- density(cells, ..., at="points") 128s + if(do.fun) { 128s + f <- densityfun(cells, ...) 128s + U <- f(0.1, 0.3) 128s + if(badones) { 128s + U2 <- f(1.1, 0.3) 128s + U3 <- f(1.1, 0.3, drop=FALSE) 128s + } 128s + } 128s + return(invisible(NULL)) 128s + } 128s + 128s + if(ALWAYS) { 128s + tryit(0.05) 128s + tryit(0.05, diggle=TRUE) 128s + tryit(0.05, se=TRUE) 128s + tryit(0.05, weights=expression(x)) 128s + tryit(0.07, kernel="epa") 128s + tryit(sigma=Inf) 128s + tryit(0.05, badones=TRUE) 128s + } 128s + if(FULLTEST) { 128s + tryit(0.07, kernel="quartic") 128s + tryit(0.07, kernel="disc") 128s + tryit(0.07, kernel="epa", weights=expression(x)) 128s + tryit(sigma=Inf, weights=expression(x)) 128s + } 128s + 128s + V <- diag(c(0.05^2, 0.07^2)) 128s + 128s + if(ALWAYS) { 128s + tryit(varcov=V) 128s + } 128s + if(FULLTEST) { 128s + tryit(varcov=V, diggle=TRUE) 128s + tryit(varcov=V, weights=expression(x)) 128s + tryit(varcov=V, weights=expression(x), diggle=TRUE) 128s + Z <- distmap(runifpoint(5, Window(cells))) 128s + tryit(0.05, weights=Z) 128s + tryit(0.05, weights=Z, diggle=TRUE) 128s + } 128s + 128s + trymost <- function(...) tryit(..., do.fun=FALSE) 128s + wdf <- data.frame(a=1:42,b=42:1) 128s + if(ALWAYS) { 128s + trymost(0.05, weights=wdf) 128s + trymost(sigma=Inf, weights=wdf) 128s + } 128s + if(FULLTEST) { 128s + trymost(0.05, weights=wdf, diggle=TRUE) 128s + trymost(varcov=V, weights=wdf) 128s + trymost(varcov=V, weights=expression(cbind(x,y))) 128s + } 128s + 128s + ## check conservation of mass 128s + checkconserve <- function(X, xname, sigma, toler=0.01) { 128s + veritas <- npoints(X) 128s + vino <- integral(density(X, sigma, diggle=TRUE)) 128s + relerr <- abs(vino - veritas)/veritas 128s + if(relerr > toler) 128s + stop(paste("density.ppp(diggle=TRUE) fails to conserve mass:", 128s + vino, "!=", veritas, 128s + "for", sQuote(xname)), 128s + call.=FALSE) 128s + return(relerr) 128s + } 128s + if(FULLTEST) { 128s + checkconserve(cells, "cells", 0.15) 128s + } 128s + if(ALWAYS) { 128s + checkconserve(split(chorley)[["lung"]], "lung", 2) 128s + } 128s + 128s + ## run C algorithm 'denspt' 128s + opa <- spatstat.options(densityC=TRUE, densityTransform=FALSE) 128s + if(ALWAYS) { 128s + tryit(varcov=V) 128s + } 128s + if(FULLTEST) { 128s + tryit(varcov=V, weights=expression(x)) 128s + trymost(varcov=V, weights=wdf) 128s + } 128s + spatstat.options(opa) 128s + 128s + crossit <- function(..., sigma=NULL) { 128s + U <- runifpoint(20, Window(cells)) 128s + a <- densitycrossEngine(cells, U, ..., sigma=sigma) 128s + a <- densitycrossEngine(cells, U, ..., sigma=sigma, diggle=TRUE) 128s + invisible(NULL) 128s + } 128s + if(ALWAYS) { 128s + crossit(varcov=V, weights=cells$x) 128s + crossit(sigma=Inf) 128s + } 128s + if(FULLTEST) { 128s + crossit(varcov=V, weights=wdf) 128s + crossit(sigma=0.1, weights=wdf) 128s + crossit(sigma=0.1, kernel="epa", weights=wdf) 128s + } 128s + 128s + ## apply different discretisation rules 128s + if(ALWAYS) { 128s + Z <- density(cells, 0.05, fractional=TRUE) 128s + } 128s + if(FULLTEST) { 128s + Z <- density(cells, 0.05, preserve=TRUE) 128s + Z <- density(cells, 0.05, fractional=TRUE, preserve=TRUE) 128s + } 128s + 128s + ## compare results with different algorithms 128s + crosscheque <- function(expr) { 128s + e <- as.expression(substitute(expr)) 128s + ename <- sQuote(deparse(substitute(expr))) 128s + ## interpreted R 128s + opa <- spatstat.options(densityC=FALSE, densityTransform=FALSE) 128s + val.interpreted <- eval(e) 128s + ## established C algorithm 'denspt' 128s + spatstat.options(densityC=TRUE, densityTransform=FALSE) 128s + val.C <- eval(e) 128s + ## new C algorithm 'Gdenspt' using transformed coordinates 128s + spatstat.options(densityC=TRUE, densityTransform=TRUE) 128s + val.Transform <- eval(e) 128s + spatstat.options(opa) 128s + if(max(abs(val.interpreted - val.C)) > 0.001) 128s + stop(paste("Numerical discrepancy between R and C algorithms in", 128s + ename)) 128s + if(max(abs(val.C - val.Transform)) > 0.001) 128s + stop(paste("Numerical discrepancy between C algorithms", 128s + "using transformed and untransformed coordinates in", 128s + ename)) 128s + invisible(NULL) 128s + } 128s + 128s + ## execute & compare results of density(at="points") with different algorithms 128s + wdfr <- cbind(1:npoints(redwood), 2) 128s + if(ALWAYS) { 128s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE)) 128s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 128s + weights=wdfr[,1])) 128s + crosscheque(density(redwood, at="points", sigma=0.13, edge=FALSE, 128s + weights=wdfr)) 128s + } 128s + 128s + ## correctness of non-Gaussian kernel calculation 128s + leavein <- function(ker, maxd=0.025) { 128s + ZI <- density(redwood, 0.12, kernel=ker, edge=FALSE, 128s + dimyx=256)[redwood] 128s + ZP <- density(redwood, 0.12, kernel=ker, edge=FALSE, 128s + at="points", leaveoneout=FALSE) 128s + discrep <- max(abs(ZP - ZI))/npoints(redwood) 128s + if(discrep > maxd) 128s + stop(paste("Discrepancy", 128s + signif(discrep, 3), 128s + "in calculation for", ker, "kernel")) 128s + return(invisible(NULL)) 128s + } 128s + if(ALWAYS) { 128s + leavein("epanechnikov", 0.015) 128s + } 128s + if(FULLTEST) { 128s + leavein("quartic", 0.010) 128s + leavein("disc", 0.100) 128s + } 128s + 128s + ## bandwidth selection code blocks 128s + sigvec <- 0.01 * 2:15 128s + sigran <- range(sigvec) 128s + if(ALWAYS) { 128s + bw.ppl(redwood, sigma=sigvec) 128s + bw.CvL(redwood, sigma=sigvec) 128s + } 128s + if(FULLTEST) { 128s + bw.ppl(redwood, srange=sigran, ns=5) 128s + bw.CvL(redwood, srange=sigran, ns=5) 128s + } 128s + ## adaptive bandwidth 128s + if(ALWAYS) { 128s + a <- bw.abram(redwood) 128s + } 128s + if(FULLTEST) { 128s + a <- bw.abram(redwood, pilot=density(redwood, 0.2)) 128s + a <- bw.abram(redwood, smoother="densityVoronoi", at="pixels") 128s + } 128s + 128s + ## Kinhom 128s + if(ALWAYS) { 128s + lam <- density(redwood) 128s + K <- Kinhom(redwood, lam) 128s + 128s + lamX <- density(redwood, at="points") 128s + KX <- Kinhom(redwood, lamX) 128s + } 128s + 128s + ## test all code cases of new 'relrisk.ppp' algorithm 128s + pants <- function(..., X=ants, sigma=100, se=TRUE) { 128s + a <- relrisk(X, sigma=sigma, se=se, ...) 128s + return(TRUE) 128s + } 128s + if(ALWAYS) { 128s + pants() 128s + pants(diggle=TRUE) 128s + pants(edge=FALSE) 128s + pants(at="points") 128s + pants(casecontrol=FALSE) 128s + pants(relative=TRUE) 128s + pants(sigma=Inf) 128s + pants(sigma=NULL, varcov=diag(c(100,100)^2)) 128s + f <- 1/area(Window(ants)) 128s + pants(fudge=f) 128s + } 128s + if(FULLTEST) { 128s + pants(diggle=TRUE, at="points") 128s + pants(edge=FALSE, at="points", fudge=f) 128s + pants(casecontrol=FALSE, relative=TRUE) 128s + pants(casecontrol=FALSE,at="points") 128s + pants(relative=TRUE,at="points", fudge=f) 128s + pants(casecontrol=FALSE, relative=TRUE,at="points") 128s + pants(relative=TRUE, control="Cataglyphis", case="Messor", fudge=f) 128s + pants(relative=TRUE, control="Cataglyphis", case="Messor", at="points") 128s + pants(casecontrol=FALSE, case="Messor", se=FALSE) 128s + pants(case=2, at="pixels", relative=TRUE) 128s + pants(case=2, at="points", relative=TRUE) 128s + pants(case=2, at="pixels", relative=FALSE) 128s + pants(case=2, at="points", relative=FALSE) 128s + } 128s + if(ALWAYS) { 128s + ## underflow example from stackoverflow! 128s + funky <- scanpp("funky.tab", owin(c(4, 38), c(0.3, 17))) 128s + P <- relrisk(funky, 0.5) 128s + R <- relrisk(funky, 0.5, relative=TRUE) 128s + } 128s + ## more than 2 types 128s + if(ALWAYS) { 128s + pants(X=sporophores) 128s + pants(X=sporophores, sigma=20, at="points") 128s + pants(X=sporophores, sigma=20, at="points", fudge=f) 128s + bw.relrisk(sporophores, method="leastsquares") 128s + } 128s + if(FULLTEST) { 128s + pants(X=sporophores, sigma=20, relative=TRUE, at="points", fudge=f) 128s + pants(X=sporophores, sigma=20, at="pixels", se=FALSE) 128s + pants(X=sporophores, sigma=20, relative=TRUE, at="pixels", se=FALSE) 128s + bw.relrisk(sporophores, method="weightedleastsquares") 128s + } 128s + 128s + ## execute Smooth.ppp and Smoothfun.ppp in all cases 128s + stroke <- function(..., Y = longleaf, FUN=TRUE) { 128s + Z <- Smooth(Y, ..., at="pixels") 128s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 128s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 128s + if(FUN) { 128s + f <- Smoothfun(Y, ...) 128s + f(120, 80) 128s + f(Y[1:2]) 128s + f(Y[FALSE]) 128s + U <- as.im(f) 128s + } 128s + return(invisible(NULL)) 128s + } 128s + if(ALWAYS) { 128s + stroke() 128s + stroke(5, diggle=TRUE) 128s + stroke(5, geometric=TRUE) 128s + stroke(1e-6) # generates warning about small bandwidth 128s + stroke(5, weights=expression(x)) 128s + stroke(5, kernel="epa") 128s + stroke(sigma=Inf) 128s + stroke(varcov1=diag(c(1,1))) # 'anisotropic' code 128s + } 128s + if(FULLTEST) { 128s + Z <- as.im(function(x,y){abs(x)+1}, Window(longleaf)) 128s + stroke(5, weights=Z) 128s + stroke(5, weights=runif(npoints(longleaf))) 128s + stroke(varcov=diag(c(25, 36))) 128s + stroke(varcov=diag(c(25, 36)), weights=runif(npoints(longleaf))) 128s + stroke(5, Y=longleaf %mark% 1) 128s + stroke(5, Y=cut(longleaf,breaks=3)) 128s + stroke(5, weights=Z, geometric=TRUE) 128s + g <- function(x,y) { dnorm(x, sd=10) * dnorm(y, sd=10) } 128s + stroke(kernel=g, cutoff=30, FUN=FALSE) 128s + stroke(kernel=g, cutoff=30, scalekernel=TRUE, sigma=1, FUN=FALSE) 128s + } 128s + if(FULLTEST) { 128s + ## standard errors - single column of marks 128s + stroke(sigma=5, se=TRUE) 128s + stroke(sigma=5, se=TRUE, loctype="f") 128s + w <- runif(npoints(longleaf)) 128s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="i") 128s + stroke(sigma=5, se=TRUE, weights=w, loctype="r", wtype="m") 128s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="i") 128s + stroke(sigma=5, se=TRUE, weights=w, loctype="f", wtype="m") 128s + } 128s + 128s + niets <- markmean(longleaf, 9) 128s + 128s + strike <- function(..., Y=finpines) { 128s + Z <- Smooth(Y, ..., at="pixels") 128s + Z <- Smooth(Y, ..., at="points", leaveoneout=TRUE) 128s + Z <- Smooth(Y, ..., at="points", leaveoneout=FALSE) 128s + f <- Smoothfun(Y, ...) 128s + f(4, 1) 128s + f(Y[1:2]) 128s + f(Y[FALSE]) 128s + U <- as.im(f) 128s + return(invisible(NULL)) 128s + } 128s + if(ALWAYS) { 128s + strike() 128s + strike(sigma=1.5, kernel="epa") 128s + strike(varcov=diag(c(1.2, 2.1))) 128s + strike(sigma=1e-6) 128s + strike(sigma=Inf) 128s + } 128s + if(FULLTEST) { 128s + strike(sigma=1e-6, kernel="epa") 128s + strike(1.5, weights=runif(npoints(finpines))) 128s + strike(1.5, weights=expression(y)) 128s + strike(1.5, geometric=TRUE) 128s + strike(1.5, Y=finpines[FALSE]) 128s + flatfin <- finpines %mark% data.frame(a=rep(1, npoints(finpines)), b=2) 128s + strike(1.5, Y=flatfin) 128s + strike(1.5, Y=flatfin, geometric=TRUE) 128s + } 128s + if(FULLTEST) { 128s + ## standard errors - multivariate marks 128s + strike(sigma=1.5, se=TRUE) 128s + strike(sigma=1.5, se=TRUE, loctype="f") 128s + w <- runif(npoints(finpines)) 128s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="i") 128s + strike(sigma=1.5, se=TRUE, weights=w, loctype="r", wtype="m") 128s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="i") 128s + strike(sigma=1.5, se=TRUE, weights=w, loctype="f", wtype="m") 128s + } 128s + opx <- spatstat.options(densityTransform=FALSE) 128s + if(ALWAYS) { 128s + stroke(5, Y=longleaf[order(longleaf$x)], sorted=TRUE) 128s + } 128s + if(FULLTEST) { 128s + strike(1.5, Y=finpines[order(finpines$x)], sorted=TRUE) 128s + } 128s + spatstat.options(opx) 128s + 128s + ## detect special cases 128s + if(ALWAYS) { 128s + Smooth(longleaf[FALSE]) 128s + Smooth(longleaf, minnndist(longleaf)) 128s + Xconst <- cells %mark% 1 128s + Smooth(Xconst, 0.1) 128s + Smooth(Xconst, 0.1, at="points") 128s + Smooth(cells %mark% runif(42), sigma=Inf) 128s + Smooth(cells %mark% runif(42), sigma=Inf, at="points") 128s + Smooth(cells %mark% runif(42), sigma=Inf, at="points", leaveoneout=FALSE) 128s + Smooth(cut(longleaf, breaks=4)) 128s + } 128s + 128s + ## code not otherwise reached 128s + if(ALWAYS) { 128s + smoothpointsEngine(cells, values=rep(1, npoints(cells)), sigma=0.2) 128s + } 128s + if(FULLTEST) { 128s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=Inf) 128s + smoothpointsEngine(cells, values=runif(npoints(cells)), sigma=1e-16) 128s + } 128s + 128s + ## validity of Smooth.ppp(at='points') 128s + Y <- longleaf %mark% runif(npoints(longleaf), min=41, max=43) 128s + Z <- Smooth(Y, 5, at="points", leaveoneout=TRUE) 128s + rZ <- range(Z) 128s + if(rZ[1] < 40 || rZ[2] > 44) 128s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=TRUE)") 128s + 128s + Z <- Smooth(Y, 5, at="points", leaveoneout=FALSE) 128s + rZ <- range(Z) 128s + if(rZ[1] < 40 || rZ[2] > 44) 128s + stop("Implausible results from Smooth.ppp(at=points, leaveoneout=FALSE)") 128s + 128s + ## compare Smooth.ppp results with different algorithms 128s + if(ALWAYS) { 128s + crosscheque(Smooth(longleaf, at="points", sigma=6)) 128s + wt <- runif(npoints(longleaf)) 128s + crosscheque(Smooth(longleaf, at="points", sigma=6, weights=wt)) 128s + } 128s + if(FULLTEST) { 128s + vc <- diag(c(25,36)) 128s + crosscheque(Smooth(longleaf, at="points", varcov=vc)) 128s + crosscheque(Smooth(longleaf, at="points", varcov=vc, weights=wt)) 128s + } 128s + ## drop-dimension coding errors 128s + if(FULLTEST) { 128s + X <- longleaf 128s + marks(X) <- cbind(marks(X), 1) 128s + Z <- Smooth(X, 5) 128s + 128s + ZZ <- bw.smoothppp(finpines, hmin=0.01, hmax=0.012, nh=2) # reshaping problem 128s + } 128s + 128s + ## geometric-mean smoothing 128s + if(ALWAYS) { 128s + U <- Smooth(longleaf, 5, geometric=TRUE) 128s + } 128s + if(FULLTEST) { 128s + UU <- Smooth(X, 5, geometric=TRUE) 128s + V <- Smooth(longleaf, 5, geometric=TRUE, at="points") 128s + VV <- Smooth(X, 5, geometric=TRUE, at="points") 128s + } 128s + 128s + if(FULLTEST) { 128s + ## isotropic and anisotropic cases of bw.smoothppp 128s + bi <- bw.smoothppp(longleaf) 128s + ba <- bw.smoothppp(longleaf, varcov1=diag(c(1,1))) 128s + ## should be equal 128s + if(abs(bi-ba) > 0.001) 128s + stop(paste("Inconsistency in bw.smoothppp: isotropic =", bi, 128s + "!=", ba, "= anisotropic")) 128s + } 128s + }) 132s > 132s > reset.spatstat.options() 132s > 132s > local({ 132s + if(ALWAYS) { 132s + #' Kmeasure, second.moment.engine 132s + #' Expansion of window 132s + Zno <- Kmeasure(redwood, sigma=0.2, expand=FALSE) 132s + Zyes <- Kmeasure(redwood, sigma=0.2, expand=TRUE) 132s + #' All code blocks 132s + sigmadouble <- rep(0.1, 2) 132s + diagmat <- diag(sigmadouble^2) 132s + generalmat <- matrix(c(1, 0.5, 0.5, 1)/100, 2, 2) 132s + Z <- Kmeasure(redwood, sigma=sigmadouble) 132s + Z <- Kmeasure(redwood, varcov=diagmat) 132s + Z <- Kmeasure(redwood, varcov=generalmat) 132s + A <- second.moment.calc(redwood, 0.1, what="all", debug=TRUE) 132s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 132s + B <- second.moment.calc(redwood, varcov=diagmat, what="all") 132s + D <- second.moment.calc(redwood, varcov=generalmat, what="all") 132s + PR <- pixellate(redwood) 132s + DRno <- second.moment.calc(PR, 0.2, debug=TRUE, expand=FALSE, 132s + npts=npoints(redwood), obswin=Window(redwood)) 132s + DRyes <- second.moment.calc(PR, 0.2, debug=TRUE, expand=TRUE, 132s + npts=npoints(redwood), obswin=Window(redwood)) 132s There were 22 warnings (use warnings() to see them) 132s + DR2 <- second.moment.calc(solist(PR, PR), 0.2, debug=TRUE, expand=TRUE, 132s + npts=npoints(redwood), obswin=Window(redwood)) 132s + Gmat <- generalmat * 100 132s + isoGauss <- function(x,y) {dnorm(x) * dnorm(y)} 132s + ee <- evaluate2Dkernel(isoGauss, runif(10), runif(10), 132s + varcov=Gmat, scalekernel=TRUE) 132s + isoGaussIm <- as.im(isoGauss, square(c(-3,3))) 132s + gg <- evaluate2Dkernel(isoGaussIm, runif(10), runif(10), 132s + varcov=Gmat, scalekernel=TRUE) 132s + ## experimental code 132s + op <- spatstat.options(developer=TRUE) 132s + DR <- density(redwood, 0.1) 132s + spatstat.options(op) 132s + } 132s + }) 132s smooth: maximum imaginary part= 4.59e-18 132s smooth: mass error= 0 132s 2nd moment measure: maximum imaginary part= 1.06e-16 132s 2nd moment measure: mass error= 0 132s smooth: maximum imaginary part= 2.27e-18 132s smooth: mass error= 0 132s 2nd moment measure: maximum imaginary part= 7.68e-17 132s 2nd moment measure: mass error= 0 132s smooth: maximum imaginary part= 6.13e-18 132s smooth: mass error= -4.97e-14 132s 2nd moment measure: maximum imaginary part= 3.87e-16 132s 2nd moment measure: mass error= 4.55e-13 132s smooth component 1 : maximum imaginary part= 6.13e-18 132s smooth component 1 : mass error= -4.97e-14 132s smooth component 2 : maximum imaginary part= 6.13e-18 132s smooth component 2 : mass error= -4.97e-14 133s 2nd moment measure: maximum imaginary part= 3.87e-16 133s 2nd moment measure: mass error= 4.55e-13 133s 2nd moment measure: maximum imaginary part= 3.87e-16 133s 2nd moment measure: mass error= 4.55e-13 133s > 133s > local({ 133s + if(FULLTEST) { 133s + #' bandwidth selection 133s + op <- spatstat.options(n.bandwidth=8) 133s + bw.diggle(cells) 133s + bw.diggle(cells, method="interpreted") # undocumented test 133s + ## bw.relrisk(urkiola, hmax=20) is tested in man/bw.relrisk.Rd 133s + bw.relrisk(urkiola, hmax=20, method="leastsquares") 133s + bw.relrisk(urkiola, hmax=20, method="weightedleastsquares") 133s + ZX <- density(swedishpines, at="points") 133s + bw.pcf(swedishpines, lambda=ZX) 133s + bw.pcf(swedishpines, lambda=ZX, 133s + bias.correct=FALSE, simple=FALSE, cv.method="leastSQ") 133s + spatstat.options(op) 133s + } 133s + }) 133s > 133s > local({ 133s + if(FULLTEST) { 133s + ## idw 133s + Z <- idw(longleaf, power=4) 133s + Z <- idw(longleaf, power=4, se=TRUE) 133s + ZX <- idw(longleaf, power=4, at="points") 133s + ZX <- idw(longleaf, power=4, at="points", se=TRUE) 133s + } 133s + if(ALWAYS) { 133s + ## former bug in densityVoronoi.ppp 133s + X <- redwood[1:2] 133s + A <- densityVoronoi(X, f=0.51, counting=FALSE, fixed=FALSE, nrep=50, verbose=FALSE) 133s + ## dodgy code blocks in densityVoronoi.R 133s + A <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE) 133s + B <- adaptive.density(nztrees, nrep=2, f=0.5, counting=TRUE, fixed=TRUE) 133s + D <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE) 133s + E <- adaptive.density(nztrees, nrep=2, f=0.5, counting=FALSE, fixed=TRUE) 133s + } 133s + if(FULLTEST) { 133s + #' adaptive kernel estimation 133s + d10 <- nndist(nztrees, k=10) 133s + d10fun <- distfun(nztrees, k=10) 133s + d10im <- as.im(d10fun) 133s + uN <- 2 * runif(npoints(nztrees)) 133s + AA <- densityAdaptiveKernel(nztrees, bw=d10) 133s + BB <- densityAdaptiveKernel(nztrees, bw=d10, weights=uN) 133s + DD <- densityAdaptiveKernel(nztrees, bw=d10fun, weights=uN) 133s + EE <- densityAdaptiveKernel(nztrees, bw=d10im, weights=uN) 133s + } 133s + }) 133s Computing 2 intensity estimates...1, 133s 2. 133s Done. 133s Computing 2 intensity estimates...1, 133s 2. 133s Done. 133s Computing 2 intensity estimates...1, 133s 2. 133s Done. 133s Computing 2 intensity estimates...1, 133s 2. 133s Done. 133s > 133s > local({ 133s + if(FULLTEST) { 133s + ## cases of 'intensity' etc 133s + a <- intensity(amacrine, weights=expression(x)) 133s + SA <- split(amacrine) 133s + a <- intensity(SA, weights=expression(x)) 133s + a <- intensity(SA, weights=amacrine$x) 133s + 133s + ## check infrastructure for 'densityfun' 133s + f <- densityfun(cells, 0.05) 133s + Z <- as.im(f) 133s + Z <- as.im(f, W=square(0.5)) 133s + } 133s + }) 133s > 133s > local({ 133s + if(FULLTEST) { 133s + ## other cases of SpatialQuantile.ppp 133s + X <- longleaf 133s + marks(X) <- round(marks(X), -1) 133s + Z <- SpatialMedian(X, 30, type=4) 133s + ZX <- SpatialMedian(X, 30, type=4, at="points") 133s + ZXP <- SpatialMedian(X, 30, at="points", leaveoneout=FALSE) 133s + } 133s + }) 133s > 133s > 133s > 133s > reset.spatstat.options() 133s > 133s > 133s BEGIN TEST testsEtoF.R 134s 134s R version 4.4.3 (2025-02-28) -- "Trophy Case" 134s Copyright (C) 2025 The R Foundation for Statistical Computing 134s Platform: aarch64-unknown-linux-gnu 134s 134s R is free software and comes with ABSOLUTELY NO WARRANTY. 134s You are welcome to redistribute it under certain conditions. 134s Type 'license()' or 'licence()' for distribution details. 134s 134s R is a collaborative project with many contributors. 134s Type 'contributors()' for more information and 134s 'citation()' on how to cite R or R packages in publications. 134s 134s Type 'demo()' for some demos, 'help()' for on-line help, or 134s 'help.start()' for an HTML browser interface to help. 134s Type 'q()' to quit R. 134s 134s > Loading required package: spatstat.explore 134s #' 134s > #' Header for all (concatenated) test files 134s > #' 134s > #' Require spatstat.explore 134s > #' Obtain environment variable controlling tests. 134s > #' 134s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 134s > 134s > require(spatstat.explore) 134s Loading required package: spatstat.data 135s Loading required package: spatstat.univar 135s spatstat.univar 3.1-2 135s Loading required package: spatstat.geom 135s spatstat.geom 3.3-6 135s Loading required package: spatstat.random 135s spatstat.random 3.3-3 135s Loading required package: nlme 135s spatstat.explore 3.3-4 135s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 135s > ALWAYS <- TRUE 135s > cat(paste("--------- Executing", 135s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 135s + "test code -----------\n")) 135s --------- Executing **RESTRICTED** subset of test code ----------- 135s > # 135s > # tests/envelopes.R 135s > # 135s > # Test validity of envelope data 135s > # 135s > # $Revision: 1.29 $ $Date: 2024/01/10 13:45:29 $ 135s > # 135s > 135s > local({ 135s + 135s + 135s + 135s + ## check envelope calls from 'alltypes' 135s + if(ALWAYS) a <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE) 135s + if(FULLTEST) b <- alltypes(demopat, Kcross, nsim=4, envelope=TRUE, global=TRUE) 135s + ## check 'transform' idioms 135s + if(ALWAYS) A <- envelope(cells, Kest, nsim=4, transform=expression(. - .x)) 135s + if(FULLTEST) B <- envelope(cells, Kest, nsim=4, transform=expression(sqrt(./pi) - .x)) 135s + 135s + 135s + # check conditional simulation 135s + if(FULLTEST) { 135s + e1 <- envelope(cells, Kest, nsim=4, fix.n=TRUE) 135s + e2 <- envelope(amacrine, Kest, nsim=4, fix.n=TRUE) 135s + e3 <- envelope(amacrine, Kcross, nsim=4, fix.marks=TRUE) 135s + e4 <- envelope(finpines, Kest, nsim=4, fix.n=TRUE) # multiple columns of marks 135s + e5 <- envelope(finpines, Kest, nsim=4, fix.marks=TRUE) 135s + } 135s + 135s + 135s + ## check pooling of envelopes in global case 135s + E1 <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE) 135s + E2 <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE) 135s + p12 <- pool(E1, E2) 135s + p12 <- pool(E1, E2, savefuns=TRUE) 135s + if(FULLTEST) { 135s + F1 <- envelope(cells, Kest, nsim=5, 135s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 135s + F2 <- envelope(cells, Kest, nsim=12, 135s + savefuns=TRUE, savepatterns=TRUE, global=TRUE) 135s + p12 <- pool(F1, F2) 135s + p12 <- pool(F1, F2, savefuns=TRUE, savepatterns=TRUE) 135s + E1r <- envelope(cells, Kest, nsim=5, savefuns=TRUE, global=TRUE, 135s + ginterval=c(0.05, 0.15)) 135s + E2r <- envelope(cells, Kest, nsim=12, savefuns=TRUE, global=TRUE, 135s + ginterval=c(0.05, 0.15)) 135s + p12r <- pool(E1r, E2r) 135s + } 135s + 135s + if(FULLTEST) { 135s + #' as.data.frame.envelope 135s + Nsim <- 5 135s + E <- envelope(cells, nsim=Nsim, savefuns=TRUE) 135s + A <- as.data.frame(E) 135s + B <- as.data.frame(E, simfuns=TRUE) 135s + stopifnot(ncol(B) - ncol(A) == Nsim) 135s + } 135s + 135s + if(FULLTEST) { 135s + #' cases not covered elsewhere 135s + A <- envelope(cells, nsim=5, alternative="less", 135s + do.pwrong=TRUE, use.theory=FALSE, 135s + savepatterns=TRUE, savefuns=TRUE) 135s + print(A) 135s + B <- envelope(A, nsim=5, savefuns=TRUE) 135s + D <- envelope(cells, "Lest", nsim=5) 135s + 135s + UU <- envelope(cells, nsim=5, foreignclass="ppp", clipdata=TRUE) 135s + 135s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", global=TRUE) 135s + AA <- envelope(cells, nsim=5, jsim=5, alternative="less", global=TRUE) 135s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 135s + AA <- envelope(cells, nsim=5, jsim=5, alternative="greater", VARIANCE=TRUE) 135s + 135s + #' spotted by Art Stock - bugs in ratfv class support 135s + BB <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="border") 135s + CC <- envelope(redwood, Kinhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="border") 135s + DD <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, ratio=TRUE, correction="trans") 135s + EE <- envelope(redwood, Finhom, nsim=5, sigma=bw.scott, global=TRUE, ratio=TRUE, correction="trans") 135s + 135s + #' envelopes based on sample variance 135s + E <- envelope(cells, nsim=8, VARIANCE=TRUE) 135s + G <- envelope(cells, nsim=8, VARIANCE=TRUE, 135s + use.theory=FALSE, do.pwrong=TRUE) 135s + print(G) 135s + #' summary method 135s + summary(E) 135s + summary(envelope(cells, nsim=5, simulate=expression(runifpoint(42)))) 135s + #' weights argument 135s + H1 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 135s + H2 <- envelope(cells, nsim=4, weights=npoints, savefuns=TRUE) 135s + J1 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 135s + J2 <- envelope(cells, nsim=4, weights=npoints, VARIANCE=TRUE) 135s + #' pooling with weights 135s + H <- pool(H1, H2) 135s + J <- pool(J1, J2) 135s + #' pooling envelopes with non-identical attributes 135s + H0 <- envelope(cells, nsim=4, savefuns=TRUE) 135s + HH <- pool(H0, H1) 135s + #' malformed argument 'simulate' 135s + A <- replicate(3, list(list(runifpoint(ex=cells)))) # list(list(ppp), list(ppp), list(ppp)) 135s + E <- envelope(cells, simulate=A, nsim=3) 135s + #' undocumented/secret 135s + K <- envelope(cells, nsim=4, saveresultof=npoints, collectrubbish=TRUE) 135s + #' so secret I've even forgotten how to do it 135s + M <- envelope(cells, nsim=4, internal=list(eject="patterns")) 135s + } 135s + 135s + 135s + if(ALWAYS) { 135s + #' Test robustness of envelope() sorting procedure when NA's are present 135s + #' Fails with spatstat.utils 1.12-0 135s + set.seed(42) 135s + EP <- envelope(longleaf, pcf, nsim=10, nrank=2) 135s + 135s + #' Test case when the maximum permitted number of failures is exceeded 135s + X <- amacrine[1:153] # contains exactly one point with mark='off' 135s + #' High probability of generating a pattern with no marks = 'off' 135s + E <- envelope(X, Kcross, nsim=39, maxnerr=2, maxerr.action="warn") 135s + A <- alltypes(X, Kcross, envelope=TRUE, nsim=39, maxnerr=2) 135s + } 135s + 135s + if(ALWAYS) { 135s + #' Internals: envelope.matrix 135s + Y <- matrix(rnorm(200), 10, 20) 135s + rr <- 1:10 135s + oo <- rnorm(10) 135s + zz <- numeric(10) 135s + E <- envelope(Y, rvals=rr, observed=oo, nsim=10) 135s + E <- envelope(Y, rvals=rr, observed=oo, jsim=1:10) 135s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 135s + type="global", use.theory=TRUE) 135s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 135s + type="global", use.theory=TRUE, nsim=10) 135s + E <- envelope(Y, rvals=rr, observed=oo, theory=zz, 135s + type="global", use.theory=FALSE, nsim=10) 135s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 135s + nsim=10, nsim2=10) 135s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 135s + jsim=1:10, jsim.mean=11:20) 135s + if(FULLTEST) print(E) 135s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 135s + nsim=10, jsim.mean=11:20) 135s + E <- envelope(Y, rvals=rr, observed=oo, type="global", 135s + jsim=1:10, nsim2=10) 135s + } 135s + 135s + if(ALWAYS) { 135s + #' quirk with handmade summary functions ('conserve' attribute) 135s + Kdif <- function(X, r=NULL) { # note no ellipsis 135s + Y <- split(X) 135s + K1 <- Kest(Y[[1]], r=r) 135s + K2 <- Kest(Y[[2]], r=r) 135s + D <- eval.fv(K1-K2) 135s + return(D) 135s + } 135s + envelope(amacrine, Kdif, nsim=3) 135s + } 135s + 135s + 135s + ## close 'local' 135s + }) 135s Generating 4 simulations of CSR ... 135s 1, 2, 3, 135s 4. 135s 135s Done. 135s Generating 5 simulations of CSR ... 136s 1, 2, 3, 4, 136s 5. 136s 136s Done. 136s Generating 12 simulations of CSR ... 136s 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 136s 12. 136s 136s Done. 136s Generating 10 simulations of CSR ... 136s 1, 2, 3, 4, 5, 6, 7, 8, 9, 136s 10. 136s 136s Done. 136s Generating 39 simulations of CSR ... 136s Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 136s No points have mark i = off 136s [retrying] 136s 1, 2, 3, 4, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 136s No points have mark i = off 136s [retrying] 136s 5, 6, Error in (function (X, i, j, r = NULL, breaks = NULL, correction = c("border", : 136s No points have mark i = off 136s 136s Done. 136s Generating 3 simulations of CSR ... 136s 1, 2, 136s 3. 136s 136s Done. 136s Pointwise critical envelopes for K1(r)-K2(r) 136s and observed value for ‘amacrine’ 136s Edge correction: “iso” 136s Obtained from 3 simulations of CSR 136s Alternative: two.sided 136s Significance level of pointwise Monte Carlo test: 2/4 = 0.5 136s ................................................................................ 136s Math.label 136s r r 136s obs hat((K1-K2))[obs](r) 136s theo (K1-K2)[theo](r) 136s lo hat((K1-K2))[lo](r) 136s hi hat((K1-K2))[hi](r) 136s Description 136s r distance argument r 136s obs observed value of K1(r)-K2(r) for data pattern 136s theo theoretical value of K1(r)-K2(r) for CSR 136s lo lower pointwise envelope of K1(r)-K2(r) from simulations 136s hi upper pointwise envelope of K1(r)-K2(r) from simulations 136s ................................................................................ 136s Default plot formula: .~r 136s where “.” stands for ‘obs’, ‘theo’, ‘hi’, ‘lo’ 136s Columns ‘lo’ and ‘hi’ will be plotted as shading (by default) 136s Recommended range of argument r: [0, 0.25] 136s Available range of argument r: [0, 0.25] 136s Unit of length: 662 microns 136s > # 136s > # tests/fastK.R 136s > # 136s > # check fast and slow code for Kest 136s > # and options not tested elsewhere 136s > # 136s > # $Revision: 1.5 $ $Date: 2020/04/28 12:58:26 $ 136s > # 136s > if(ALWAYS) { 136s + local({ 136s + ## fast code 136s + Kb <- Kest(cells, nlarge=0) 136s + Ku <- Kest(cells, correction="none") 136s + Kbu <- Kest(cells, correction=c("none", "border")) 136s + ## slow code, full set of corrections, sqrt transformation, ratios 136s + Ldd <- Lest(unmark(demopat), correction="all", var.approx=TRUE, ratio=TRUE) 136s + ## Lotwick-Silverman var approx (rectangular window) 136s + Loo <- Lest(cells, correction="all", var.approx=TRUE, ratio=TRUE) 136s + ## Code for large dataset 136s + nbig <- .Machine$integer.max 136s + if(!is.null(nbig)) { 136s + Warning messages: 136s 1: Exceeded maximum permissible number of (maxnerr = 2) when evaluating summary function for simulated point patterns 136s 2: In alltypes(X, Kcross, envelope = TRUE, nsim = 39, maxnerr = 2) : 136s 3 out of 4 envelopes were not computed, due to errors in evaluating the summary functions for simulated patterns 136s nn <- ceiling(sqrt(nbig)) 136s + if(nn < 1e6) Kbig <- Kest(runifpoint(nn), 136s + correction=c("border", "bord.modif", "none"), 136s + ratio=TRUE) 136s + } 136s + 136s + ## Kinhom 136s + lam <- density(cells, at="points", leaveoneout=TRUE) 136s + ## fast code 136s + Kib <- Kinhom(cells, lam, nlarge=0) 136s + Kiu <- Kest(cells, lam, correction="none") 136s + Kibu <- Kest(cells, lam, correction=c("none", "border")) 136s + ## slow code 136s + Lidd <- Linhom(unmark(demopat), sigma=bw.scott) 136s + }) 136s + 136s + } 136s number of data points exceeds 0 - computing border correction estimate only 138s number of data points exceeds 0 - computing border correction estimate only 139s > ## 139s > ## tests/fvproblems.R 139s > ## 139s > ## problems with fv, ratfv and fasp code 139s > ## 139s > Warning message: 139s Periodic correction is not defined for non-rectangular windows 139s ## $Revision: 1.15 $ $Date: 2020/04/28 12:58:26 $ 139s > 139s > #' This appears in the workshop notes 139s > #' Problem detected by Martin Bratschi 139s > 139s > if(FULLTEST) { 139s + local({ 139s + Jdif <- function(X, ..., i) { 139s + Jidot <- Jdot(X, ..., i=i) 139s + J <- Jest(X, ...) 139s + dif <- eval.fv(Jidot - J) 139s + return(dif) 139s + } 139s + Z <- Jdif(amacrine, i="on") 139s + }) 139s + } 139s > #' 139s > #' Test mathlegend code 139s > #' 139s > local({ 139s + K <- Kest(cells) 139s + if(FULLTEST) { 139s + plot(K) 139s + plot(K, . ~ r) 139s + plot(K, . - theo ~ r) 139s + } 139s + if(ALWAYS) { 139s + plot(K, sqrt(./pi) ~ r) 139s + } 139s + if(FULLTEST) { 139s + plot(K, cbind(iso, theo) ~ r) 139s + plot(K, cbind(iso, theo) - theo ~ r) 139s + plot(K, sqrt(cbind(iso, theo)/pi) ~ r) 139s + plot(K, cbind(iso/2, -theo) ~ r) 139s + plot(K, cbind(iso/2, trans/2) - theo ~ r) 139s + } 139s + if(FULLTEST) { 139s + ## test expansion of .x and .y 139s + plot(K, . ~ .x) 139s + plot(K, . - theo ~ .x) 139s + plot(K, .y - theo ~ .x) 139s + } 139s + if(ALWAYS) { 139s + plot(K, sqrt(.y) - sqrt(theo) ~ .x) 139s + } 139s + 139s + # problems with parsing weird strings in levels(marks(X)) 139s + # noted by Ulf Mehlig 139s + if(ALWAYS) { 139s + levels(marks(amacrine)) <- c("Nasticreechia krorluppia", "Homo habilis") 139s + plot(Kcross(amacrine)) 139s + plot(alltypes(amacrine, "K")) 139s + } 139s + if(FULLTEST) { 139s + plot(alltypes(amacrine, "J")) 139s + plot(alltypes(amacrine, pcfcross)) 139s + } 139s + }) 139s > 139s > #' 139s > #' Test quirks related to 'alim' attribute 139s > 139s > if(FULLTEST) { 139s + local({ 139s + K <- Kest(cells) 139s + attr(K, "alim") <- NULL 139s + plot(K) 139s + attr(K, "alim") <- c(0, 0.1) 139s + plot(tail(K)) 139s + }) 139s + } 139s > 139s > #' 139s > #' Check that default 'r' vector passes the test for fine spacing 139s > 139s > if(ALWAYS) { 139s + local({ 139s + a <- Fest(cells) 139s + A <- Fest(cells, r=a$r) 139s + b <- Hest(heather$coarse) 139s + B <- Hest(heather$coarse, r=b$r) 139s + # from Cenk Icos 139s + X <- runifpoint(100, owin(c(0,3), c(0,10))) 139s + FX <- Fest(X) 139s + FXr <- Fest(X, r=FX$r) 139s + JX <- Jest(X) 139s + }) 139s + } 139s > 139s > ##' various functionality in fv.R 139s > 139s > if(ALWAYS) { 139s + local({ 139s + M <- cbind(1:20, matrix(runif(100), 20, 5)) 139s + A <- as.fv(M) 139s + fvlabels(A) <- c("r","%s(r)", "%s[A](r)", "%s[B](r)", "%s[C](r)", "%s[D](r)") 139s + A <- rename.fv(A, "M", quote(M(r))) 139s + A <- tweak.fv.entry(A, "V1", new.tag="r") 139s + A[,3] <- NULL 139s + A$hogwash <- runif(nrow(A)) 139s + fvnames(A, ".") <- NULL 139s + #' bind.fv with qualitatively different functions 139s + GK <- harmonise(G=Gest(cells), K=Kest(cells)) 139s + G <- GK$G 139s + K <- GK$K 139s + ss <- c(rep(TRUE, nrow(K)-10), rep(FALSE, 10)) 139s + U <- bind.fv(G, K[ss, ], clip=TRUE) 139s + #' 139s + H <- rebadge.as.crossfun(K, "H", "inhom", 1, 2) 139s + H <- rebadge.as.dotfun(K, "H", "inhom", 3) 139s + #' text layout 139s + op <- options(width=27) 139s + print(K) 139s + options(width=18) 139s + print(K) 139s + options(op) 139s + #' collapse.fv 139s + Kb <- Kest(cells, correction="border") 139s + Ki <- Kest(cells, correction="isotropic") 139s + collapse.fv(Kb, Ki, same="theo") 139s + collapse.fv(anylist(B=Kb, I=Ki), same="theo") 139s + collapse.fv(anylist(B=Kb), I=Ki, same="theo") 139s + Xlist <- replicate(3, runifpoint(30), simplify=FALSE) 139s + Klist <- anylapply(Xlist, Kest) 139s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 139s + names(Klist) <- LETTERS[24:26] 139s + collapse.fv(Klist, same="theo", different=c("iso", "border")) 139s + }) 139s + } 139s Function value object 139s (class ‘fv’) 139s for the function r -> K(r) 139s ........................... 139s Math.label 139s r r 139s theo K[pois](r) 139s border hat(K)[bord](r) 139s trans hat(K)[trans](r) 139s iso hat(K)[iso](r) 139s Description 139s r distance argument r 139s theo theoretical [..] 139s border [..] 139s trans [..] 139s iso [..] 139s ........................... 139s Default plot formula: .~r 139s where “.” stands for 139s ‘iso’, ‘trans’, 139s ‘border’, ‘theo’ 139s Recommended range of 139s argument r: [0, 0.25] 139s Available range of 139s argument r: [0, 0.25] 139s Function value 139s object (class 139s ‘fv’) 139s for the function 139s r -> K(r) 139s .................. 139s Math.label 139s r r 139s theo K[pois](r) 139s border hat(K)[bord](r) 139s trans hat(K)[trans](r) 139s iso hat(K)[iso](r) 139s Description 139s r [..] 139s theo [..] 139s border [..] 139s trans [..] 139s iso [..] 139s .................. 139s Default plot 139s formula: .~r 139s where “.” 139s stands for 139s ‘iso’, 139s ‘trans’, 139s ‘border’, 139s ‘theo’ 139s Recommended range 139s of argument r: 139s [0, 0.25] 139s Available range 139s of argument r: 139s [0, 0.25] 139s Function value object (class ‘fv’) 139s for the function r -> K(r) 139s ................................................................ 139s Math.label Description 139s r r distance argument r 139s theo K[pois](r) theoretical Poisson K(r) 139s Xborder X~hat(K)[bord](r) X border-corrected estimate of K(r) 139s Xiso X~hat(K)[iso](r) X isotropic-corrected estimate of K(r) 139s Yborder Y~hat(K)[bord](r) Y border-corrected estimate of K(r) 139s Yiso Y~hat(K)[iso](r) Y isotropic-corrected estimate of K(r) 139s Zborder Z~hat(K)[bord](r) Z border-corrected estimate of K(r) 139s Ziso Z~hat(K)[iso](r) Z isotropic-corrected estimate of K(r) 139s ................................................................ 139s Default plot formula: .~.x 139s where “.” stands for ‘theo’, ‘Xborder’, ‘Xiso’, ‘Yborder’, 139s ‘Yiso’, ‘Zborder’, ‘Ziso’ 139s Recommended range of argument r: [0, 0.25] 139s Available range of argument r: [0, 0.25] 139s > 139s > if(FULLTEST) { 139s + local({ 139s + ## rat 139s + K <- Kest(cells, ratio=TRUE) 139s + G <- Gest(cells, ratio=TRUE) 139s + print(K) 139s + compatible(K, K) 139s + compatible(K, G) 139s + H <- rat(K, attr(K, "numerator"), attr(K, "denominator"), check=TRUE) 139s + }) 139s + } 139s > 139s > if(FULLTEST) { 139s + local({ 139s + ## bug in Jmulti.R colliding with breakpts.R 139s + B <- owin(c(0,3), c(0,10)) 139s + Y <- superimpose(A=runifpoint(1212, B), B=runifpoint(496, B)) 139s + JDX <- Jdot(Y) 139s + JCX <- Jcross(Y) 139s + Jdif <- function(X, ..., i) { 139s + Jidot <- Jdot(X, ..., i=i) 139s + J <- Jest(X, ...) 139s Warning message: 139s In bind.fv(G, K[ss, ], clip = TRUE) : 139s The column name ‘theo’ was duplicated. Unique names were generated 139s + dif <- eval.fv(Jidot - J) 139s + return(dif) 139s + } 139s + E <- envelope(Y, Jdif, nsim=19, i="A", simulate=expression(rlabel(Y))) 139s + }) 139s + } 139s > 139s > if(FULLTEST) { 139s + local({ 139s + #' fasp axes, title, dimnames 139s + a <- alltypes(amacrine) 139s + a$title <- NULL 139s + plot(a, samex=TRUE, samey=TRUE) 139s + dimnames(a) <- lapply(dimnames(a), toupper) 139s + 139s + b <- as.fv(a) 139s + }) 139s + } 139s > 139s > if(FULLTEST) { 139s + local({ 139s + ## plot.anylist (fv) 139s + b <- anylist(A=Kcross(amacrine), B=Kest(amacrine)) 139s + plot(b, equal.scales=TRUE, main=expression(sqrt(pi))) 139s + plot(b, arrange=FALSE) 139s + }) 139s + } 139s > 139s BEGIN TEST testsGtoJ.R 139s 139s R version 4.4.3 (2025-02-28) -- "Trophy Case" 139s Copyright (C) 2025 The R Foundation for Statistical Computing 139s Platform: aarch64-unknown-linux-gnu 139s 139s R is free software and comes with ABSOLUTELY NO WARRANTY. 139s You are welcome to redistribute it under certain conditions. 139s Type 'license()' or 'licence()' for distribution details. 139s 139s R is a collaborative project with many contributors. 139s Type 'contributors()' for more information and 139s 'citation()' on how to cite R or R packages in publications. 139s 139s Type 'demo()' for some demos, 'help()' for on-line help, or 139s 'help.start()' for an HTML browser interface to help. 139s Type 'q()' to quit R. 139s 139s > #' 139s > #' Header for all (concatenated) test files 139s > #' 139s > #' Require spatstat.explore 139s > #' Obtain environment variable controlling tests. 139s > #' 139s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 139s > 139s > require(spatstat.explore) 139s Loading required package: spatstat.explore 139s Loading required package: spatstat.data 140s Loading required package: spatstat.univar 140s spatstat.univar 3.1-2 140s Loading required package: spatstat.geom 140s spatstat.geom 3.3-6 140s Loading required package: spatstat.random 140s spatstat.random 3.3-3 140s Loading required package: nlme 141s spatstat.explore 3.3-4 141s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 141s > ALWAYS <- TRUE 141s > cat(paste("--------- Executing", 141s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 141s + "test code -----------\n")) 141s --------- Executing **RESTRICTED** subset of test code ----------- 141s > ## 141s > ## tests/gcc323.R 141s > ## 141s > ## $Revision: 1.3 $ $Date: 2020/04/28 12:58:26 $ 141s > ## 141s > if(ALWAYS) { # depends on hardware 141s + local({ 141s + # critical R values that provoke GCC bug #323 141s + a <- marktable(lansing, R=0.25) 141s + a <- marktable(lansing, R=0.21) 141s + a <- marktable(lansing, R=0.20) 141s + a <- marktable(lansing, R=0.10) 141s + }) 141s + } 141s > #' tests/hypotests.R 141s > #' Hypothesis tests 141s > #' 141s > #' $Revision: 1.10 $ $Date: 2023/07/17 07:30:48 $ 141s > 141s > if(FULLTEST) { 141s + local({ 141s + 141s + hopskel.test(redwood, method="MonteCarlo", nsim=5) 141s + 141s + #' quadrat test - spatial methods 141s + a <- quadrat.test(redwood, 3) 141s + domain(a) 141s + shift(a, c(1,1)) 141s + 141s + #' quadrat test - correctness of mapping from table to quadrats 141s + Q2 <- quadratcount(humberside, 2, 3) 141s + T2 <- suppressWarnings(quadrat.test(Q2)) 141s + R2 <- cbind(as.numeric(t(Q2)), round(10 * residuals(T2))) 141s + R2correct <- cbind(c(2, 20, 13, 11, 34, 123), 141s + c(-46, -12, -62, -41, 50, 134)) 141s + if(!all(R2 == R2correct)) 141s + stop("Incorrect count-residual map for quadrat.test(2,3)") 141s + 141s + Q5 <- quadratcount(humberside, 5, 3) 141s + T5 <- suppressWarnings(quadrat.test(Q5)) 141s + R5 <- cbind(as.numeric(t(Q5)), round(10 * residuals(T5))) 141s + R5correct <- cbind( 141s + c( 0, 0, 3, 19, 3, 2, 14, 5, 0, 2, 117, 35, 3), 141s + c(-19, -33, -42, 16, -37, -49, -28, -35, -5, -21, 295, 40, -32)) 141s + if(!all(R5 == R5correct)) 141s + stop("Incorrect count-residual map for quadrat.test(5,3)") 141s + 141s + #' cases of studpermu.test 141s + #' X is a hyperframe 141s + b <- studpermu.test(pyramidal, nperm=9) 141s + b <- studpermu.test(pyramidal, nperm=9, use.Tbar=TRUE) 141s + #' X is a list of lists of ppp 141s + ZZ <- split(pyramidal$Neurons, pyramidal$group) 141s + bb <- studpermu.test(ZZ, nperm=9) 141s + 141s + #' Issue #115 141s + X <- runifpoint(50, nsim = 3) 141s + Y <- runifpoint(3000, nsim = 3) 141s + h <- hyperframe(ppp = c(X, Y), group = rep(1:2, 3)) 141s + studpermu.test(h, ppp ~ group) 141s + 141s + #' scan test 141s + Z <- scanmeasure(cells, 0.1, method="fft") 141s + rr <- c(0.05, 1) 141s + scan.test(amacrine, rr, nsim=5, 141s + method="binomial", alternative="less") 141s + }) 141s + } 141s > # 141s > # tests/imageops.R 141s > # 141s > # $Revision: 1.43 $ $Date: 2023/08/29 01:03:59 $ 141s > # 141s > 141s > 141s > if(FULLTEST) { 141s + local({ 141s + #' case of "[.im" and "[<-.im" where index is an ssf 141s + d <- distmap(cells, dimyx=32) 141s + Empty <- cells[FALSE] 141s + EmptyFun <- ssf(Empty, numeric(0)) 141s + ff <- d[EmptyFun] 141s + d[EmptyFun] <- 42 141s + 141s + #' Smooth.im -> blur.im with sigma=NULL 141s + Z <- as.im(function(x,y) { x - y }, letterR, dimyx=32) 141s + ZS <- Smooth(Z) 141s + 141s + #' deprecated -> im.apply(DA, which.max) 141s + Z <- which.max.im(bei.extra) 141s + 141s + #' rotmean 141s + U <- rotmean(Z, origin="midpoint", result="im", padzero=FALSE) 141s + 141s + #' cases of distcdf 141s + distcdf(cells[1:5]) 141s + distcdf(W=cells[1:5], dW=1:5) 141s + distcdf(W=Window(cells), V=cells[1:5]) 141s + distcdf(W=Window(cells), V=cells[1:5], dV=1:5) 141s + }) 141s + } 141s > 141s > 141s BEGIN TEST testsK.R 141s 141s R version 4.4.3 (2025-02-28) -- "Trophy Case" 141s Copyright (C) 2025 The R Foundation for Statistical Computing 141s Platform: aarch64-unknown-linux-gnu 141s 141s R is free software and comes with ABSOLUTELY NO WARRANTY. 141s You are welcome to redistribute it under certain conditions. 141s Type 'license()' or 'licence()' for distribution details. 141s 141s R is a collaborative project with many contributors. 141s Type 'contributors()' for more information and 141s 'citation()' on how to cite R or R packages in publications. 141s 141s Type 'demo()' for some demos, 'help()' for on-line help, or 141s 'help.start()' for an HTML browser interface to help. 141s Type 'q()' to quit R. 141s 141s > #' 141s > Loading required package: spatstat.explore 141s #' Header for all (concatenated) test files 141s > #' 141s > #' Require spatstat.explore 141s > #' Obtain environment variable controlling tests. 141s > #' 141s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 141s > 141s > require(spatstat.explore) 141s Loading required package: spatstat.data 142s Loading required package: spatstat.univar 142s spatstat.univar 3.1-2 142s Loading required package: spatstat.geom 142s spatstat.geom 3.3-6 142s Loading required package: spatstat.random 142s spatstat.random 3.3-3 142s Loading required package: nlme 143s spatstat.explore 3.3-4 143s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 143s > ALWAYS <- TRUE 143s > cat(paste("--------- Executing", 143s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 143s + "test code -----------\n")) 143s --------- Executing **RESTRICTED** subset of test code ----------- 143s > #' 143s > #' tests/kernelstuff.R 143s > #' 143s > #' $Revision: 1.2 $ $Date: 2023/11/05 01:49:45 $ 143s > 143s > local({ 143s + if(FULLTEST) { 143s + #' test all cases in kernels.R 143s + kernames <- c("gaussian", "rectangular", "triangular", 143s + "epanechnikov", "biweight", "cosine", "optcosine") 143s + X <- rnorm(20) 143s + U <- runif(20) 143s + for(ker in kernames) { 143s + dX <- dkernel(X, ker) 143s + fX <- pkernel(X, ker) 143s + qU <- qkernel(U, ker) 143s + m0 <- kernel.moment(0, 0, ker) 143s + m1 <- kernel.moment(1, 0, ker) 143s + m2 <- kernel.moment(2, 0, ker) 143s + m3 <- kernel.moment(3, 0, ker) 143s + } 143s + } 143s + }) 143s > 143s > #' 143s > #' tests/Kfuns.R 143s > #' 143s > #' Various K and L functions and pcf 143s > #' 143s > #' $Revision: 1.43 $ $Date: 2022/06/17 01:47:08 $ 143s > #' 143s > #' Assumes 'EveryStart.R' was run 143s > 143s > if(FULLTEST) { 143s + Cells <- cells 143s + Amacrine <- amacrine 143s + Redwood <- redwood 143s + } else { 143s + ## reduce numbers of data + dummy points 143s + spatstat.options(npixel=32, ndummy.min=16) 143s + Cells <- cells[c(FALSE, TRUE)] 143s + Amacrine <- amacrine[c(FALSE, TRUE)] 143s + Redwood <- redwood[c(FALSE, TRUE)] 143s + } 143s > 143s > 143s > myfun <- function(x,y){(x+1) * y } # must be outside 143s > 143s > local({ 143s + if(FULLTEST) { 143s + #' supporting code 143s + rmax.rule("Kscaled", owin(), 42) 143s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 143s + "polygonal", TRUE) 143s + implemented.for.K(c("border", "bord.modif", "translate", "good", "best"), 143s + "mask", TRUE) 143s + implemented.for.K(c("border", "isotropic"), "mask", TRUE) 143s + implemented.for.K(c("border", "isotropic"), "mask", FALSE) 143s + #' shortcuts 143s + D <- density(Cells) 143s + K <- Kborder.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 143s + K <- Knone.engine(Cells, rmax=0.4, weights=D, ratio=TRUE) 143s + allcor <- c("none", "border", "bord.modif","isotropic", "translate") 143s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor) 143s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 143s + weights=D) 143s + K <- Krect.engine(Cells, rmax=0.4, ratio=TRUE, correction=allcor, 143s + use.integers=FALSE) 143s + #' Kest special code blocks 143s + K <- Kest(Cells, var.approx=TRUE, ratio=FALSE) 143s + Z <- distmap(Cells) + 1 143s + Kb <- Kest(Cells, correction=c("border","bord.modif"), 143s + weights=Z, ratio=TRUE) 143s + Kn <- Kest(Cells, correction="none", 143s + weights=Z, ratio=TRUE) 143s + Knb <- Kest(Cells, correction=c("border","bord.modif","none"), 143s + weights=Z, ratio=TRUE) 143s + } 143s + if(ALWAYS) { 143s + bigint <- 50000 # This is only "big" on a 32-bit system where 143s + # sqrt(.Machine$integer.max) = 46340.9 143s + X <- runifpoint(bigint) 143s + Z <- as.im(1/bigint, owin()) 143s + Kb <- Kest(X, correction=c("border","bord.modif"), 143s + rmax=0.02, weights=Z, ratio=TRUE) 143s + } 143s + if(FULLTEST) { 143s + Kn <- Kest(X, correction="none", 143s + rmax=0.02, weights=Z, ratio=TRUE) 143s + Knb <- Kest(X, correction=c("border","bord.modif","none"), 143s + rmax=0.02, weights=Z, ratio=TRUE) 143s + #' pcf.ppp special code blocks 143s + pr <- pcf(Cells, ratio=TRUE, var.approx=TRUE) 143s + pc <- pcf(Cells, domain=square(0.5)) 143s + pcr <- pcf(Cells, domain=square(0.5), ratio=TRUE) 143s + pw <- pcf(Redwood, correction="none") 143s + pwr <- pcf(Redwood, correction="none", ratio=TRUE) 143s + pv <- pcf(Redwood, kernel="rectangular") 143s + p1 <- pcf(Redwood[1]) 143s + #' pcf.fv 143s + K <- Kest(Redwood) 143s + g <- pcf(K, method="a") 143s + g <- pcf(K, method="c") 143s + g <- pcf(K, method="d") 143s + #' Kinhom code blocks 143s + X <- rpoispp(function(x,y) { 100 * x }, 100, square(1)) 143s + lambda <- 100 * X$x 143s + Kin <- Kinhom(X, lambda, correction=c("none", "border")) 143s + lambda2 <- outer(lambda, lambda, "*") 143s + Ki2 <- Kinhom(X, lambda2=lambda2, diagonal=FALSE, 143s + correction=c("translate", "isotropic")) 143s + } 143s + if(ALWAYS) { 143s + #' edge corrections 143s + rr <- rep(0.1, npoints(Cells)) 143s + eC <- edge.Ripley(Cells, rr) 143s + eI <- edge.Ripley(Cells, rr, method="interpreted") 143s + if(max(abs(eC-eI)) > 0.1) 143s + stop("Ripley edge correction results do not match") 143s + } 143s + if(FULLTEST) { 143s + a <- rmax.Ripley(square(1)) 143s + a <- rmax.Rigid(square(1)) 143s + a <- rmax.Ripley(as.polygonal(square(1))) 143s + a <- rmax.Rigid(as.polygonal(square(1))) 143s + a <- rmax.Ripley(letterR) 143s + a <- rmax.Rigid(letterR) 143s + } 143s + if(ALWAYS) { 143s + #' run slow code for edge correction and compare results 143s + op <- spatstat.options(npixel=128) 143s + X <- Redwood[c(TRUE, FALSE, FALSE, FALSE)] 143s + Window(X) <- as.polygonal(Window(X)) 143s + Eapprox <- edge.Trans(X) 143s + Eexact <- edge.Trans(X, exact=TRUE) 143s + maxrelerr <- max(abs(1 - range(Eapprox/Eexact))) 143s + if(maxrelerr > 0.1) 143s + stop(paste("Exact and approximate algorithms for edge.Trans disagree by", 143s + paste0(round(100*maxrelerr), "%")), 143s + call.=FALSE) 143s + spatstat.options(op) 143s + } 143s + }) 143s > 143s > local({ 143s + if(FULLTEST) { 143s + #' ---- multitype ------ 143s + K <- Kcross(Amacrine, correction=c("none", "bord.modif")) 143s + K <- Kcross(Amacrine, correction=c("none", "bord", "bord.modif"), 143s + ratio=TRUE) 143s + #' inhomogeneous multitype 143s + K2 <- Kcross.inhom(Amacrine, lambdaX=densityfun(Amacrine)) 143s + K3 <- Kcross.inhom(Amacrine, lambdaX=density(Amacrine, at="points")) 143s + K5 <- Kcross.inhom(Amacrine, correction="bord.modif") 143s + #' markconnect, markcorr 143s + M <- markconnect(Amacrine, "on", "off", normalise=TRUE) 143s + M <- markcorr(longleaf, normalise=TRUE, 143s + correction=c("isotropic", "translate", "border", "none")) 143s + M <- markcorr(longleaf, normalise=TRUE, fargs=list()) 143s + #' Kmark (=markcorrint) 143s + X <- runifpoint(100) %mark% runif(100) 143s + km <- Kmark(X, f=atan2) 143s + km <- Kmark(X, f1=sin) 143s + km <- Kmark(X, f="myfun") 143s + aa <- Kmark(X, normalise=FALSE, returnL=FALSE) 143s + aa <- Kmark(X, normalise=FALSE, returnL=TRUE) 143s + aa <- Kmark(X, normalise=TRUE, returnL=FALSE) 143s + aa <- Kmark(X, normalise=TRUE, returnL=TRUE) 143s + } 143s + }) 143s > 143s > local({ 143s + if(FULLTEST) { 143s + #' various modified K functions 143s + #' 143s + #' directional K functions 143s + #' 143s + a <- Ksector(swedishpines, 143s + -pi/2, pi/2, units="radians", 143s + correction=c("none", "border", "bord.modif", 143s + "Ripley", "translate"), 143s + ratio=TRUE) 143s + plot(a) 143s + #' 143s + #' local K functions 143s + #' 143s + Z <- as.im(intensity(swedishpines), W=Window(swedishpines)) 143s + ZX <- Z[swedishpines] 143s + a <- localLinhom(swedishpines, lambda=Z) 143s + a <- localLinhom(swedishpines, lambda=ZX) 143s + a <- localLinhom(swedishpines, lambda=Z, correction="none") 143s + a <- localLinhom(swedishpines, lambda=Z, correction="translate") 143s + a <- localLcross(Amacrine) 143s + a <- localLcross(Amacrine, from="off", to="off") 143s + a <- localKdot(Amacrine) 143s + a <- localLdot(Amacrine) 143s + a <- localKcross.inhom(Amacrine) 143s + a <- localLcross.inhom(Amacrine) 143s + Zed <- solapply(intensity(amacrine), as.im, W=Window(amacrine)) 143s + Lum <- evaluateCovariateAtPoints(Zed, Amacrine) 143s + moff <- (marks(Amacrine) == "off") 143s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed) 143s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Lum) 143s + a <- localLcross.inhom(Amacrine, from="off", to="on", 143s + lambdaFrom=Lum[moff], lambdaTo=Lum[!moff]) 143s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 143s + correction="none") 143s + a <- localLcross.inhom(Amacrine, from="off", to="on", lambdaX=Zed, 143s + correction="translate") 143s + #' 143s + #' cases of resolve.lambdacross 143s + #' 143s + h <- resolve.lambdacross(Amacrine, moff, !moff) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Zed) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=Lum) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, 143s + lambdaI=Zed[["off"]], lambdaJ=Zed[["on"]]) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, 143s + lambdaI=Lum[moff], lambdaJ=Lum[!moff]) 143s + d <- densityfun(unmark(Amacrine), sigma=0.1) 143s + dm <- lapply(split(Amacrine), densityfun, sigma=0.1) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, lambdaX=d) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, 143s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 143s + h <- resolve.lambdacross(Amacrine, moff, !moff, 143s + lambdaX=function(x,y,m){ d(x,y) }) 143s + #' 143s + #' multitype inhomogeneous pcf 143s + #' 143s + g <- pcfcross.inhom(Amacrine, 143s + lambdaI=dm[["off"]], lambdaJ=dm[["on"]]) 143s + 143s + #' 143s + #' lohboot code blocks 143s + #' 143s + Ared <- lohboot(Redwood, fun="Kest", block=TRUE, 143s + Vcorrection=TRUE, global=FALSE, correction="none") 143s + Bred <- lohboot(Redwood, block=TRUE, basicboot=TRUE, global=FALSE) 143s + Cred <- lohboot(Redwood, fun=Kest, block=TRUE, global=TRUE, 143s + correction="translate") 143s + Dred <- lohboot(Redwood, Lest) 143s + Kred <- lohboot(Redwood, Kinhom) 143s + Lred <- lohboot(Redwood, Linhom) 143s + gred <- lohboot(Redwood, pcfinhom, sigma=0.1) 143s + #' 143s + X <- runifpoint(100, letterR) 143s + AX <- lohboot(X, block=TRUE, nx=7, ny=10) 143s + #' multitype 143s + b <- lohboot(Amacrine, Kcross) 143s + b <- lohboot(Amacrine, Lcross) 143s + b <- lohboot(Amacrine, Kdot) 143s + b <- lohboot(Amacrine, Ldot) 143s + b <- lohboot(Amacrine, Kcross.inhom) 143s + b <- lohboot(Amacrine, Lcross.inhom) 143s + 143s + ## Kscaled 143s + A <- Lscaled(japanesepines, renormalise=TRUE, correction="all") 143s + } 143s + }) 143s > 143s > local({ 143s + if(ALWAYS) { 143s + #' From Ege, in response to a stackoverflow question. 143s + #' The following example has two points separated by r = 1 with 1/4 of the 143s + #' circumference outside the 10x10 window (i.e. area 100). 143s + #' Thus the value of K^(r) should jump from 0 to 143s + #' 100/(2\cdot 1)\cdot ((3/4)^{-1} + (3/4)^{-1}) = 100 \cdot 4/3 = 133.333. 143s + x <- c(4.5,5.5) 143s + y <- c(10,10)-sqrt(2)/2 143s + W <- square(10) 143s + X <- ppp(x, y, W) 143s + compere <- function(a, b, where, tol=1e-6) { 143s + descrip <- paste("discrepancy in isotropic edge correction", where) 143s + err <- as.numeric(a) - as.numeric(b) 143s + maxerr <- max(abs(err)) 143s + blurb <- paste(descrip, "is", paste0(signif(maxerr, 4), ","), 143s + discrepancy in isotropic edge correction at interior point of rectangle is 2.22e-16, within tolerance of 1e-06 143s discrepancy in isotropic edge correction near corner of rectangle is 8.882e-16, within tolerance of 1e-06 143s if(maxerr > tol) "exceeding" else "within", 143s + "tolerance of", tol) 143s + message(blurb) 143s + if(maxerr > tol) { 143s + message(paste("Discrepancies:", paste(err, collapse=", "))) 143s + stop(paste("excessive", descrip), call.=FALSE) 143s + } 143s + invisible(TRUE) 143s + } 143s + ## Testing: 143s + eX <- edge.Ripley(X, c(1,1)) 143s + compere(eX, c(4/3,4/3), "at interior point of rectangle") 143s + ## Corner case: 143s + Y <- X 143s + Y$x <- X$x-4.5+sqrt(2)/2 143s + eY <- edge.Ripley(Y, c(1,1)) 143s + compere(eY, c(2,4/3), "near corner of rectangle") 143s + ## Invoke polygonal code 143s + Z <- rotate(Y, pi/4) 143s + eZdebug <- edge.Ripley(Z, c(1,1), internal=list(debug=TRUE)) 143s + compere(eZdebug, c(2,4/3), "at interior point of polygon (debug on)") 143s + ## test validity without debugger,in case of quirks of compiler optimisation 143s + eZ <- edge.Ripley(Z, c(1,1)) 143s + compere(eZ, c(2,4/3), "at interior point of polygon (debug off)") 143s + } 143s + }) 143s /// Debug level 3 /// 143s ------- centre[0] = (-6.071068, 7.071068) ------ 143s boundary distance 0.707107 143s radius[0] = 1.000000 143s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 143s Left: det = -35.857864 143s Right: det = -171.715729 143s Top: det = -34143.145751 143s Finished cutting; ncut = 0 143s contrib = -0.000000 143s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 143s Left: det = -171.715729 143s Right: det = -35.857864 143s Top: det = -34143.145751 143s discrepancy in isotropic edge correction at interior point of polygon (debug on) is 6.439e-15, within tolerance of 1e-06 143s discrepancy in isotropic edge correction at interior point of polygon (debug off) is 6.439e-15, within tolerance of 1e-06 143s Finished cutting; ncut = 0 143s contrib = 0.000000 143s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 143s Left: det = -35.857864 143s Right: det = 0.000000 143s det = 0 143s Top: det = 200.000000 143s det > 0 143s hits + segment: t = 1.000000, theta = 3.141593 143s hits - segment: t = 0.858579, theta = 1.570796 143s Finished cutting; ncut = 2 143s theta[0] = 1.570796 143s theta[1] = 3.141593 143s Interval 0, width 1.570796:inside 143s Interval 1, width 1.570796:outside 143s Interval 2, width 3.141593:inside 143s contrib = 4.712389 143s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 143s Left: det = 0.000000 143s det = 0 143s Right: det = -35.857864 143s Top: det = 200.000000 143s det > 0 143s hits + segment: t = 0.141421, theta = -1.570796 143s hits - segment: t = 0.000000, theta = 3.141593 143s Finished cutting; ncut = 2 143s theta[0] = 3.141593 143s theta[1] = 4.712389 143s Interval 0, width 3.141593:outside 143s Interval 1, width 1.570796:inside 143s Interval 2, width 1.570796:outside 143s contrib = -1.570796 143s 143s Total = 3.141593 = 0.500000 * (2 * pi) 143s ------- centre[1] = (-5.363961, 7.778175) ------ 143s boundary distance 0.707107 143s radius[0] = 1.000000 143s ... Edge[0] = (0.000000,0.000000) to (7.071068,7.071068) 143s Left: det = -27.772078 143s Right: det = -153.629942 143s Top: det = -34143.145751 143s Finished cutting; ncut = 0 143s contrib = -0.000000 143s ... Edge[1] = (7.071068,7.071068) to (0.000000,14.142136) 143s Left: det = -153.629942 143s Right: det = -27.772078 143s Top: det = -27108.831175 143s Finished cutting; ncut = 0 143s contrib = 0.000000 143s ... Edge[2] = (0.000000,14.142136) to (-7.071068,7.071068) 143s Left: det = -27.772078 143s Right: det = -1.914214 143s Top: det = 200.000000 143s det > 0 143s hits + segment: t = 0.900000, theta = 3.141593 143s hits - segment: t = 0.758579, theta = 1.570796 143s Finished cutting; ncut = 2 143s theta[0] = 1.570796 143s theta[1] = 3.141593 143s Interval 0, width 1.570796:inside 143s Interval 1, width 1.570796:outside 143s Interval 2, width 3.141593:inside 143s contrib = 4.712389 143s ... Edge[3] = (-7.071068,7.071068) to (0.000000,0.000000) 143s Left: det = -1.914214 143s Right: det = -27.772078 143s Top: det = -765.685425 143s Finished cutting; ncut = 0 143s contrib = -0.000000 143s 143s Total = 4.712389 = 0.750000 * (2 * pi) 143s > 143s > 143s > 143s > reset.spatstat.options() 143s > 143s BEGIN TEST testsL.R 143s 143s R version 4.4.3 (2025-02-28) -- "Trophy Case" 143s Copyright (C) 2025 The R Foundation for Statistical Computing 143s Platform: aarch64-unknown-linux-gnu 143s 143s R is free software and comes with ABSOLUTELY NO WARRANTY. 143s You are welcome to redistribute it under certain conditions. 143s Type 'license()' or 'licence()' for distribution details. 143s 143s R is a collaborative project with many contributors. 143s Type 'contributors()' for more information and 143s 'citation()' on how to cite R or R packages in publications. 143s 143s Type 'demo()' for some demos, 'help()' for on-line help, or 143s 'help.start()' for an HTML browser interface to help. 143s Type 'q()' to quit R. 143s 143s > #' 143s > #' Header for all (concatenated) test files 143s > #' 143s > #' Require spatstat.explore 143s > #' Obtain environment variable controlling tests. 143s > #' 143s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 143s > 143s > require(spatstat.explore) 143s Loading required package: spatstat.explore 143s Loading required package: spatstat.data 144s Loading required package: spatstat.univar 144s spatstat.univar 3.1-2 144s Loading required package: spatstat.geom 144s spatstat.geom 3.3-6 144s Loading required package: spatstat.random 144s spatstat.random 3.3-3 144s Loading required package: nlme 144s spatstat.explore 3.3-4 144s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 144s > ALWAYS <- TRUE 144s > cat(paste("--------- Executing", 144s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 144s + "test code -----------\n")) 144s --------- Executing **RESTRICTED** subset of test code ----------- 144s > ## 144s > ## tests/localpcf.R 144s > ## 144s > ## temporary test file for localpcfmatrix 144s > ## $Revision: 1.2 $ $Date: 2015/12/29 08:54:49 $ 144s > 144s > local({ 144s + a <- localpcfmatrix(redwood) 144s + if(FULLTEST) { 144s + a 144s + plot(a) 144s + a[, 3:5] 144s + } 144s + }) 144s > 144s BEGIN TEST testsM.R 144s 144s R version 4.4.3 (2025-02-28) -- "Trophy Case" 144s Copyright (C) 2025 The R Foundation for Statistical Computing 144s Platform: aarch64-unknown-linux-gnu 144s 144s R is free software and comes with ABSOLUTELY NO WARRANTY. 144s You are welcome to redistribute it under certain conditions. 144s Type 'license()' or 'licence()' for distribution details. 144s 144s R is a collaborative project with many contributors. 144s Type 'contributors()' for more information and 144s 'citation()' on how to cite R or R packages in publications. 144s 144s Type 'demo()' for some demos, 'help()' for on-line help, or 144s 'help.start()' for an HTML browser interface to help. 144s Type 'q()' to quit R. 144s 144s > #' 144s > #' Header for all (concatenated) test files 144s > #' 144s > #' Require spatstat.explore 144s > #' Obtain environment variable controlling tests. 144s > #' 144s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 144s > 144s > require(spatstat.explore) 144s Loading required package: spatstat.explore 144s Loading required package: spatstat.data 145s Loading required package: spatstat.univar 145s spatstat.univar 3.1-2 145s Loading required package: spatstat.geom 145s spatstat.geom 3.3-6 146s Loading required package: spatstat.random 146s spatstat.random 3.3-3 146s Loading required package: nlme 146s spatstat.explore 3.3-4 146s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 146s > ALWAYS <- TRUE 146s > cat(paste("--------- Executing", 146s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 146s + "test code -----------\n")) 146s --------- Executing **RESTRICTED** subset of test code ----------- 146s > ## 146s > ## tests/markcor.R 146s > ## 146s > ## Tests of mark correlation code (etc) 146s > ## 146s > ## $Revision: 1.7 $ $Date: 2020/11/25 01:23:32 $ 146s > 146s > local({ 146s + if(ALWAYS) { 146s + ## check.testfun checks equality of functions 146s + ## and is liable to break if the behaviour of all.equal is changed 146s + fe <- function(m1, m2) {m1 == m2} 146s + fm <- function(m1, m2) {m1 * m2} 146s + fs <- function(m1, m2) {sqrt(m1)} 146s + if(check.testfun(fe, X=amacrine)$ftype != "equ") 146s + warning("check.testfun fails to recognise mark equality function") 146s + if(check.testfun(fm, X=longleaf)$ftype != "mul") 146s + warning("check.testfun fails to recognise mark product function") 146s + check.testfun(fs, X=longleaf) 146s + check.testfun("mul") 146s + check.testfun("equ") 146s + } 146s + 146s + if(FULLTEST) { 146s + ## test all is well in Kmark -> Kinhom 146s + MA <- Kmark(amacrine,function(m1,m2){m1==m2}) 146s + set.seed(42) 146s + AR <- rlabel(amacrine) 146s + MR <- Kmark(AR,function(m1,m2){m1==m2}) 146s + if(isTRUE(all.equal(MA,MR))) 146s + stop("Kmark unexpectedly ignores marks") 146s + 146s + ## cover code blocks in markcorr() 146s + X <- runifpoint(100) %mark% runif(100) 146s + Y <- X %mark% data.frame(u=runif(100), v=runif(100)) 146s + ww <- runif(100) 146s + fone <- function(x) { x/2 } 146s + ffff <- function(x,y) { fone(x) * fone(y) } 146s + aa <- markcorr(Y) 146s + bb <- markcorr(Y, ffff, weights=ww, normalise=TRUE) 146s + bb <- markcorr(Y, ffff, weights=ww, normalise=FALSE) 146s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=TRUE) 146s + bb <- markcorr(Y, f1=fone, weights=ww, normalise=FALSE) 146s + 146s + ## markcrosscorr 146s + a <- markcrosscorr(betacells, normalise=FALSE) 146s Warning messages: 146s 1: In eval(quote({ : 146s check.testfun fails to recognise mark equality function 146s 2: In eval(quote({ : 146s check.testfun fails to recognise mark product function 146s + if(require(sm)) { 146s + b <- markcrosscorr(betacells, method="sm") 146s + } 146s + 146s + ## Vmark with normalisation 146s + v <- Vmark(spruces, normalise=TRUE) 146s + v <- Vmark(finpines, normalise=TRUE) 146s + } 146s + }) 146s > #' tests/mctests.R 146s > #' Monte Carlo tests 146s > #' (mad.test, dclf.test, envelopeTest, hasenvelope) 146s > #' $Revision: 1.5 $ $Date: 2022/05/23 04:09:49 $ 146s > 146s > local({ 146s + if(FULLTEST) { 146s + envelopeTest(cells, Lest, exponent=1, nsim=9, savepatterns=TRUE) 146s + (a3 <- envelopeTest(cells, Lest, exponent=3, nsim=9, savepatterns=TRUE)) 146s + 146s + envelopeTest(a3, Lest, exponent=3, nsim=9, alternative="less") 146s + 146s + envelopeTest(redwood, Lest, exponent=1, nsim=19, 146s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 146s + envelopeTest(redwood, pcf, exponent=Inf, nsim=19, 146s + rinterval=c(0, 0.1), alternative="greater", clamp=TRUE) 146s + } 146s + }) 146s > 146s > 146s > 146s BEGIN TEST testsNtoO.R 146s 146s R version 4.4.3 (2025-02-28) -- "Trophy Case" 146s Copyright (C) 2025 The R Foundation for Statistical Computing 146s Platform: aarch64-unknown-linux-gnu 146s 146s R is free software and comes with ABSOLUTELY NO WARRANTY. 146s You are welcome to redistribute it under certain conditions. 146s Type 'license()' or 'licence()' for distribution details. 146s 146s R is a collaborative project with many contributors. 146s Type 'contributors()' for more information and 146s 'citation()' on how to cite R or R packages in publications. 146s 146s Type 'demo()' for some demos, 'help()' for on-line help, or 146s 'help.start()' for an HTML browser interface to help. 146s Type 'q()' to quit R. 146s 146s > #' 146s > #' Header for all (concatenated) test files 146s > #' 146s > #' Require spatstat.explore 146s > #' Obtain environment variable controlling tests. 146s > #' 146s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 146s > 146s > require(spatstat.explore) 146s Loading required package: spatstat.explore 146s Loading required package: spatstat.data 147s Loading required package: spatstat.univar 147s spatstat.univar 3.1-2 147s Loading required package: spatstat.geom 147s spatstat.geom 3.3-6 147s Loading required package: spatstat.random 147s spatstat.random 3.3-3 147s Loading required package: nlme 147s spatstat.explore 3.3-4 147s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 147s > ALWAYS <- TRUE 147s > cat(paste("--------- Executing", 147s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 147s + "test code -----------\n")) 147s --------- Executing **RESTRICTED** subset of test code ----------- 147s > # 147s > # tests/nnstat.R 147s > # 147s > # Check code that uses nndist/nnwhich 147s > # 147s > # nnorient() 147s > # stienen() 147s > # 147s > # $Revision: 1.1 $ $Date: 2020/12/04 03:45:44 $ 147s > # 147s > 147s > 147s > local({ 147s + if(FULLTEST) { 147s + #' test nnorient 147s + nnorient(cells, domain=erosion(Window(cells), 0.1)) 147s + #' degenerate case 147s + X <- cells[nndist(cells) > bdist.points(cells)] 147s + f <- nnorient(X) 147s + #' nnclean 147s + A <- nnclean(shapley, k=17, edge.correct=TRUE) 147s + B <- nnclean(runifpoint3(300), 3) 147s + #' stienen set 147s + #' bug when disc radius is zero 147s + Y <- unmark(humberside)[40:100] # contains duplicated points 147s + stienen(Y) 147s + Z <- stienenSet(Y) 147s + #' other cases 147s + U <- stienen(cells[1]) 147s + V <- stienenSet(cells, edge=FALSE) 147s + } 147s + }) 147s > 147s > 147s > 147s > 147s BEGIN TEST testsP1.R 147s 147s R version 4.4.3 (2025-02-28) -- "Trophy Case" 147s Copyright (C) 2025 The R Foundation for Statistical Computing 147s Platform: aarch64-unknown-linux-gnu 147s 147s R is free software and comes with ABSOLUTELY NO WARRANTY. 147s You are welcome to redistribute it under certain conditions. 147s Type 'license()' or 'licence()' for distribution details. 147s 147s R is a collaborative project with many contributors. 147s Type 'contributors()' for more information and 147s 'citation()' on how to cite R or R packages in publications. 147s 147s Type 'demo()' for some demos, 'help()' for on-line help, or 147s 'help.start()' for an HTML browser interface to help. 147s Type 'q()' to quit R. 147s 147s > Loading required package: spatstat.explore 147s #' 147s > #' Header for all (concatenated) test files 147s > #' 147s > #' Require spatstat.explore 147s > #' Obtain environment variable controlling tests. 147s > #' 147s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 147s > 147s > require(spatstat.explore) 147s Loading required package: spatstat.data 148s Loading required package: spatstat.univar 148s spatstat.univar 3.1-2 148s Loading required package: spatstat.geom 148s spatstat.geom 3.3-6 148s Loading required package: spatstat.random 148s spatstat.random 3.3-3 148s Loading required package: nlme 148s spatstat.explore 3.3-4 148s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 148s > ALWAYS <- TRUE 148s > cat(paste("--------- Executing", 148s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 148s + "test code -----------\n")) 148s --------- Executing **RESTRICTED** subset of test code ----------- 148s > ## 148s > ## tests/pixelgripes.R 148s > ## Problems related to pixellation of windows 148s > ## 148s > ## $Revision: 1.8 $ $Date: 2022/10/23 06:21:10 $ 148s > 148s > if(FULLTEST) { 148s + local({ 148s + 148s + 148s + }) 148s + } 148s > 148s BEGIN TEST testsP2.R 149s 149s R version 4.4.3 (2025-02-28) -- "Trophy Case" 149s Copyright (C) 2025 The R Foundation for Statistical Computing 149s Platform: aarch64-unknown-linux-gnu 149s 149s R is free software and comes with ABSOLUTELY NO WARRANTY. 149s You are welcome to redistribute it under certain conditions. 149s Type 'license()' or 'licence()' for distribution details. 149s 149s R is a collaborative project with many contributors. 149s Type 'contributors()' for more information and 149s 'citation()' on how to cite R or R packages in publications. 149s 149s Type 'demo()' for some demos, 'help()' for on-line help, or 149s 'help.start()' for an HTML browser interface to help. 149s Type 'q()' to quit R. 149s 149s > #' 149s > #' Header for all (concatenated) test files 149s > Loading required package: spatstat.explore 149s #' 149s > #' Require spatstat.explore 149s > #' Obtain environment variable controlling tests. 149s > #' 149s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 149s > 149s > require(spatstat.explore) 149s Loading required package: spatstat.data 150s Loading required package: spatstat.univar 150s spatstat.univar 3.1-2 150s Loading required package: spatstat.geom 150s spatstat.geom 3.3-6 150s Loading required package: spatstat.random 150s spatstat.random 3.3-3 150s Loading required package: nlme 150s spatstat.explore 3.3-4 150s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 150s > ALWAYS <- TRUE 150s > cat(paste("--------- Executing", 150s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 150s + "test code -----------\n")) 150s --------- Executing **RESTRICTED** subset of test code ----------- 150s > 150s BEGIN TEST testsQ.R 150s 150s R version 4.4.3 (2025-02-28) -- "Trophy Case" 150s Copyright (C) 2025 The R Foundation for Statistical Computing 150s Platform: aarch64-unknown-linux-gnu 150s 150s R is free software and comes with ABSOLUTELY NO WARRANTY. 150s You are welcome to redistribute it under certain conditions. 150s Type 'license()' or 'licence()' for distribution details. 150s 150s R is a collaborative project with many contributors. 150s Type 'contributors()' for more information and 150s 'citation()' on how to cite R or R packages in publications. 150s 150s Type 'demo()' for some demos, 'help()' for on-line help, or 150s 'help.start()' for an HTML browser interface to help. 150s Type 'q()' to quit R. 150s 150s > #' 150s > #' Header for all (concatenated) test files 150s > #' 150s > #' Require spatstat.explore 150s > #' Obtain environment variable controlling tests. 150s > #' 150s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 150s > 150s > require(spatstat.explore) 150s Loading required package: spatstat.explore 150s Loading required package: spatstat.data 151s Loading required package: spatstat.univar 151s spatstat.univar 3.1-2 151s Loading required package: spatstat.geom 151s spatstat.geom 3.3-6 151s Loading required package: spatstat.random 151s spatstat.random 3.3-3 151s Loading required package: nlme 151s spatstat.explore 3.3-4 151s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 151s > ALWAYS <- TRUE 151s > cat(paste("--------- Executing", 151s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 151s + "test code -----------\n")) 151s --------- Executing **RESTRICTED** subset of test code ----------- 151s > 151s BEGIN TEST testsR1.R 151s 151s R version 4.4.3 (2025-02-28) -- "Trophy Case" 151s Copyright (C) 2025 The R Foundation for Statistical Computing 151s Platform: aarch64-unknown-linux-gnu 151s 151s R is free software and comes with ABSOLUTELY NO WARRANTY. 151s You are welcome to redistribute it under certain conditions. 151s Type 'license()' or 'licence()' for distribution details. 151s 151s R is a collaborative project with many contributors. 151s Type 'contributors()' for more information and 151s 'citation()' on how to cite R or R packages in publications. 151s 151s Type 'demo()' for some demos, 'help()' for on-line help, or 151s 'help.start()' for an HTML browser interface to help. 151s Type 'q()' to quit R. 151s 151s > #' 151s Loading required package: spatstat.explore 151s > #' Header for all (concatenated) test files 151s > #' 151s > #' Require spatstat.explore 151s > #' Obtain environment variable controlling tests. 151s > #' 151s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 151s > 151s > require(spatstat.explore) 151s Loading required package: spatstat.data 152s Loading required package: spatstat.univar 152s spatstat.univar 3.1-2 152s Loading required package: spatstat.geom 152s spatstat.geom 3.3-6 152s Loading required package: spatstat.random 152s spatstat.random 3.3-3 152s Loading required package: nlme 153s spatstat.explore 3.3-4 153s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 153s > ALWAYS <- TRUE 153s > cat(paste("--------- Executing", 153s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 153s + "test code -----------\n")) 153s --------- Executing **RESTRICTED** subset of test code ----------- 153s > ## 153s > ## tests/rhohat.R 153s > ## 153s > ## Test all combinations of options for rhohatCalc 153s > ## 153s > ## $Revision: 1.6 $ $Date: 2022/05/22 08:03:48 $ 153s > 153s > local({ 153s + if(FULLTEST) { 153s + X <- rpoispp(function(x,y){exp(3+3*x)}) 153s + Z <- as.im(function(x,y) { x }, Window(X)) 153s + f <- funxy(function(x,y) { y + 1 }, Window(X)) 153s + 153s + ## rhohat.ppp 153s + ## done in example(rhohat): 153s + ## rhoA <- rhohat(X, "x") 153s + ## rhoB <- rhohat(X, "x", method="reweight") 153s + ## rhoC <- rhohat(X, "x", method="transform") 153s + ## alternative smoother (if package locfit available) 153s + rhoA <- rhohat(X, "x", smoother="local") 153s + rhoB <- rhohat(X, "x", smoother="local", method="reweight") 153s + rhoC <- rhohat(X, "x", smoother="local", method="transform") 153s + 153s + #' code blocks 153s + rhoD <- rhohat(X, "y", positiveCI=TRUE) 153s + rhoE <- rhohat(X, Z, positiveCI=TRUE) 153s + #' weights 153s + rhoF <- rhohat(X, Z, weights=f(X)) 153s + rhoG <- rhohat(X, Z, weights=f) 153s + rhoH <- rhohat(X, Z, weights=as.im(f)) 153s + 153s + lam <- as.im(function(x,y) {exp(3+2*x)}, W=Window(Z)) 153s + 153s + ## Baseline 153s + rhoAb <- rhohat(X, "x", baseline=lam) 153s + rhoBb <- rhohat(X, "x", method="reweight", baseline=lam) 153s + rhoCb <- rhohat(X, "x", method="transform", baseline=lam) 153s + 153s + ## Horvitz-Thompson 153s + rhoAH <- rhohat(X, "x", horvitz=TRUE) 153s + rhoBH <- rhohat(X, "x", method="reweight", horvitz=TRUE) 153s + rhoCH <- rhohat(X, "x", method="transform", horvitz=TRUE) 153s + 153s + ## class support 153s + plot(rhoA) 153s + plot(rhoA, rho ~ x, shade=NULL) 153s + plot(rhoA, log(rho) ~ x, shade=NULL) 153s + plot(rhoA, log(.) ~ x) 153s + 153s + ## rho2hat 153s + r2xy <- rho2hat(X, "x", "y") 153s + r2xyw <- rho2hat(X, "x", "y", method="reweight") 153s + print(r2xyw) 153s + plot(r2xy, do.points=TRUE) 153s + xcoord <- function(x,y) x 153s + ycoord <- function(x,y) y 153s + xim <- as.im(xcoord, W=Window(X)) 153s + r2fi <- rho2hat(X, ycoord, xim) 153s + r2if <- rho2hat(X, xim, ycoord) 153s + } 153s + }) 153s > 153s BEGIN TEST testsR2.R 153s 153s R version 4.4.3 (2025-02-28) -- "Trophy Case" 153s Copyright (C) 2025 The R Foundation for Statistical Computing 153s Platform: aarch64-unknown-linux-gnu 153s 153s R is free software and comes with ABSOLUTELY NO WARRANTY. 153s You are welcome to redistribute it under certain conditions. 153s Type 'license()' or 'licence()' for distribution details. 153s 153s R is a collaborative project with many contributors. 153s Type 'contributors()' for more information and 153s 'citation()' on how to cite R or R packages in publications. 153s 153s Type 'demo()' for some demos, 'help()' for on-line help, or 153s 'help.start()' for an HTML browser interface to help. 153s Type 'q()' to quit R. 153s 153s > #' 153s > #' Header for all (concatenated) test files 153s > #' 153s > #' Require spatstat.explore 153s > #' Obtain environment variable controlling tests. 153s > #' 153s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 153s > 153s > require(spatstat.explore) 153s Loading required package: spatstat.explore 153s Loading required package: spatstat.data 154s Loading required package: spatstat.univar 154s spatstat.univar 3.1-2 154s Loading required package: spatstat.geom 154s spatstat.geom 3.3-6 154s Loading required package: spatstat.random 154s spatstat.random 3.3-3 154s Loading required package: nlme 154s spatstat.explore 3.3-4 154s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 154s > ALWAYS <- TRUE 154s > cat(paste("--------- Executing", 154s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 154s + "test code -----------\n")) 154s --------- Executing **RESTRICTED** subset of test code ----------- 154s > 154s BEGIN TEST testsS.R 154s 154s R version 4.4.3 (2025-02-28) -- "Trophy Case" 154s Copyright (C) 2025 The R Foundation for Statistical Computing 154s Platform: aarch64-unknown-linux-gnu 154s 154s R is free software and comes with ABSOLUTELY NO WARRANTY. 154s You are welcome to redistribute it under certain conditions. 154s Type 'license()' or 'licence()' for distribution details. 154s 154s R is a collaborative project with many contributors. 154s Type 'contributors()' for more information and 154s 'citation()' on how to cite R or R packages in publications. 154s 154s Type 'demo()' for some demos, 'help()' for on-line help, or 154s 'help.start()' for an HTML browser interface to help. 154s Type 'q()' to quit R. 154s 154s > #' 154s > #' Header for all (concatenated) test files 154s > #' 154s > Loading required package: spatstat.explore 154s #' Require spatstat.explore 154s > #' Obtain environment variable controlling tests. 154s > #' 154s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 154s > 154s > require(spatstat.explore) 154s Loading required package: spatstat.data 155s Loading required package: spatstat.univar 155s spatstat.univar 3.1-2 155s Loading required package: spatstat.geom 155s spatstat.geom 3.3-6 155s Loading required package: spatstat.random 155s spatstat.random 3.3-3 155s Loading required package: nlme 155s spatstat.explore 3.3-4 155s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 155s > ALWAYS <- TRUE 155s > cat(paste("--------- Executing", 155s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 155s + "test code -----------\n")) 155s --------- Executing **RESTRICTED** subset of test code ----------- 155s > #' tests/sdr.R 155s > #' 155s > #' $Revision: 1.2 $ $Date: 2020/05/01 09:59:59 $ 155s > 155s > if(FULLTEST) { 155s + local({ 155s + AN <- sdr(bei, bei.extra, method="NNIR") 155s + AV <- sdr(bei, bei.extra, method="SAVE") 155s + AI <- sdr(bei, bei.extra, method="SIR") 155s + AT <- sdr(bei, bei.extra, method="TSE") 155s + subspaceDistance(AN$B, AV$B) 155s + dimhat(AN$M) 155s + }) 155s + } 155s > ## 155s > ## tests/segments.R 155s > ## Tests of psp class and related code 155s > ## [SEE ALSO: tests/xysegment.R] 155s > ## 155s > ## $Revision: 1.33 $ $Date: 2022/05/22 08:39:47 $ 155s > 155s > 155s > local({ 155s + if(ALWAYS) { # C code 155s + #' tests of density.psp 155s + Y <- edges(letterR) 155s + Window(Y) <- grow.rectangle(Frame(Y), 0.4) 155s + YC <- density(Y, 0.2, method="C", edge=FALSE, dimyx=64) 155s + YI <- density(Y, 0.2, method="interpreted", edge=FALSE, dimyx=64) 155s + YF <- density(Y, 0.2, method="FFT", edge=FALSE, dimyx=64) 156s + xCI <- max(abs(YC/YI - 1)) 156s + xFI <- max(abs(YF/YI - 1)) 156s + cat(paste("xCI =", xCI, "\txFI =", signif(xFI, 5)), fill=TRUE) 156s + if(xCI > 0.01) stop(paste("density.psp C algorithm relative error =", xCI)) 156s + if(xFI > 0.1) stop(paste("density.psp FFT algorithm relative error =", xFI)) 156s + 156s + B <- square(0.3) 156s + density(Y, 0.2, at=B) 156s + density(Y, 0.2, at=B, edge=TRUE, method="C") 156s + Z <- runifrect(3, B) 156s + density(Y, 0.2, at=Z) 156s + density(Y, 0.2, at=Z, edge=TRUE, method="C") 156s + } 156s + 156s + if(FULLTEST) { 156s + #' segment clipping in window (bug found by Rolf) 156s + set.seed(42) 156s + X <- runifpoint(50, letterR) 156s + SP <- dirichletEdges(X) #' clip to polygonal window 156s + Window(X) <- as.mask(Window(X)) 156s + SM <- dirichletEdges(X) #' clip to mask window 156s + } 156s + 156s + if(FULLTEST) { 156s + #' test rshift.psp and append.psp with marks (Ute Hahn) 156s + m <- data.frame(A=1:10, B=letters[1:10]) 156s + g <- gl(3, 3, length=10) 156s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=m) 156s + Y <- rshift(X, radius = 0.1) 156s + Y <- rshift(X, radius = 0.1, group=g) 156s + #' mark management 156s + b <- data.frame(A=1:10) 156s + X <- psp(runif(10), runif(10), runif(10), runif(10), window=owin(), marks=b) 156s + stopifnot(is.data.frame(marks(X))) 156s + Y <- rshift(X, radius = 0.1) 156s + Y <- rshift(X, radius = 0.1, group=g) 156s + } 156s + 156s + }) 156s xCI = 2.55351295663786e-15 xFI = 0.073128 157s > 157s > 157s > 157s > # 157s > ## tests/sigtraceprogress.R 157s > # 157s > ## Tests of *.sigtrace and *.progress 157s > # 157s > ## $Revision: 1.5 $ $Date: 2020/05/01 09:59:59 $ 157s > 157s > if(FULLTEST) { 157s + local({ 157s Warning message: 157s the images ‘dens’ and ‘edg’ were not compatible 157s + plot(dclf.sigtrace(redwood, nsim=19, alternative="greater", rmin=0.02, 157s + verbose=FALSE)) 157s + plot(dclf.progress(redwood, nsim=19, alternative="greater", rmin=0.02, 157s + verbose=FALSE)) 157s + plot(dg.sigtrace(redwood, nsim=5, alternative="greater", rmin=0.02, 157s + verbose=FALSE)) 157s + plot(dg.progress(redwood, nsim=5, alternative="greater", rmin=0.02, 157s + verbose=FALSE)) 157s + ## test 'leave-two-out' algorithm 157s + a <- dclf.sigtrace(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 157s + verbose=FALSE) 157s + aa <- dclf.progress(redwood, Lest, nsim=9, use.theory=FALSE, leaveout=2, 157s + verbose=FALSE) 157s + b <- dg.sigtrace(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2) 157s + bb <- dg.progress(redwood, Lest, nsim=5, use.theory=FALSE, leaveout=2, 157s + verbose=FALSE) 157s + ## other code blocks 157s + e <- mad.progress(redwood, nsim=5) 157s + e <- mad.progress(redwood, nsim=19, alpha=0.05) 157s + f <- dclf.progress(redwood, nsim=5, scale=function(x) x^2) 157s + f <- dclf.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 157s + g <- dg.progress(redwood, nsim=5, scale=function(x) x^2) 157s + g <- dg.progress(redwood, nsim=5, normalize=TRUE, deflate=TRUE) 157s + }) 157s + } 157s > #' 157s > #' tests/ssf.R 157s > #' 157s > #' Tests of 'ssf' class 157s > #' 157s > #' $Revision: 1.5 $ $Date: 2020/12/04 08:02:25 $ 157s > #' 157s > 157s > if(FULLTEST) { 157s + local({ 157s + Y <- cells[1:5] 157s + X <- rsyst(Window(Y), 5) 157s + Z <- runifpoint(3, Window(Y)) 157s + f1 <- ssf(X, nncross(X,Y,what="dist")) 157s + f2 <- ssf(X, nncross(X,Y,what="dist", k=1:2)) 157s + image(f1) 157s + g1 <- as.function(f1) 157s + g1(Z) 157s + g2 <- as.function(f2) 157s + g2(Z) 157s + plot(f1, style="contour") 157s + plot(f1, style="imagecontour") 157s + contour(f1) 157s + apply.ssf(f2, 1, sum) 157s + range(f1) 157s + min(f1) 157s + max(f1) 157s + integral(f1, weights=tile.areas(dirichlet(X))) 157s + }) 157s + } 157s > #' 157s > #' tests/sumfun.R 157s > #' 157s > #' Tests of code for summary functions 157s > #' 157s > #' $Revision: 1.9 $ $Date: 2022/05/22 08:45:23 $ 157s > 157s > if(ALWAYS) { # involves C code 157s + local({ 157s + W <- owin(c(0,1), c(-1/2, 0)) 157s + Gr <- Gest(redwood, correction="all",domain=W) 157s + Fr <- Fest(redwood, correction="all",domain=W) 157s + Jr <- Jest(redwood, correction="all",domain=W) 157s + 157s + F0 <- Fest(redwood[FALSE], correction="all") 157s + Fh <- Fest(humberside, domain=erosion(Window(humberside), 100)) 157s + 157s + FIr <- Finhom(redwood, savelambda=TRUE, ratio=TRUE) 157s + JIr <- Jinhom(redwood, savelambda=TRUE, ratio=TRUE) 157s + 157s + Ga <- Gcross(amacrine, correction="all") 157s + Ia <- Iest(amacrine, correction="all") 157s + lam <- intensity(amacrine) 157s + lmin <- 0.9 * min(lam) 157s + nJ <- sum(marks(amacrine) == "off") 157s + FM <- FmultiInhom(amacrine, marks(amacrine) == "off", 157s + lambdaJ=rep(lam["off"], nJ), 157s + lambdamin = lmin) 157s + GM <- GmultiInhom(amacrine, marks(amacrine) == "on", 157s + marks(amacrine) == "off", 157s + lambda=lam[marks(amacrine)], 157s + lambdamin=lmin, 157s + ReferenceMeasureMarkSetI=42) 157s + 157s + a <- compileCDF(D=nndist(redwood), 157s + B=bdist.points(redwood), 157s + r=seq(0, 1, length=256)) 157s + 157s + #' Tstat (triplet) function, all code blocks 157s + a <- Tstat(redwood, ratio=TRUE, 157s + correction=c("none", "border", "bord.modif", "translate")) 157s + 157s + ## distance argument spacing and breakpoints 157s + e <- check.finespacing(c(0,1,2), eps=0.1, action="silent") 157s + b <- as.breakpts(pi, 20) 157s + b <- as.breakpts(42, max=pi, npos=20) 157s + b <- even.breaks.owin(letterR) 157s + }) 157s + } 159s Searching 59340 potential triangles; estimated time 0.000426 sec 159s > 159s BEGIN TEST testsT.R 159s 159s R version 4.4.3 (2025-02-28) -- "Trophy Case" 159s Copyright (C) 2025 The R Foundation for Statistical Computing 159s Platform: aarch64-unknown-linux-gnu 159s 159s R is free software and comes with ABSOLUTELY NO WARRANTY. 159s You are welcome to redistribute it under certain conditions. 159s Type 'license()' or 'licence()' for distribution details. 159s 159s R is a collaborative project with many contributors. 159s Type 'contributors()' for more information and 159s 'citation()' on how to cite R or R packages in publications. 159s 159s Type 'demo()' for some demos, 'help()' for on-line help, or 159s 'help.start()' for an HTML browser interface to help. 159s Type 'q()' to quit R. 159s 159s > #' 159s > #' Header for all (concatenated) test files 159s > #' 159s > #' Require spatstat.explore 159s > #' Obtain environment variable controlling tests. 159s > #' 159s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 159s > 159s > require(spatstat.explore) 159s Loading required package: spatstat.explore 159s Loading required package: spatstat.data 160s Loading required package: spatstat.univar 160s spatstat.univar 3.1-2 160s Loading required package: spatstat.geom 160s spatstat.geom 3.3-6 160s Loading required package: spatstat.random 160s spatstat.random 3.3-3 160s Loading required package: nlme 161s spatstat.explore 3.3-4 161s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 161s > ALWAYS <- TRUE 161s > cat(paste("--------- Executing", 161s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 161s + "test code -----------\n")) 161s --------- Executing **RESTRICTED** subset of test code ----------- 161s > #' 161s > #' tests/threedee.R 161s > #' 161s > #' Tests of 3D code 161s > #' 161s > #' $Revision: 1.8 $ $Date: 2020/05/02 01:32:58 $ 161s > #' 161s > 161s > local({ 161s + X <- runifpoint3(30) 161s + Y <- runifpoint3(20) 161s + if(FULLTEST) { 161s + A <- runifpoint3(10, nsim=2) 161s + Z <- ppsubset(X, 2:4) 161s + } 161s + ## 161s + if(ALWAYS) { # includes C code 161s + d <- pairdist(X, periodic=TRUE, squared=TRUE) 161s + d <- crossdist(X, Y, squared=TRUE) 161s + d <- crossdist(X, Y, squared=TRUE, periodic=TRUE) 161s + #' 161s + h <- has.close(X, 0.2) 161s + h <- has.close(X, 0.2, periodic=TRUE) 161s + h <- has.close(X, 0.2, Y=Y) 161s + h <- has.close(X, 0.2, Y=Y, periodic=TRUE) 161s + #' code blocks not otherwise reached 161s + rmax <- 0.6 * max(nndist(X)) 161s + g <- G3est(X, rmax=rmax, correction="rs") 161s + g <- G3est(X, rmax=rmax, correction="km") 161s + g <- G3est(X, rmax=rmax, correction="Hanisch") 161s + g <- G3est(X, rmax=rmax, sphere="ideal") 161s + g <- G3est(X, rmax=rmax, sphere="digital") 161s + v <- sphere.volume() 161s + v <- digital.volume() 161s + #' older code 161s + co <- coords(X) 161s + xx <- co$x 161s + yy <- co$y 161s + zz <- co$z 161s + gg1 <- g3engine(xx, yy, zz, correction="Hanisch G3") 161s + gg2 <- g3engine(xx, yy, zz, correction="minus sampling") 161s + ff1 <- f3engine(xx, yy, zz, correction="no") 161s + ff2 <- f3engine(xx, yy, zz, correction="minus sampling") 161s + } 161s + ## 161s + if(ALWAYS) { 161s + #'class support 161s + X <- runifpoint3(10) 161s + print(X) 161s + print(X %mark% runif(10)) 161s + print(X %mark% factor(letters[c(1:5,5:1)])) 161s + print(X %mark% data.frame(a=1:10, b=runif(10))) 161s + da <- as.Date(paste0("2020-01-0", c(1:5,5:1))) 161s + print(X %mark% da) 161s + print(X %mark% data.frame(a=1:10, b=da)) 161s + } 161s + }) 161s Three-dimensional point pattern: 10 points 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s Marked three-dimensional point pattern: 10 points 161s marks are numeric, of storage type ‘double’ 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s Marked three-dimensional point pattern: 10 points 161s Multitype, with levels = a, b, c, d, e 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s Marked three-dimensional point pattern: 10 points 161s Mark variables: a, b 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s Marked three-dimensional point pattern: 10 points 161s marks are dates, of class ‘Date’ 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s Warning messages: 161s Marked three-dimensional point pattern: 10 points 161s Mark variables: a, b 161s Box: [0, 1] x [0, 1] x [0, 1] units 161s 1: In G3est: unrecognised argument ‘sphere’ was ignored 161s 2: In G3est: unrecognised argument ‘sphere’ was ignored 161s > 161s BEGIN TEST testsUtoZ.R 161s 161s R version 4.4.3 (2025-02-28) -- "Trophy Case" 161s Copyright (C) 2025 The R Foundation for Statistical Computing 161s Platform: aarch64-unknown-linux-gnu 161s 161s R is free software and comes with ABSOLUTELY NO WARRANTY. 161s You are welcome to redistribute it under certain conditions. 161s Type 'license()' or 'licence()' for distribution details. 161s 161s R is a collaborative project with many contributors. 161s Type 'contributors()' for more information and 161s 'citation()' on how to cite R or R packages in publications. 161s 161s Type 'demo()' for some demos, 'help()' for on-line help, or 161s 'help.start()' for an HTML browser interface to help. 161s Type 'q()' to quit R. 161s 161s > #' 161s > #' Header for all (concatenated) test files 161s > #' 161s > #' Require spatstat.explore 161s > #' Obtain environment variable controlling tests. 161s > #' 161s > #' $Revision: 1.5 $ $Date: 2020/04/30 05:31:37 $ 161s > 161s > require(spatstat.explore) 161s Loading required package: spatstat.explore 161s Loading required package: spatstat.data 162s Loading required package: spatstat.univar 162s spatstat.univar 3.1-2 162s Loading required package: spatstat.geom 162s spatstat.geom 3.3-6 162s Loading required package: spatstat.random 162s spatstat.random 3.3-3 162s Loading required package: nlme 162s spatstat.explore 3.3-4 162s > FULLTEST <- (nchar(Sys.getenv("SPATSTAT_TEST", unset="")) > 0) 162s > ALWAYS <- TRUE 162s > cat(paste("--------- Executing", 162s + if(FULLTEST) "** ALL **" else "**RESTRICTED** subset of", 162s + "test code -----------\n")) 162s --------- Executing **RESTRICTED** subset of test code ----------- 162s > 162s autopkgtest [10:51:44]: test run-unit-test: -----------------------] 163s autopkgtest [10:51:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 163s run-unit-test PASS 163s autopkgtest [10:51:45]: test pkg-r-autopkgtest: preparing testbed 264s autopkgtest [10:53:26]: testbed dpkg architecture: arm64 264s autopkgtest [10:53:26]: testbed apt version: 3.0.0 264s autopkgtest [10:53:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 264s autopkgtest [10:53:26]: testbed release detected to be: questing 265s autopkgtest [10:53:27]: updating testbed package index (apt update) 265s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 266s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 266s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 266s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 266s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [2076 kB] 266s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [175 kB] 266s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [44.4 kB] 266s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [219 kB] 266s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1509 kB] 266s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [15.4 kB] 267s Fetched 4149 kB in 1s (3089 kB/s) 268s Reading package lists... 268s autopkgtest [10:53:30]: upgrading testbed (apt dist-upgrade and autopurge) 269s Reading package lists... 269s Building dependency tree... 269s Reading state information... 270s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 270s Starting 2 pkgProblemResolver with broken count: 0 270s Done 270s Entering ResolveByKeep 271s 271s Calculating upgrade... 271s The following packages will be upgraded: 271s htop mtd-utils nano 272s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 272s Need to get 936 kB of archives. 272s After this operation, 727 kB of additional disk space will be used. 272s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 nano arm64 8.4-1 [290 kB] 272s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 htop arm64 3.4.1-4 [177 kB] 272s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 mtd-utils arm64 1:2.3.0-1ubuntu1 [469 kB] 273s Fetched 936 kB in 1s (1696 kB/s) 273s (Reading 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mtd-utils (1:2.3.0-1ubuntu1) ... 273s Setting up nano (8.4-1) ... 273s Installing new version of config file /etc/nanorc ... 273s Processing triggers for man-db (2.13.0-1) ... 274s Processing triggers for install-info (7.1.1-1) ... 275s Reading package lists... 275s Building dependency tree... 275s Reading state information... 276s Starting pkgProblemResolver with broken count: 0 276s Starting 2 pkgProblemResolver with broken count: 0 276s Done 276s Solving dependencies... 277s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Starting pkgProblemResolver with broken count: 0 281s Starting 2 pkgProblemResolver with broken count: 0 281s Done 282s The following NEW packages will be installed: 282s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 282s dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 282s g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 282s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gfortran gfortran-14 282s gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu icu-devtools 282s libasan8 libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 282s libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev 282s libgfortran5 libgomp1 libgraphite2-3 libgsl28 libgslcblas0 libharfbuzz0b 282s libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev 282s libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev 282s liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev 282s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 282s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 282s libpixman-1-0 libpkgconf3 libpng-dev libreadline-dev libsharpyuv0 libsm6 282s libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-dev 282s libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0 libxft2 282s libxrender1 libxss1 libxt6t64 pkg-r-autopkgtest pkgconf pkgconf-bin 282s r-base-core r-base-dev r-cran-abind r-cran-deldir r-cran-goftest r-cran-gsl 282s r-cran-lattice r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-polyclip 282s r-cran-rpart r-cran-sm r-cran-spatial r-cran-spatstat r-cran-spatstat.data 282s r-cran-spatstat.explore r-cran-spatstat.geom r-cran-spatstat.linnet 282s r-cran-spatstat.model r-cran-spatstat.random r-cran-spatstat.sparse 282s r-cran-spatstat.univar r-cran-spatstat.utils r-cran-survival r-cran-tensor 282s unzip x11-common xdg-utils zip zlib1g-dev 282s 0 upgraded, 124 newly installed, 0 to remove and 0 not upgraded. 282s Need to get 176 MB of archives. 282s After this operation, 473 MB of additional disk space will be used. 282s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 libisl23 arm64 0.27-1 [676 kB] 282s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 282s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [10.6 MB] 283s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-14 arm64 14.2.0-19ubuntu2 [1026 B] 283s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [5558 B] 283s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 cpp arm64 4:14.2.0-1ubuntu1 [22.4 kB] 283s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libcc1-0 arm64 15-20250404-0ubuntu1 [49.1 kB] 283s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 283s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 libitm1 arm64 15-20250404-0ubuntu1 [27.8 kB] 283s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 libasan8 arm64 15-20250404-0ubuntu1 [2922 kB] 283s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 liblsan0 arm64 15-20250404-0ubuntu1 [1318 kB] 283s Get:12 http://ftpmaster.internal/ubuntu questing/main arm64 libtsan2 arm64 15-20250404-0ubuntu1 [2692 kB] 283s Get:13 http://ftpmaster.internal/ubuntu questing/main arm64 libubsan1 arm64 15-20250404-0ubuntu1 [1177 kB] 283s Get:14 http://ftpmaster.internal/ubuntu questing/main arm64 libhwasan0 arm64 15-20250404-0ubuntu1 [1640 kB] 283s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 libgcc-14-dev arm64 14.2.0-19ubuntu2 [2593 kB] 283s Get:16 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [20.9 MB] 284s Get:17 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-14 arm64 14.2.0-19ubuntu2 [529 kB] 284s Get:18 http://ftpmaster.internal/ubuntu questing/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1200 B] 284s Get:19 http://ftpmaster.internal/ubuntu questing/main arm64 gcc arm64 4:14.2.0-1ubuntu1 [4998 B] 284s Get:20 http://ftpmaster.internal/ubuntu questing/main arm64 libstdc++-14-dev arm64 14.2.0-19ubuntu2 [2501 kB] 284s Get:21 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [12.1 MB] 284s Get:22 http://ftpmaster.internal/ubuntu questing/main arm64 g++-14 arm64 14.2.0-19ubuntu2 [23.0 kB] 284s Get:23 http://ftpmaster.internal/ubuntu questing/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [956 B] 284s Get:24 http://ftpmaster.internal/ubuntu questing/main arm64 g++ arm64 4:14.2.0-1ubuntu1 [1080 B] 284s Get:25 http://ftpmaster.internal/ubuntu questing/main arm64 build-essential arm64 12.12ubuntu1 [5082 B] 284s Get:26 http://ftpmaster.internal/ubuntu questing/main arm64 dctrl-tools arm64 2.24-3build3 [103 kB] 284s Get:27 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 284s Get:28 http://ftpmaster.internal/ubuntu questing/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 284s Get:29 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig-config arm64 2.15.0-2.2ubuntu1 [37.9 kB] 284s Get:30 http://ftpmaster.internal/ubuntu questing/main arm64 libfontconfig1 arm64 2.15.0-2.2ubuntu1 [144 kB] 284s Get:31 http://ftpmaster.internal/ubuntu questing/main arm64 fontconfig arm64 2.15.0-2.2ubuntu1 [191 kB] 284s Get:32 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran5 arm64 15-20250404-0ubuntu1 [444 kB] 284s Get:33 http://ftpmaster.internal/ubuntu questing/main arm64 libgfortran-14-dev arm64 14.2.0-19ubuntu2 [498 kB] 284s Get:34 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-19ubuntu2 [11.4 MB] 285s Get:35 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-14 arm64 14.2.0-19ubuntu2 [14.2 kB] 285s Get:36 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1ubuntu1 [1022 B] 285s Get:37 http://ftpmaster.internal/ubuntu questing/main arm64 gfortran arm64 4:14.2.0-1ubuntu1 [1166 B] 285s Get:38 http://ftpmaster.internal/ubuntu questing/main arm64 icu-devtools arm64 76.1-1ubuntu2 [213 kB] 285s Get:39 http://ftpmaster.internal/ubuntu questing/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 285s Get:40 http://ftpmaster.internal/ubuntu questing/main arm64 libblas-dev arm64 3.12.1-2 [126 kB] 285s Get:41 http://ftpmaster.internal/ubuntu questing/main arm64 libbz2-dev arm64 1.0.8-6 [36.1 kB] 285s Get:42 http://ftpmaster.internal/ubuntu questing/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 285s Get:43 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 285s Get:44 http://ftpmaster.internal/ubuntu questing/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 285s Get:45 http://ftpmaster.internal/ubuntu questing/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 285s Get:46 http://ftpmaster.internal/ubuntu questing/main arm64 libcairo2 arm64 1.18.4-1 [560 kB] 285s Get:47 http://ftpmaster.internal/ubuntu questing/main arm64 libdatrie1 arm64 0.2.13-3build1 [19.2 kB] 285s Get:48 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 285s Get:49 http://ftpmaster.internal/ubuntu questing/main arm64 libdeflate-dev arm64 1.23-1 [53.7 kB] 285s Get:50 http://ftpmaster.internal/ubuntu questing/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 285s Get:51 http://ftpmaster.internal/ubuntu questing/universe arm64 libgslcblas0 arm64 2.8+dfsg-5ubuntu1 [87.4 kB] 285s Get:52 http://ftpmaster.internal/ubuntu questing/universe arm64 libgsl28 arm64 2.8+dfsg-5ubuntu1 [982 kB] 285s Get:53 http://ftpmaster.internal/ubuntu questing/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 285s Get:54 http://ftpmaster.internal/ubuntu questing/main arm64 x11-common all 1:7.7+23ubuntu4 [21.8 kB] 285s Get:55 http://ftpmaster.internal/ubuntu questing/main arm64 libice6 arm64 2:1.1.1-1 [42.3 kB] 285s Get:56 http://ftpmaster.internal/ubuntu questing/main arm64 libicu-dev arm64 76.1-1ubuntu2 [12.2 MB] 285s Get:57 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 285s Get:58 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-turbo8-dev arm64 2.1.5-3ubuntu2 [306 kB] 285s Get:59 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 285s Get:60 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] 285s Get:61 http://ftpmaster.internal/ubuntu questing/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] 285s Get:62 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 285s Get:63 http://ftpmaster.internal/ubuntu questing/main arm64 liblapack-dev arm64 3.12.1-2 [4439 kB] 286s Get:64 http://ftpmaster.internal/ubuntu questing/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 286s Get:65 http://ftpmaster.internal/ubuntu questing/main arm64 libncurses-dev arm64 6.5+20250216-2 [389 kB] 286s Get:66 http://ftpmaster.internal/ubuntu questing/main arm64 libthai-data all 0.1.29-2build1 [158 kB] 286s Get:67 http://ftpmaster.internal/ubuntu questing/main arm64 libthai0 arm64 0.1.29-2build1 [18.2 kB] 286s Get:68 http://ftpmaster.internal/ubuntu questing/main arm64 libpango-1.0-0 arm64 1.56.3-1 [238 kB] 286s Get:69 http://ftpmaster.internal/ubuntu questing/main arm64 libpangoft2-1.0-0 arm64 1.56.3-1 [49.8 kB] 286s Get:70 http://ftpmaster.internal/ubuntu questing/main arm64 libpangocairo-1.0-0 arm64 1.56.3-1 [27.6 kB] 286s Get:71 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper2 arm64 2.2.5-0.3 [17.3 kB] 286s Get:72 http://ftpmaster.internal/ubuntu questing/main arm64 libpaper-utils arm64 2.2.5-0.3 [15.4 kB] 286s Get:73 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-16-0 arm64 10.45-1 [222 kB] 286s Get:74 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-32-0 arm64 10.45-1 [210 kB] 286s Get:75 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-posix3 arm64 10.45-1 [7084 B] 286s Get:76 http://ftpmaster.internal/ubuntu questing/main arm64 libpcre2-dev arm64 10.45-1 [768 kB] 286s Get:77 http://ftpmaster.internal/ubuntu questing/main arm64 libpkgconf3 arm64 1.8.1-4 [31.4 kB] 286s Get:78 http://ftpmaster.internal/ubuntu questing/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 286s Get:79 http://ftpmaster.internal/ubuntu questing/main arm64 libpng-dev arm64 1.6.47-1.1 [269 kB] 286s Get:80 http://ftpmaster.internal/ubuntu questing/main arm64 libreadline-dev arm64 8.2-6 [179 kB] 286s Get:81 http://ftpmaster.internal/ubuntu questing/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 286s Get:82 http://ftpmaster.internal/ubuntu questing/main arm64 libsm6 arm64 2:1.2.4-1 [16.4 kB] 286s Get:83 http://ftpmaster.internal/ubuntu questing/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [987 kB] 286s Get:84 http://ftpmaster.internal/ubuntu questing/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 286s Get:85 http://ftpmaster.internal/ubuntu questing/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 286s Get:86 http://ftpmaster.internal/ubuntu questing/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 286s Get:87 http://ftpmaster.internal/ubuntu questing/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 286s Get:88 http://ftpmaster.internal/ubuntu questing/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 286s Get:89 http://ftpmaster.internal/ubuntu questing/main arm64 libtk8.6 arm64 8.6.16-1 [776 kB] 286s Get:90 http://ftpmaster.internal/ubuntu questing/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] 286s Get:91 http://ftpmaster.internal/ubuntu questing/main arm64 zip arm64 3.0-14ubuntu2 [173 kB] 286s Get:92 http://ftpmaster.internal/ubuntu questing/main arm64 unzip arm64 6.0-28ubuntu6 [178 kB] 286s Get:93 http://ftpmaster.internal/ubuntu questing/main arm64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 286s Get:94 http://ftpmaster.internal/ubuntu questing/universe arm64 r-base-core arm64 4.4.3-1 [28.4 MB] 287s Get:95 http://ftpmaster.internal/ubuntu questing/main arm64 liblzma-dev arm64 5.6.4-1ubuntu1 [180 kB] 287s Get:96 http://ftpmaster.internal/ubuntu questing/main arm64 pkgconf-bin arm64 1.8.1-4 [20.9 kB] 287s Get:97 http://ftpmaster.internal/ubuntu questing/main arm64 pkgconf arm64 1.8.1-4 [16.7 kB] 287s Get:98 http://ftpmaster.internal/ubuntu questing/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] 287s Get:99 http://ftpmaster.internal/ubuntu questing/universe arm64 r-base-dev all 4.4.3-1 [4176 B] 287s Get:100 http://ftpmaster.internal/ubuntu questing/universe arm64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 287s Get:101 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-abind all 1.4-8-1 [66.9 kB] 287s Get:102 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-deldir arm64 2.0-4-1build1 [270 kB] 287s Get:103 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-goftest arm64 1.2-3-1 [60.2 kB] 287s Get:104 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-gsl arm64 2.1-8-1build1 [485 kB] 288s Get:105 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-lattice arm64 0.22-6-1 [1363 kB] 288s Get:106 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-matrix arm64 1.7-3-1 [4045 kB] 288s Get:107 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 r-cran-nlme arm64 3.1.168-1 [2310 kB] 289s Get:108 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-mgcv arm64 1.9-1-1 [3248 kB] 289s Get:109 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-polyclip arm64 1.10-7-1 [113 kB] 289s Get:110 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-survival arm64 3.8-3-1 [8213 kB] 289s Get:111 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-rpart arm64 4.1.24-1 [665 kB] 290s Get:112 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-sm arm64 2.2-6.0-1 [787 kB] 290s Get:113 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatial arm64 7.3-18-1 [133 kB] 290s Get:114 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.utils arm64 3.1-3-1 [386 kB] 290s Get:115 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.data all 3.1-6-1 [4153 kB] 290s Get:116 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.univar arm64 3.1-2-1 [314 kB] 290s Get:117 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.geom arm64 3.3-6-1 [3941 kB] 290s Get:118 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.random arm64 3.3-3-1 [1163 kB] 290s Get:119 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-tensor all 1.5-4 [15.7 kB] 290s Get:120 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.sparse arm64 3.1-0-1 [218 kB] 290s Get:121 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.explore arm64 3.3-4-1 [3272 kB] 290s Get:122 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.model arm64 3.3-4-1 [3398 kB] 290s Get:123 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat.linnet arm64 3.2-5-1 [1507 kB] 290s Get:124 http://ftpmaster.internal/ubuntu questing/universe arm64 r-cran-spatstat arm64 3.3-1-1 [4120 kB] 291s Preconfiguring packages ... 291s Fetched 176 MB in 9s (19.8 MB/s) 291s Selecting previously unselected package libisl23:arm64. 291s (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 ... 117821 files and directories currently installed.) 291s Preparing to unpack .../000-libisl23_0.27-1_arm64.deb ... 291s Unpacking libisl23:arm64 (0.27-1) ... 292s Selecting previously unselected package libmpc3:arm64. 292s Preparing to unpack .../001-libmpc3_1.3.1-1build2_arm64.deb ... 292s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 292s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 292s Preparing to unpack .../002-cpp-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 292s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 292s Selecting previously unselected package cpp-14. 292s Preparing to unpack .../003-cpp-14_14.2.0-19ubuntu2_arm64.deb ... 292s Unpacking cpp-14 (14.2.0-19ubuntu2) ... 292s Selecting previously unselected package cpp-aarch64-linux-gnu. 292s Preparing to unpack .../004-cpp-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 292s Unpacking cpp-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 292s Selecting previously unselected package cpp. 292s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_arm64.deb ... 292s Unpacking cpp (4:14.2.0-1ubuntu1) ... 292s Selecting previously unselected package libcc1-0:arm64. 292s Preparing to unpack .../006-libcc1-0_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking libcc1-0:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package libgomp1:arm64. 292s Preparing to unpack .../007-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package libitm1:arm64. 292s Preparing to unpack .../008-libitm1_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking libitm1:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package libasan8:arm64. 292s Preparing to unpack .../009-libasan8_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking libasan8:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package liblsan0:arm64. 292s Preparing to unpack .../010-liblsan0_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking liblsan0:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package libtsan2:arm64. 292s Preparing to unpack .../011-libtsan2_15-20250404-0ubuntu1_arm64.deb ... 292s Unpacking libtsan2:arm64 (15-20250404-0ubuntu1) ... 292s Selecting previously unselected package libubsan1:arm64. 293s Preparing to unpack .../012-libubsan1_15-20250404-0ubuntu1_arm64.deb ... 293s Unpacking libubsan1:arm64 (15-20250404-0ubuntu1) ... 293s Selecting previously unselected package libhwasan0:arm64. 293s Preparing to unpack .../013-libhwasan0_15-20250404-0ubuntu1_arm64.deb ... 293s Unpacking libhwasan0:arm64 (15-20250404-0ubuntu1) ... 293s Selecting previously unselected package libgcc-14-dev:arm64. 293s Preparing to unpack .../014-libgcc-14-dev_14.2.0-19ubuntu2_arm64.deb ... 293s Unpacking libgcc-14-dev:arm64 (14.2.0-19ubuntu2) ... 293s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 293s Preparing to unpack .../015-gcc-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 293s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 293s Selecting previously unselected package gcc-14. 293s Preparing to unpack .../016-gcc-14_14.2.0-19ubuntu2_arm64.deb ... 293s Unpacking gcc-14 (14.2.0-19ubuntu2) ... 293s Selecting previously unselected package gcc-aarch64-linux-gnu. 293s Preparing to unpack .../017-gcc-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 293s Unpacking gcc-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 293s Selecting previously unselected package gcc. 293s Preparing to unpack .../018-gcc_4%3a14.2.0-1ubuntu1_arm64.deb ... 293s Unpacking gcc (4:14.2.0-1ubuntu1) ... 294s Selecting previously unselected package libstdc++-14-dev:arm64. 294s Preparing to unpack .../019-libstdc++-14-dev_14.2.0-19ubuntu2_arm64.deb ... 294s Unpacking libstdc++-14-dev:arm64 (14.2.0-19ubuntu2) ... 294s Selecting previously unselected package g++-14-aarch64-linux-gnu. 294s Preparing to unpack .../020-g++-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 294s Unpacking g++-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 294s Selecting previously unselected package g++-14. 294s Preparing to unpack .../021-g++-14_14.2.0-19ubuntu2_arm64.deb ... 294s Unpacking g++-14 (14.2.0-19ubuntu2) ... 294s Selecting previously unselected package g++-aarch64-linux-gnu. 294s Preparing to unpack .../022-g++-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 294s Unpacking g++-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 294s Selecting previously unselected package g++. 294s Preparing to unpack .../023-g++_4%3a14.2.0-1ubuntu1_arm64.deb ... 294s Unpacking g++ (4:14.2.0-1ubuntu1) ... 294s Selecting previously unselected package build-essential. 294s Preparing to unpack .../024-build-essential_12.12ubuntu1_arm64.deb ... 294s Unpacking build-essential (12.12ubuntu1) ... 294s Selecting previously unselected package dctrl-tools. 294s Preparing to unpack .../025-dctrl-tools_2.24-3build3_arm64.deb ... 294s Unpacking dctrl-tools (2.24-3build3) ... 294s Selecting previously unselected package fonts-dejavu-mono. 294s Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... 294s Unpacking fonts-dejavu-mono (2.37-8) ... 294s Selecting previously unselected package fonts-dejavu-core. 294s Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ... 294s Unpacking fonts-dejavu-core (2.37-8) ... 294s Selecting previously unselected package fontconfig-config. 294s Preparing to unpack .../028-fontconfig-config_2.15.0-2.2ubuntu1_arm64.deb ... 295s Unpacking fontconfig-config (2.15.0-2.2ubuntu1) ... 295s Selecting previously unselected package libfontconfig1:arm64. 295s Preparing to unpack .../029-libfontconfig1_2.15.0-2.2ubuntu1_arm64.deb ... 295s Unpacking libfontconfig1:arm64 (2.15.0-2.2ubuntu1) ... 295s Selecting previously unselected package fontconfig. 295s Preparing to unpack .../030-fontconfig_2.15.0-2.2ubuntu1_arm64.deb ... 295s Unpacking fontconfig (2.15.0-2.2ubuntu1) ... 295s Selecting previously unselected package libgfortran5:arm64. 295s Preparing to unpack .../031-libgfortran5_15-20250404-0ubuntu1_arm64.deb ... 295s Unpacking libgfortran5:arm64 (15-20250404-0ubuntu1) ... 295s Selecting previously unselected package libgfortran-14-dev:arm64. 295s Preparing to unpack .../032-libgfortran-14-dev_14.2.0-19ubuntu2_arm64.deb ... 295s Unpacking libgfortran-14-dev:arm64 (14.2.0-19ubuntu2) ... 295s Selecting previously unselected package gfortran-14-aarch64-linux-gnu. 295s Preparing to unpack .../033-gfortran-14-aarch64-linux-gnu_14.2.0-19ubuntu2_arm64.deb ... 295s Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-19ubuntu2) ... 295s Selecting previously unselected package gfortran-14. 295s Preparing to unpack .../034-gfortran-14_14.2.0-19ubuntu2_arm64.deb ... 295s Unpacking gfortran-14 (14.2.0-19ubuntu2) ... 295s Selecting previously unselected package gfortran-aarch64-linux-gnu. 295s Preparing to unpack .../035-gfortran-aarch64-linux-gnu_4%3a14.2.0-1ubuntu1_arm64.deb ... 295s Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1ubuntu1) ... 295s Selecting previously unselected package gfortran. 295s Preparing to unpack .../036-gfortran_4%3a14.2.0-1ubuntu1_arm64.deb ... 295s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 295s Selecting previously unselected package icu-devtools. 295s Preparing to unpack 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296s Selecting previously unselected package libxcb-shm0:arm64. 296s Preparing to unpack .../043-libxcb-shm0_1.17.0-2_arm64.deb ... 296s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 296s Selecting previously unselected package libxrender1:arm64. 296s Preparing to unpack .../044-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 296s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 296s Selecting previously unselected package libcairo2:arm64. 296s Preparing to unpack .../045-libcairo2_1.18.4-1_arm64.deb ... 296s Unpacking libcairo2:arm64 (1.18.4-1) ... 296s Selecting previously unselected package libdatrie1:arm64. 296s Preparing to unpack .../046-libdatrie1_0.2.13-3build1_arm64.deb ... 296s Unpacking libdatrie1:arm64 (0.2.13-3build1) ... 296s Selecting previously unselected package libdeflate0:arm64. 296s Preparing to unpack .../047-libdeflate0_1.23-1_arm64.deb ... 296s Unpacking libdeflate0:arm64 (1.23-1) ... 296s Selecting previously unselected package libdeflate-dev:arm64. 296s 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297s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 297s Selecting previously unselected package libjpeg8-dev:arm64. 297s Preparing to unpack .../059-libjpeg8-dev_8c-2ubuntu11_arm64.deb ... 297s Unpacking libjpeg8-dev:arm64 (8c-2ubuntu11) ... 297s Selecting previously unselected package libjpeg-dev:arm64. 297s Preparing to unpack .../060-libjpeg-dev_8c-2ubuntu11_arm64.deb ... 297s Unpacking libjpeg-dev:arm64 (8c-2ubuntu11) ... 297s Selecting previously unselected package liblapack3:arm64. 297s Preparing to unpack .../061-liblapack3_3.12.1-2_arm64.deb ... 297s Unpacking liblapack3:arm64 (3.12.1-2) ... 297s Selecting previously unselected package liblapack-dev:arm64. 297s Preparing to unpack .../062-liblapack-dev_3.12.1-2_arm64.deb ... 297s Unpacking liblapack-dev:arm64 (3.12.1-2) ... 298s Selecting previously unselected package liblerc4:arm64. 298s Preparing to unpack .../063-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 298s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 298s Selecting previously unselected package libncurses-dev:arm64. 298s Preparing to unpack .../064-libncurses-dev_6.5+20250216-2_arm64.deb ... 298s Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... 298s Selecting previously unselected package libthai-data. 298s Preparing to unpack .../065-libthai-data_0.1.29-2build1_all.deb ... 298s Unpacking libthai-data (0.1.29-2build1) ... 298s Selecting previously unselected package libthai0:arm64. 298s Preparing to unpack .../066-libthai0_0.1.29-2build1_arm64.deb ... 298s Unpacking libthai0:arm64 (0.1.29-2build1) ... 298s Selecting previously unselected package libpango-1.0-0:arm64. 298s Preparing to unpack .../067-libpango-1.0-0_1.56.3-1_arm64.deb ... 298s Unpacking libpango-1.0-0:arm64 (1.56.3-1) ... 298s Selecting previously unselected package libpangoft2-1.0-0:arm64. 298s Preparing to unpack .../068-libpangoft2-1.0-0_1.56.3-1_arm64.deb ... 298s Unpacking libpangoft2-1.0-0:arm64 (1.56.3-1) ... 298s Selecting previously unselected package libpangocairo-1.0-0:arm64. 298s Preparing to unpack .../069-libpangocairo-1.0-0_1.56.3-1_arm64.deb ... 298s Unpacking libpangocairo-1.0-0:arm64 (1.56.3-1) ... 298s Selecting previously unselected package libpaper2:arm64. 298s Preparing to unpack .../070-libpaper2_2.2.5-0.3_arm64.deb ... 298s Unpacking libpaper2:arm64 (2.2.5-0.3) ... 298s Selecting previously unselected package libpaper-utils. 298s Preparing to unpack .../071-libpaper-utils_2.2.5-0.3_arm64.deb ... 298s Unpacking libpaper-utils (2.2.5-0.3) ... 298s Selecting previously unselected package libpcre2-16-0:arm64. 298s Preparing to unpack .../072-libpcre2-16-0_10.45-1_arm64.deb ... 298s Unpacking libpcre2-16-0:arm64 (10.45-1) ... 298s Selecting previously unselected package libpcre2-32-0:arm64. 298s Preparing to unpack .../073-libpcre2-32-0_10.45-1_arm64.deb ... 298s Unpacking libpcre2-32-0:arm64 (10.45-1) ... 298s Selecting previously unselected package libpcre2-posix3:arm64. 298s Preparing to unpack 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299s Unpacking libreadline-dev:arm64 (8.2-6) ... 299s Selecting previously unselected package libsharpyuv0:arm64. 299s Preparing to unpack .../080-libsharpyuv0_1.5.0-0.1_arm64.deb ... 299s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 299s Selecting previously unselected package libsm6:arm64. 299s Preparing to unpack .../081-libsm6_2%3a1.2.4-1_arm64.deb ... 299s Unpacking libsm6:arm64 (2:1.2.4-1) ... 299s Selecting previously unselected package libtcl8.6:arm64. 299s Preparing to unpack .../082-libtcl8.6_8.6.16+dfsg-1_arm64.deb ... 299s Unpacking libtcl8.6:arm64 (8.6.16+dfsg-1) ... 299s Selecting previously unselected package libjbig0:arm64. 299s Preparing to unpack .../083-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 299s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 299s Selecting previously unselected package libwebp7:arm64. 299s Preparing to unpack .../084-libwebp7_1.5.0-0.1_arm64.deb ... 299s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 299s Selecting previously unselected package libtiff6:arm64. 299s Preparing to unpack .../085-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 299s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 299s Selecting previously unselected package libxft2:arm64. 299s Preparing to unpack .../086-libxft2_2.3.6-1build1_arm64.deb ... 299s Unpacking libxft2:arm64 (2.3.6-1build1) ... 299s Selecting previously unselected package libxss1:arm64. 299s Preparing to unpack .../087-libxss1_1%3a1.2.3-1build3_arm64.deb ... 299s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 299s Selecting previously unselected package libtk8.6:arm64. 299s Preparing to unpack .../088-libtk8.6_8.6.16-1_arm64.deb ... 299s Unpacking libtk8.6:arm64 (8.6.16-1) ... 299s Selecting previously unselected package libxt6t64:arm64. 299s Preparing to unpack .../089-libxt6t64_1%3a1.2.1-1.2build1_arm64.deb ... 299s Unpacking libxt6t64:arm64 (1:1.2.1-1.2build1) ... 299s Selecting previously unselected package zip. 299s Preparing to unpack .../090-zip_3.0-14ubuntu2_arm64.deb ... 299s Unpacking zip (3.0-14ubuntu2) ... 299s Selecting previously unselected package unzip. 299s Preparing to unpack .../091-unzip_6.0-28ubuntu6_arm64.deb ... 299s Unpacking unzip (6.0-28ubuntu6) ... 299s Selecting previously unselected package xdg-utils. 299s Preparing to unpack .../092-xdg-utils_1.2.1-2ubuntu1_all.deb ... 299s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 299s Selecting previously unselected package r-base-core. 299s Preparing to unpack .../093-r-base-core_4.4.3-1_arm64.deb ... 299s Unpacking r-base-core (4.4.3-1) ... 300s Selecting previously unselected package liblzma-dev:arm64. 300s Preparing to unpack .../094-liblzma-dev_5.6.4-1ubuntu1_arm64.deb ... 300s Unpacking liblzma-dev:arm64 (5.6.4-1ubuntu1) ... 300s Selecting previously unselected package pkgconf-bin. 300s Preparing to unpack .../095-pkgconf-bin_1.8.1-4_arm64.deb ... 300s Unpacking pkgconf-bin (1.8.1-4) ... 300s Selecting previously unselected package pkgconf:arm64. 300s Preparing to unpack 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previously unselected package r-cran-goftest. 300s Preparing to unpack .../102-r-cran-goftest_1.2-3-1_arm64.deb ... 300s Unpacking r-cran-goftest (1.2-3-1) ... 300s Selecting previously unselected package r-cran-gsl. 300s Preparing to unpack .../103-r-cran-gsl_2.1-8-1build1_arm64.deb ... 300s Unpacking r-cran-gsl (2.1-8-1build1) ... 300s Selecting previously unselected package r-cran-lattice. 300s Preparing to unpack .../104-r-cran-lattice_0.22-6-1_arm64.deb ... 300s Unpacking r-cran-lattice (0.22-6-1) ... 300s Selecting previously unselected package r-cran-matrix. 300s Preparing to unpack .../105-r-cran-matrix_1.7-3-1_arm64.deb ... 300s Unpacking r-cran-matrix (1.7-3-1) ... 300s Selecting previously unselected package r-cran-nlme. 300s Preparing to unpack .../106-r-cran-nlme_3.1.168-1_arm64.deb ... 300s Unpacking r-cran-nlme (3.1.168-1) ... 300s Selecting previously unselected package r-cran-mgcv. 300s Preparing to unpack .../107-r-cran-mgcv_1.9-1-1_arm64.deb ... 300s Unpacking 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(4:14.2.0-1ubuntu1) ... 305s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 305s 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 305s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 305s 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 305s Setting up r-cran-spatstat.data (3.1-6-1) ... 305s Setting up r-cran-spatstat.geom (3.3-6-1) ... 305s Setting up r-base-dev (4.4.3-1) ... 305s Setting up r-cran-rpart (4.1.24-1) ... 305s Setting up r-cran-spatstat.random (3.3-3-1) ... 305s Setting up r-cran-spatstat.explore (3.3-4-1) ... 305s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 305s Setting up r-cran-spatstat.model (3.3-4-1) ... 305s Setting up r-cran-spatstat.linnet (3.2-5-1) ... 305s Setting up r-cran-spatstat (3.3-1-1) ... 305s Processing triggers for install-info (7.1.1-1) ... 305s Processing triggers for libc-bin (2.41-6ubuntu1) ... 305s Processing triggers for man-db (2.13.0-1) ... 309s autopkgtest [10:54:11]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 309s autopkgtest [10:54:11]: test pkg-r-autopkgtest: [----------------------- 309s Test: Try to load the R library spatstat.explore 309s 309s R version 4.4.3 (2025-02-28) -- "Trophy Case" 309s Copyright (C) 2025 The R Foundation for Statistical Computing 309s Platform: aarch64-unknown-linux-gnu 309s 309s R is free software and comes with ABSOLUTELY NO WARRANTY. 309s You are welcome to redistribute it under certain conditions. 309s Type 'license()' or 'licence()' for distribution details. 309s 309s R is a collaborative project with many contributors. 309s Type 'contributors()' for more information and 309s 'citation()' on how to cite R or R packages in publications. 309s 309s Type 'demo()' for some demos, 'help()' for on-line help, or 309s 'help.start()' for an HTML browser interface to help. 309s Type 'q()' to quit R. 309s 309s > library('spatstat.explore') 309s Loading required package: spatstat.data 310s Loading required package: spatstat.univar 310s spatstat.univar 3.1-2 310s Loading required package: spatstat.geom 310s spatstat.geom 3.3-6 310s Loading required package: spatstat.random 310s spatstat.random 3.3-3 310s Loading required package: nlme 310s spatstat.explore 3.3-4 310s > 310s > 310s Other tests are currently unsupported! 310s They will be progressively added. 311s autopkgtest [10:54:13]: test pkg-r-autopkgtest: -----------------------] 311s autopkgtest [10:54:13]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 311s pkg-r-autopkgtest PASS 312s autopkgtest [10:54:14]: @@@@@@@@@@@@@@@@@@@@ summary 312s run-unit-test PASS 312s pkg-r-autopkgtest PASS 329s nova [W] Using flock in prodstack6-arm64 329s Creating nova instance adt-questing-arm64-r-cran-spatstat.explore-20250502-104902-juju-7f2275-prod-proposed-migration-environment-23-91a488c2-ddb4-4d55-ac1d-1054177d0d9f from image adt/ubuntu-questing-arm64-server-20250502.img (UUID a0b7b7fd-ad05-4ea9-97eb-0f52dbbe98e1)... 329s nova [W] Timed out waiting for 28df7ac7-f4a9-4540-9190-0d1f2f91c845 to get deleted. 329s nova [W] Using flock in prodstack6-arm64 329s Creating nova instance adt-questing-arm64-r-cran-spatstat.explore-20250502-104902-juju-7f2275-prod-proposed-migration-environment-23-91a488c2-ddb4-4d55-ac1d-1054177d0d9f from image adt/ubuntu-questing-arm64-server-20250502.img (UUID a0b7b7fd-ad05-4ea9-97eb-0f52dbbe98e1)... 329s nova [W] Timed out waiting for 0f00e4c9-1cd8-44c3-b13d-452967debb44 to get deleted.