* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/spatialClust.Rcheck’ * using R Under development (unstable) (2021-06-19 r80532) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘spatialClust/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spatialClust’ version ‘1.1.1’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘spatialClust’ can be installed ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘spatialClust-Ex.R’ failed The error most likely occurred in: > ### Name: visualize > ### Title: Cluster Visualization > ### Aliases: visualize > > ### ** Examples > > #load data example > X <- example > > #if using matrix distance > #distance <- dist > > #if using shapefile > #library(rgdal) for call readOGR > #distance <- readOGR(dsn = 'folder/.',"shapefile name") > distance <- map > > #load population data > pop <- population > > clust <- fgwc(X,pop,distance,K=2,m=1.5,beta=0.5) Warning in wkt(obj) : CRS object has no comment Warning in wkt(obj) : CRS object has no comment $func.obj [1] 4125426791 $U Clust 1 Clust 2 [1,] 0.9555792 0.04442076 [2,] 0.9573443 0.04265572 [3,] 0.9574918 0.04250824 [4,] 0.9491605 0.05083953 [5,] 0.9455637 0.05443632 [6,] 0.9329619 0.06703808 [7,] 0.9377566 0.06224345 [8,] 0.8864878 0.11351222 [9,] 0.8805349 0.11946505 [10,] 0.6509285 0.34907146 [11,] 0.3936940 0.60630602 [12,] 0.8748924 0.12510755 [13,] 0.7182103 0.28178973 [14,] 0.8893098 0.11069017 [15,] 0.9044826 0.09551740 [16,] 0.9209480 0.07905205 [17,] 0.9296572 0.07034277 [18,] 0.9254795 0.07452050 [19,] 0.8638785 0.13612153 [20,] 0.9210192 0.07898080 [21,] 0.8932737 0.10672629 [22,] 0.8772784 0.12272155 [23,] 0.9124931 0.08750692 [24,] 0.8479640 0.15203596 [25,] 0.9330618 0.06693824 [26,] 0.9501669 0.04983310 [27,] 0.9486172 0.05138282 [28,] 0.9472578 0.05274219 [29,] 0.9473690 0.05263104 [30,] 0.4511240 0.54887597 [31,] 0.4023037 0.59769632 [32,] 0.4521152 0.54788479 [33,] 0.4696957 0.53030426 [34,] 0.9473918 0.05260825 [35,] 0.4802399 0.51976009 $V AMH APM.SD APM.SMP Rata.Rata.Lama.Sekolah [1,] 93.05576 96.49064 78.57197 7.390587 [2,] 94.62494 96.51878 82.51334 9.160928 Angka.Harapan.Lama.Sekolah Pengeluaran.Per.Kapita.Pendidikan.Bln [1,] 11.98999 24300.58 [2,] 13.13530 47619.01 rasio.murid.sekolah.smp rasio.murid.guru.smp rasio.murid.sekolah.sd [1,] 382.6765 16.13324 201.1935 [2,] 414.3785 15.11344 210.1145 rasio.murid.guru.sd APtS APBD [1,] 14.94752 0.9480584 42.41571 [2,] 15.35785 0.5677409 40.24574 $D [,1] [,2] [1,] 1167383.2 494579695 [2,] 6719183.4 429654362 [3,] 33829284.3 848794509 [4,] 48956361.5 919009066 [5,] 15401863.6 376128583 [6,] 5315988.3 441550705 [7,] 2197903.4 614765160 [8,] 21233616.0 779863464 [9,] 9512272.6 409458818 [10,] 132929889.6 138981174 [11,] 328497244.1 26981025 [12,] 33267741.7 845912832 [13,] 111582619.9 162732009 [14,] 2660694.7 621904023 [15,] 135438913.8 1221933177 [16,] 55112069.6 945077157 [17,] 26727379.3 811573604 [18,] 550940.4 578698410 [19,] 82029252.4 203409841 [20,] 18263642.9 761320746 [21,] 7150223.8 426218910 [22,] 1839526.8 608810649 [23,] 64028683.2 980950004 [24,] 72904971.9 218542325 [25,] 64667550.4 983453093 [26,] 8162787.0 685094138 [27,] 115129215.0 1159270708 [28,] 62184272.0 973691770 [29,] 91197659.3 1080309007 [30,] 394603346.6 11942685 [31,] 2082318223.7 497942602 [32,] 2248508262.2 580810564 [33,] 1629125228.1 290499414 [34,] 8132406.7 684869636 [35,] 275614168.8 45131797 $m [1] 1.5 $data AMH APM.SD APM.SMP Rata.Rata.Lama.Sekolah Angka.Harapan.Lama.Sekolah [1,] 92.65 97.80 73.31 6.99 12.27 [2,] 94.78 93.39 79.18 7.51 12.56 [3,] 95.77 97.28 79.78 6.76 11.51 [4,] 93.44 92.46 71.34 6.38 10.70 [5,] 91.85 93.72 81.77 7.19 12.07 [6,] 94.98 97.49 82.37 7.98 13.03 [7,] 95.75 99.07 66.63 6.63 11.34 [8,] 92.89 98.57 74.13 7.64 12.00 [9,] 88.46 97.16 77.07 7.70 11.65 [10,] 92.44 98.48 76.07 8.33 12.74 [11,] 92.17 99.29 79.17 9.12 12.96 [12,] 85.94 97.23 85.62 7.00 11.94 [13,] 93.15 98.43 90.67 8.04 13.26 [14,] 87.25 96.90 80.09 7.08 12.19 [15,] 94.90 96.68 86.65 6.89 12.24 [16,] 89.42 96.20 85.75 6.63 11.75 [17,] 91.31 94.78 90.42 7.15 11.46 [18,] 92.11 95.58 80.91 7.20 11.24 [19,] 95.49 97.57 74.08 8.34 12.58 [20,] 94.91 98.25 79.30 7.66 12.25 [21,] 94.60 90.38 78.45 7.55 11.84 [22,] 94.83 98.74 79.86 7.83 12.81 [23,] 92.35 97.13 72.69 7.22 11.69 [24,] 91.50 98.36 80.22 7.40 11.83 [25,] 94.37 95.77 76.37 6.76 10.65 [26,] 96.17 97.93 71.32 6.79 11.93 [27,] 89.58 97.26 71.78 6.65 11.26 [28,] 94.48 97.48 79.73 6.78 11.99 [29,] 88.51 97.54 70.54 6.02 11.03 [30,] 96.78 100.00 84.81 10.10 12.98 [31,] 97.62 96.95 83.90 10.64 13.92 [32,] 95.41 94.16 88.05 9.99 14.95 [33,] 97.54 91.14 89.19 10.27 13.97 [34,] 98.26 94.06 76.84 8.48 11.93 [35,] 93.61 94.53 76.50 8.38 11.96 Pengeluaran.Per.Kapita.Pendidikan.Bln rasio.murid.sekolah.smp [1,] 25380 347.9469 [2,] 26891 476.8155 [3,] 18485 451.2800 [4,] 17304 319.0918 [5,] 28225 402.7155 [6,] 26606 351.9574 [7,] 22825 336.9182 [8,] 19693 441.9574 [9,] 27384 437.6974 [10,] 35830 428.2243 [11,] 42425 404.3165 [12,] 18535 324.9496 [13,] 34863 395.8312 [14,] 22682 227.0702 [15,] 12663 336.7536 [16,] 16877 355.6092 [17,] 19131 342.4444 [18,] 23563 421.9390 [19,] 33357 478.8333 [20,] 20027 375.8889 [21,] 26974 419.8039 [22,] 22945 358.3871 [23,] 16299 335.1096 [24,] 32837 349.1237 [25,] 16259 366.6866 [26,] 21445 305.0610 [27,] 13571 438.1290 [28,] 16415 412.8037 [29,] 14751 416.5252 [30,] 44165 355.6786 [31,] 69932 667.6667 [32,] 71719 401.9565 [33,] 64663 373.5747 [34,] 21449 405.5862 [35,] 40902 299.1275 rasio.murid.guru.smp rasio.murid.sekolah.sd rasio.murid.guru.sd APtS [1,] 16.02336 170.0588 9.572848 3.36 [2,] 18.47010 205.5938 12.824561 0.00 [3,] 19.26352 260.4000 9.169014 1.30 [4,] 15.72197 209.3077 14.550802 3.44 [5,] 16.29404 182.4737 11.996540 0.00 [6,] 16.58346 197.2222 8.198614 0.00 [7,] 15.07771 336.0000 3.326733 1.30 [8,] 23.12282 187.6739 14.014610 0.00 [9,] 14.30138 159.8421 12.549587 0.00 [10,] 13.46063 215.7925 14.495564 1.92 [11,] 14.44640 154.8235 5.927928 0.65 [12,] 11.96812 52.6800 0.371614 0.00 [13,] 14.21595 304.3333 98.323077 0.00 [14,] 17.85241 330.0625 10.604418 0.61 [15,] 16.50870 142.7333 15.077465 0.59 [16,] 16.37798 160.0000 13.636364 0.00 [17,] 16.09399 169.3333 12.390244 0.00 [18,] 13.64314 128.4231 7.258696 0.00 [19,] 16.12912 236.3333 15.005291 0.65 [20,] 17.00000 195.6000 22.101695 1.35 [21,] 14.09480 161.2941 10.968000 0.00 [22,] 22.29431 236.7778 15.033510 0.92 [23,] 15.57161 224.9565 14.214286 1.52 [24,] 13.42251 382.8889 34.288557 1.10 [25,] 18.22552 186.5000 10.970588 1.31 [26,] 13.41287 152.9688 11.278802 2.36 [27,] 11.39191 155.2174 15.127119 1.57 [28,] 18.76381 172.6667 26.086331 1.57 [29,] 17.32406 157.6667 12.128205 2.21 [30,] 19.97793 115.8667 5.347692 0.00 [31,] 14.86150 304.3333 15.064231 0.00 [32,] 13.09490 238.4286 14.326180 0.00 [33,] 14.24233 212.4389 12.944821 1.07 [34,] 15.85175 214.4615 13.700246 0.84 [35,] 13.30051 195.4667 11.453125 1.08 APBD [1,] 42.911 [2,] 46.023 [3,] 47.264 [4,] 46.045 [5,] 47.605 [6,] 45.603 [7,] 41.848 [8,] 47.990 [9,] 48.376 [10,] 52.672 [11,] 44.747 [12,] 51.581 [13,] 47.857 [14,] 45.204 [15,] 42.060 [16,] 42.948 [17,] 38.937 [18,] 43.812 [19,] 36.229 [20,] 43.845 [21,] 36.973 [22,] 38.056 [23,] 20.000 [24,] 45.990 [25,] 39.963 [26,] 41.846 [27,] 45.687 [28,] 45.394 [29,] 42.515 [30,] 34.761 [31,] 40.528 [32,] 37.507 [33,] 34.582 [34,] 30.318 [35,] 35.297 $call fgwc(X = X, population = pop, distance = distance, K = 2, m = 1.5, beta = 0.5) $Clust.desc AMH APM.SD APM.SMP Rata.Rata.Lama.Sekolah Angka.Harapan.Lama.Sekolah 1 92.65 97.80 73.31 6.99 12.27 2 94.78 93.39 79.18 7.51 12.56 3 95.77 97.28 79.78 6.76 11.51 4 93.44 92.46 71.34 6.38 10.70 5 91.85 93.72 81.77 7.19 12.07 6 94.98 97.49 82.37 7.98 13.03 7 95.75 99.07 66.63 6.63 11.34 8 92.89 98.57 74.13 7.64 12.00 9 88.46 97.16 77.07 7.70 11.65 10 92.44 98.48 76.07 8.33 12.74 11 92.17 99.29 79.17 9.12 12.96 12 85.94 97.23 85.62 7.00 11.94 13 93.15 98.43 90.67 8.04 13.26 14 87.25 96.90 80.09 7.08 12.19 15 94.90 96.68 86.65 6.89 12.24 16 89.42 96.20 85.75 6.63 11.75 17 91.31 94.78 90.42 7.15 11.46 18 92.11 95.58 80.91 7.20 11.24 19 95.49 97.57 74.08 8.34 12.58 20 94.91 98.25 79.30 7.66 12.25 21 94.60 90.38 78.45 7.55 11.84 22 94.83 98.74 79.86 7.83 12.81 23 92.35 97.13 72.69 7.22 11.69 24 91.50 98.36 80.22 7.40 11.83 25 94.37 95.77 76.37 6.76 10.65 26 96.17 97.93 71.32 6.79 11.93 27 89.58 97.26 71.78 6.65 11.26 28 94.48 97.48 79.73 6.78 11.99 29 88.51 97.54 70.54 6.02 11.03 30 96.78 100.00 84.81 10.10 12.98 31 97.62 96.95 83.90 10.64 13.92 32 95.41 94.16 88.05 9.99 14.95 33 97.54 91.14 89.19 10.27 13.97 34 98.26 94.06 76.84 8.48 11.93 35 93.61 94.53 76.50 8.38 11.96 Pengeluaran.Per.Kapita.Pendidikan.Bln rasio.murid.sekolah.smp 1 25380 347.9469 2 26891 476.8155 3 18485 451.2800 4 17304 319.0918 5 28225 402.7155 6 26606 351.9574 7 22825 336.9182 8 19693 441.9574 9 27384 437.6974 10 35830 428.2243 11 42425 404.3165 12 18535 324.9496 13 34863 395.8312 14 22682 227.0702 15 12663 336.7536 16 16877 355.6092 17 19131 342.4444 18 23563 421.9390 19 33357 478.8333 20 20027 375.8889 21 26974 419.8039 22 22945 358.3871 23 16299 335.1096 24 32837 349.1237 25 16259 366.6866 26 21445 305.0610 27 13571 438.1290 28 16415 412.8037 29 14751 416.5252 30 44165 355.6786 31 69932 667.6667 32 71719 401.9565 33 64663 373.5747 34 21449 405.5862 35 40902 299.1275 rasio.murid.guru.smp rasio.murid.sekolah.sd rasio.murid.guru.sd APtS APBD 1 16.02336 170.0588 9.572848 3.36 42.911 2 18.47010 205.5938 12.824561 0.00 46.023 3 19.26352 260.4000 9.169014 1.30 47.264 4 15.72197 209.3077 14.550802 3.44 46.045 5 16.29404 182.4737 11.996540 0.00 47.605 6 16.58346 197.2222 8.198614 0.00 45.603 7 15.07771 336.0000 3.326733 1.30 41.848 8 23.12282 187.6739 14.014610 0.00 47.990 9 14.30138 159.8421 12.549587 0.00 48.376 10 13.46063 215.7925 14.495564 1.92 52.672 11 14.44640 154.8235 5.927928 0.65 44.747 12 11.96812 52.6800 0.371614 0.00 51.581 13 14.21595 304.3333 98.323077 0.00 47.857 14 17.85241 330.0625 10.604418 0.61 45.204 15 16.50870 142.7333 15.077465 0.59 42.060 16 16.37798 160.0000 13.636364 0.00 42.948 17 16.09399 169.3333 12.390244 0.00 38.937 18 13.64314 128.4231 7.258696 0.00 43.812 19 16.12912 236.3333 15.005291 0.65 36.229 20 17.00000 195.6000 22.101695 1.35 43.845 21 14.09480 161.2941 10.968000 0.00 36.973 22 22.29431 236.7778 15.033510 0.92 38.056 23 15.57161 224.9565 14.214286 1.52 20.000 24 13.42251 382.8889 34.288557 1.10 45.990 25 18.22552 186.5000 10.970588 1.31 39.963 26 13.41287 152.9688 11.278802 2.36 41.846 27 11.39191 155.2174 15.127119 1.57 45.687 28 18.76381 172.6667 26.086331 1.57 45.394 29 17.32406 157.6667 12.128205 2.21 42.515 30 19.97793 115.8667 5.347692 0.00 34.761 31 14.86150 304.3333 15.064231 0.00 40.528 32 13.09490 238.4286 14.326180 0.00 37.507 33 14.24233 212.4389 12.944821 1.07 34.582 34 15.85175 214.4615 13.700246 0.84 30.318 35 13.30051 195.4667 11.453125 1.08 35.297 cluster 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 2 12 1 13 1 14 1 15 1 16 1 17 1 18 1 19 1 20 1 21 1 22 1 23 1 24 1 25 1 26 1 27 1 28 1 29 1 30 2 31 2 32 2 33 2 34 1 35 2 attr(,"class") [1] "fgwc" > > #cluster visualization > ## No test: > visualize(clust) Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) : Discarded ellps Indonesian National Spheroid in Proj4 definition: +proj=longlat +a=6378160 +rf=298.247 +no_defs Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) : Discarded datum Indonesian_Datum_1974 in Proj4 definition Warning in wkt(obj) : CRS object has no comment Warning in `proj4string<-`(`*tmp*`, value = CRS("+init=epsg:4238")) : A new CRS was assigned to an object with an existing CRS: +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0 without reprojecting. For reprojection, use function spTransform Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) : Discarded ellps Indonesian National Spheroid in Proj4 definition: +proj=longlat +a=6378160 +rf=298.247 +no_defs Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj = prefer_proj) : Discarded datum Indonesian_Datum_1974 in Proj4 definition Warning in RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") : Ring Self-intersection at or near point 109.81203154000001 -7.6121331699999999 Warning in RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") : Ring Self-intersection at or near point 111.05316051 -7.50904507 Warning in RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") : Ring Self-intersection at or near point 111.46853969999999 -6.7392702 Warning in RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") : Ring Self-intersection at or near point 110.25272179 -7.0253181500000004 Warning in RGEOSUnaryPredFunc(spgeom, byid, "rgeos_isvalid") : Ring Self-intersection at or near point 109.11365244 -6.8982939500000002 SpP is invalid Warning in rgeos::gUnaryUnion(spgeom = SpP, id = IDs) : Invalid objects found; consider using set_RGEOS_CheckValidity(2L) $clusterMap Error: Unknown colour name: stateblue4 Execution halted * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/spatialClust.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 0:48.67, 42.00 + 6.28