* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/rtop.Rcheck’ * using R Under development (unstable) (2025-06-30 r88364) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘rtop/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rtop’ version ‘0.6-9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘intamap’ * 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 ‘rtop’ can be installed ... [21s/39s] OK * used C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * used Fortran compiler: ‘GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * 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 code 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 use of S3 registration ... 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 ... [39s/99s] 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking examples ... [4s/10s] ERROR Running examples in ‘rtop-Ex.R’ failed The error most likely occurred in: > ### Name: useRtopWithIntamap > ### Title: Integrates the rtop package with the 'intamap' package > ### Aliases: useRtopWithIntamap > ### Keywords: plot > > ### ** Examples > > library(intamap) Error in library(intamap) : there is no package called ‘intamap’ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘rtop.R’ [19s/38s] Running ‘rtop_sf.R’ [79s/163s] Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK [99s/202s] ERROR Running the tests in ‘tests/rtop.R’ failed. Complete output: > set.seed(1501) > #----------------------------- > ## IGNORE_RDIFF_BEGIN > library(rtop) > if (interactive()) options(error = recover) > # Read directly from shape-files in data directory > rpath = system.file("extdata",package="rtop") > library(sf) Linking to GEOS 3.13.0, GDAL 3.10.3, PROJ 9.6.2; sf_use_s2() is TRUE > observations = st_read(rpath, "observations") Reading layer `observations' from data source `/data/gannet/ripley/R/packages/tests-Suggests/rtop.Rcheck/rtop/extdata' using driver `ESRI Shapefile' Simple feature collection with 57 features and 7 fields Geometry type: POLYGON Dimension: XY Bounding box: xmin: 392041.1 ymin: 454983.1 xmax: 512819.5 ymax: 543984.4 Projected CRS: Lambert_Conformal_Conic > predictionLocations = st_read(rpath, "predictionLocations") Reading layer `predictionLocations' from data source `/data/gannet/ripley/R/packages/tests-Suggests/rtop.Rcheck/rtop/extdata' using driver `ESRI Shapefile' Simple feature collection with 235 features and 5 fields Geometry type: POLYGON Dimension: XY Bounding box: xmin: 393416.8 ymin: 454919.1 xmax: 519903.3 ymax: 543984.4 Projected CRS: Lambert_Conformal_Conic > ## IGNORE_RDIFF_END > > > observations = as(observations, "Spatial") > predictionLocations = as(predictionLocations, "Spatial") > #Finding a few prediction locations of them > > observations = observations[1:30,] > predictionLocations = predictionLocations[1:2,] > > observations$obs = observations$QSUMMER_OB/observations$AREASQKM > > # Setting some parameters > params = list(gDist = TRUE, cloud = FALSE, rresol = 25, hresol = 3, debug.level = -1) > # Build an object > rtopObj = createRtopObject(observations,predictionLocations, params = params, formulaString = "obs ~ 1" ) > # Fit a variogram (function also creates it) > rtopObj = rtopFitVariogram(rtopObj, iprint = -1) > print(rtopObj$variogramModel, 3) $model [1] "Ex1" $params [1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01 attr(,"class") [1] "rtopVariogramModel" attr(,"SSErr") [1] 0.557 attr(,"criterion") [1] 0.0981 > #rtopObj = checkVario(rtopObj) > rtopObj2 = rtopKrige(rtopObj, cv = TRUE) [1] "Sampling points from 30 areas" > > > print(attr(rtopObj2$varMatObs,"variogramModel"), 3) $model [1] "Ex1" $params [1] 2.51e-04 4.26e+05 0.00e+00 1.01e-05 9.23e-01 attr(,"class") [1] "rtopVariogramModel" attr(,"SSErr") [1] 0.557 attr(,"criterion") [1] 0.0981 > > rtopObj3 = rtopKrige(rtopObj) [1] "Sampling points from 30 areas" [1] "Sampling points from 2 areas" [1] "Creating prediction semivariance matrix. This can take some time." > > > varmat = varMat(observations, predictionLocations, variogramModel = rtopObj$variogramModel, + gDistEst = TRUE, gDistPred = TRUE, rresol = 25, hresol = 3) [1] "Sampling points from 30 areas" [1] "Sampled on average 54.2 points from 30 areas" [1] "Sampling points from 2 areas" [1] "Sampled on average 77 points from 2 areas" > > all.equal(varmat$varMatObs, rtopObj2$varMatObs) [1] TRUE > rtopObj4 = rtopKrige(rtopObj2) [1] "Sampling points from 2 areas" [1] "Creating prediction semivariance matrix. This can take some time." > > #debug(rtop:::rtopDisc.SpatialPolygons) > # rtopObj5 = rtopKrige(rtopObj, params = list(cnAreas = 5, cDlim = 10, nclus = 2)) > > print(summary(rtopObj2$predictions)) Length Class Mode 30 SpatialPolygonsDataFrame S4 > print(summary(rtopObj3$predictions)) Length Class Mode 2 SpatialPolygonsDataFrame S4 > print(summary(rtopObj4$predictions)) Length Class Mode 2 SpatialPolygonsDataFrame S4 > print(all.equal(rtopObj4$predictions, rtopObj3$predictions)) [1] TRUE > #spplot(rtopObj$predictions,col.regions = bpy.colors(), c("var1.pred","var1.var")) > > # Cross-validation > #spplot(rtopObj2$predictions,col.regions = bpy.colors(), c("observed","var1.pred")) > print(cor(rtopObj2$predictions$observed,rtopObj2$predictions$var1.pred)) [1] 0.1678744 > > > > > set.seed(1501) > library(intamap) Error in library(intamap) : there is no package called 'intamap' Execution halted * checking PDF version of manual ... [9s/19s] OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/gannet/ripley/R/packages/tests-Suggests/rtop.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 9:16.41, 232.66 + 14.44