• 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/62s] OK See the install log for details.
• 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 ... [38s/82s] 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 ... 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 ... [97s/148s] ERROR   Running ‘rtop.R’ [19s/36s]   Running ‘rtop_sf.R’ [77s/111s]   Comparing ‘rtop_sf.Rout’ to ‘rtop_sf.Rout.save’ ... OK 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-devel/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-devel/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/14s] 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