* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/geostatsp.Rcheck’
* using R Under development (unstable) (2025-02-15 r87723)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘geostatsp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geostatsp’ version ‘2.0.8’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘RandomFields’
* checking if this is a source package ... WARNING
Subdirectory ‘geostatsp/src’ contains apparent object files/libraries
  Matrix_stubs_here.o gmrfEdge.o gmrfLik.o matern.o maternLogL.o
  maternLogLopt.o optimize.o register.o
Object files/libraries should not be included in a source package.

Subdirectory ‘src’ contains:
  symbols.rds
These are unlikely file names for src files.
* 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 ‘geostatsp’ can be installed ... [62s/88s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/geostatsp-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* checking package directory ... OK
* checking ‘build’ 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 ... [14s/18s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/17s] OK
* checking whether the package can be unloaded cleanly ... [14s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/19s] OK
* checking loading without being on the library search path ... [14s/18s] 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 ... [93s/126s] 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 ... [14s/19s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31m/22m] ERROR
Running examples in ‘geostatsp-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFsimulate
> ### Title: Simulation of Random Fields
> ### Aliases: RFsimulate modelRandomFields RFsimulate RFsimulate-methods
> ###   RFsimulate,ANY,SpatRaster-method RFsimulate,numeric,SpatRaster-method
> ###   RFsimulate,numeric,SpatVector-method
> ###   RFsimulate,RMmodel,SpatVector-method
> ###   RFsimulate,RMmodel,SpatRaster-method
> ###   RFsimulate,matrix,SpatRaster-method
> ###   RFsimulate,matrix,SpatVector-method RFsimulate,data.frame,ANY-method
> ### Keywords: spatial
> 
> ### ** Examples
> 
> library('geostatsp')
> 
> # exclude this line to use the RandomFields package
> options(useRandomFields = FALSE)
> 
> model1 <- c(var=5, range=1,shape=0.5)
> 
> 
> myraster = rast(nrows=20,ncols=30,extent = ext(0,6,0,4), 
+ 	crs="+proj=utm +zone=17 +datum=NAD27 +units=m +no_defs")
> 
> set.seed(0) 
> 
> simu <- RFsimulate(model1, x=myraster, n=3)
install the RandomFields package for faster simulations
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [0m/90m] ERROR
  Running ‘RFsimulate.R’ [31m/22m]
  Running ‘krige.R’ [25s/33s]
  Running ‘lgcp.R’ [88s/91s]
  Running ‘lgm.R’ [71s/83s]
  Running ‘lgmRaster.R’ [31m/21m]
  Running ‘likfitLgm.R’ [28s/33s]
  Running ‘matern.R’ [15s/18s]
  Running ‘maternGmrfPrec.R’ [31m/21m]
  Running ‘profLlgm.R’ [0m/22m]
  Running ‘simLgcp.R’
Running the tests in ‘tests/RFsimulate.R’ failed.
Complete output:
  > library("geostatsp")
  Loading required package: Matrix
  Loading required package: terra
  terra 1.8.21
  > 
  > model <- c(var=5, range=20,shape=0.5)
  > 
  > # any old crs
  > theCrs = "+proj=utm +zone=17 +datum=NAD27 +units=m +no_defs"
  > 
  > # don't test using the randomFields package, it's currently broken on some R builds
  > options(useRandomFields = FALSE)
  > 
  >   myraster = rast(nrows=20,ncols=20,extent = ext(100,110,100,110), 
  +     crs=theCrs)
  > 
  > set.seed(0)
  > simu = RFsimulate(model = rbind(a=model, b=model+0.1), 
  +   x=myraster, n=4
  + )
Running the tests in ‘tests/lgmRaster.R’ failed.
Complete output:
  > #+ setup
  > library('geostatsp')
  Loading required package: Matrix
  Loading required package: terra
  terra 1.8.21
  > #'
  > 
  > #' # simulated data
  > 
  > # exclude this line to use the RandomFields package
  > options(useRandomFields = FALSE)
  > 
  > Ncell =  40
  > 
  > myRaster = squareRaster(ext(0,6000,0,6000), Ncell)
  > 
  > myParam=c(oneminusar=0.1, conditionalVariance=2.5^2,shape=2)
  > myQ = maternGmrfPrec(myRaster, param=myParam)
  > attributes(myQ)$info$optimalShape
       shape   variance      range   cellSize 
    4.092496 110.524266 900.000000 150.000000 
  > set.seed(0)
  > mySim = RFsimulate(attributes(myQ)$info$optimalShape, myRaster)
  install the RandomFields package for faster simulations
Running the tests in ‘tests/maternGmrfPrec.R’ failed.
Complete output:
  > library('geostatsp')
  Loading required package: Matrix
  Loading required package: terra
  terra 1.8.21
  > matrix(NNmat(7, 7)[,25], 7, 7)
       [,1] [,2] [,3] [,4] [,5] [,6] [,7]
  [1,]    0    0    0    6    0    0    0
  [2,]    0    0    5    4    5    0    0
  [3,]    0    5    3    2    3    5    0
  [4,]    6    4    2    1    2    4    6
  [5,]    0    5    3    2    3    5    0
  [6,]    0    0    5    4    5    0    0
  [7,]    0    0    0    6    0    0    0
  > 
  > myr = squareRaster(ext(0,600,0,300), 60)
  > theNN = NNmat(myr)
  > 
  > 
  > params=c(range = 6*xres(myr),
  + 		cellSize=xres(myr),
  + 		shape=2,
  + 		variance=1600)
  > 
  > 
  > # precision matrix without adjusting for edge effects
  > system.time({precMat = maternGmrfPrec(N=theNN, param=params,
  + 					adjustEdges=FALSE)})
     user  system elapsed 
    0.484   0.012   0.608 
  > 
  > 
  > system.time({theNNadj = NNmat(N=myr, nearest=params['shape']+1, adjustEdges=TRUE)})
     user  system elapsed 
    0.225   0.021   0.324 
  > # and with the adjustment
  > system.time({precMatCorr =maternGmrfPrec(N=theNNadj, param=params, 
  + 					adjustEdges=TRUE)}) 
Running the tests in ‘tests/profLlgm.R’ failed.
Complete output:
  > 
  > library('geostatsp')
  Loading required package: Matrix
  Loading required package: terra
  terra 1.8.21
  > data('swissRain')
  > swissRain = unwrap(swissRain)
  > swissAltitude = unwrap(swissAltitude)
  > 
  > Ncores = c(1,2)[1+(.Platform$OS.type=='unix')]
  > 
  > 
  > 
  > sr2 = swissRain
  > sr2$elev = extract(swissAltitude, sr2)
  Warning message:
  [`[[<-`] only using the first column 
  > swissFit = likfitLgm(
  +     data=sr2, 
  +     formula=rain~ elev,
  +     param=c(range=10000,shape=1,nugget=0,boxcox=0.5,anisoRatio=2,anisoAngleDegrees=45),
  +     paramToEstimate = c("range",'anisoAngleDegrees','anisoRatio'),
  +     reml=FALSE,
  +     verbose=FALSE
  + )
  > 
  > 
  > # calculate log-likelihood at the MLE's, but re-estimate variance
  > sl = loglikLgm(
  +     swissFit$param[c('range','shape','boxcox', 'anisoRatio', 'anisoAngleRadians')],
  +     data=sr2, 
  +     formula=rain~ elev,
  +     reml=swissFit$model$reml)  
  > 
  > 
  > # calculate log-likelihood without re-estimating variance
  > sigSqHat = attributes(sl)$totalVarHat
  > sl1 = loglikLgm(
  +     c(attributes(sl)$param[
  +             c('boxcox','anisoRatio','anisoAngleRadians','shape', 'range')], 
  +         variance=sigSqHat),
  +     data=sr2, 
  +     formula=rain~ elev,
  +     reml=swissFit$model$reml)  
  >  
  > 
  > # re=estimate the anisotropy parameters but not the range
  > sf2 = likfitLgm(
  +     data=swissFit$data, 
  +     formula=swissFit$model$formula,
  +     param= swissFit$param[c('range','nugget','shape','boxcox', 'anisoRatio', 'anisoAngleRadians')],
  +     paramToEstimate = c('variance','anisoAngleRadians','anisoRatio'),
  +     reml=swissFit$model$reml)  
  > 
  > # these should all be the same
  > as.numeric(sl1)
  [1] 644.4812
  > as.numeric(sl) 
  [1] 644.4812
  > swissFit$optim$logL
  m2logL.ml   logL.ml 
   644.4812 -322.2406 
  > sf2$optim$logL
  m2logL.ml   logL.ml 
   644.4812 -322.2406 
  > 
  > date()
  [1] "Sat Feb 15 16:36:24 2025"
  > x=profLlgm(swissFit, mc.cores=Ncores,
  +     range=seq(15000, 55000 , len=12)
  + )
  
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [506s/479s] OK
* checking PDF version of manual ... [10s/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, 1 WARNING