• using R version 2.15.2 (2012-10-26)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'psgp/DESCRIPTION' ... OK
• this is package 'psgp' version '0.3-2'
• 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 whether package 'psgp' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 10.8Mb
  sub-directories of 1Mb or more:
  libs 10.6Mb
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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
• loading checks for arch 'i386'
  ** 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
• loading checks for arch 'x86_64'
  ** 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 for unstated 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 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 line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking examples ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x86_64' ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ...
  ** running tests for arch 'i386' OK
  Running 'meuse_psgp.R'
  Comparing 'meuse_psgp.Rout' to 'meuse_psgp.Rout.save' ...1,36d0
  <
  <
  < > library(psgp)
  <
  < Attaching package: 'lattice'
  <
  < The following object(s) are masked from 'package:evd':
  <
  < qq
  <
  < > set.seed(100)
  < > # set up data:
  < > data(meuse)
  < > coordinates(meuse) = ~x+y
  < > meuse$value = log(meuse$zinc)
  < > data(meuse.grid)
  < > gridded(meuse.grid) = ~x+y
  < > proj4string(meuse) = CRS("+init=epsg:28992")
  < > proj4string(meuse.grid) = CRS("+init=epsg:28992")
  < >
  < > # set up intamap object:
  < > psgpObject = createIntamapObject(
  < + observations = meuse,
  < + formulaString=as.formula(value~1),
  < + predictionLocations = meuse.grid,
  < + class = "psgp"
  < + )
  < rgdal: version: 0.8-5, (SVN revision 449)
  < Geospatial Data Abstraction Library extensions to R successfully loaded
  < Loaded GDAL runtime: GDAL 1.9.0, released 2011/12/29
  < Path to GDAL shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/gdal
  < Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
  < Path to PROJ.4 shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/proj
  < >
  < > # run test:
  < > checkSetup(psgpObject)
  38,40d1
  < >
  < > # do interpolation steps:
  < > psgpObject = estimateParameters(psgpObject)
  390,392d350
  < >
  < > # make prediction
  < > psgpObject = spatialPredict(psgpObject)
  717c675
  < Range (P0) :844.492804
  ---
  > Range (P0) :844.492816
  721c679
  < Length scale (P0) :1752.485473
  ---
  > Length scale (P0) :1752.485482
  726,730d683
  < >
  < > # Plot prediction
  < > # plotIntamap(psgpObject)
  < > # plotIntamap(meuse, pch=1, cex=sqrt(meuse$value)/20, add=TRUE)
  < >
  Running 'psgp.R'
  Comparing 'psgp.Rout' to 'psgp.Rout.save' ...1,28d0
  <
  <
  < > library(psgp) # requires intamap
  <
  < Attaching package: 'lattice'
  <
  < The following object(s) are masked from 'package:evd':
  <
  < qq
  <
  < >
  < > data(meuse)
  < > observations = data.frame(x = meuse$x,y = meuse$y,value = log(meuse$zinc))
  < > coordinates(observations) = ~x+y
  < > set.seed(13531)
  < > predictionLocations = spsample(observations, 50, "regular")
  < >
  < > krigingObject = createIntamapObject(
  < + observations = observations,
  < + predictionLocations = predictionLocations,
  < + formulaString = as.formula(value~1),
  < + params = list(doAnisotropy = TRUE, thresh = quantile(observations$value,0.9)),
  < + outputWhat = list(mean=TRUE, variance=TRUE, excprob = 5.9, cumdistr = 5.9,
  < + quantile = .1)
  < + )
  < > class(krigingObject) = c("psgp")
  < >
  < > checkSetup(krigingObject)
  30,31d1
  < > krigingObject = preProcess(krigingObject)
  < > krigingObject = estimateParameters(krigingObject)
  381d350
  < > krigingObject = spatialPredict(krigingObject)
  700,701c669,670
  < Range (P0) :844.492766
  < Variance (P1) :1.111597
  ---
  > Range (P0) :844.492802
  > Variance (P1) :1.111596
  704c673
  < Length scale (P0) :1752.485458
  ---
  > Length scale (P0) :1752.485475
  709,745d677
  < > krigingObject = postProcess(krigingObject)
  < rgdal: version: 0.8-5, (SVN revision 449)
  < Geospatial Data Abstraction Library extensions to R successfully loaded
  < Loaded GDAL runtime: GDAL 1.9.0, released 2011/12/29
  < Path to GDAL shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/gdal
  < Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
  < Path to PROJ.4 shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/proj
  < >
  < > # Send predictions back to Java. Not sure how to deal with this spatial object though...?
  < > summary(krigingObject$outputTable)
  < x y mean variance
  < Min. :179019 Min. :330013 Min. :4.762 Min. :0.03763
  < 1st Qu.:179485 1st Qu.:330829 1st Qu.:5.314 1st Qu.:0.07613
  < Median :180183 Median :331644 Median :5.875 Median :0.25617
  < Mean :180183 Mean :331644 Mean :6.235 Mean :0.45727
  < 3rd Qu.:180882 3rd Qu.:332459 3rd Qu.:7.411 3rd Qu.:0.64259
  < Max. :181348 Max. :333275 Max. :8.015 Max. :1.81668
  < excprob5.9 cumdistr5.9 quantile0.1
  < Min. :0.0000153 Min. :0.0000 Min. :4.048
  < 1st Qu.:0.0561274 1st Qu.:0.0210 1st Qu.:4.646
  < Median :0.4838715 Median :0.5161 Median :5.176
  < Mean :0.5164961 Mean :0.4835 Mean :5.479
  < 3rd Qu.:0.9790042 3rd Qu.:0.9439 3rd Qu.:6.461
  < Max. :1.0000000 Max. :1.0000 Max. :7.228
  < > summary(krigingObject$observations)
  < Object of class SpatialPointsDataFrame
  < Coordinates:
  < min max
  < x 178605 181390
  < y 329714 333611
  < Is projected: NA
  < proj4string : [NA]
  < Number of points: 155
  < Data attributes:
  < Min. 1st Qu. Median Mean 3rd Qu. Max.
  < 4.727 5.288 5.787 5.886 6.514 7.517
  < > summary(autoKrige(value~1,krigingObject$observations,predictionLocations)$krige_output)
  747,767d678
  < Object of class SpatialPointsDataFrame
  < Coordinates:
  < min max
  < x1 179018.6 181348.1
  < x2 330013.4 333274.7
  < Is projected: NA
  < proj4string : [NA]
  < Number of points: 48
  < Data attributes:
  < var1.pred var1.var var1.stdev
  < Min. :4.929 Min. :0.1153 Min. :0.3395
  < 1st Qu.:5.518 1st Qu.:0.1615 1st Qu.:0.4018
  < Median :6.047 Median :0.3582 Median :0.5963
  < Mean :5.978 Mean :0.3827 Mean :0.5909
  < 3rd Qu.:6.337 3rd Qu.:0.6026 3rd Qu.:0.7762
  < Max. :7.472 Max. :0.6752 Max. :0.8217
  < > autofitVariogram(value~1,krigingObject$observations)$var_model
  < model psill range
  < 1 Nug 0.04847876 0.0000
  < 2 Sph 0.58754476 889.8912
  < >
  ** running tests for arch 'x86_64' OK
  Running 'meuse_psgp.R'
  Comparing 'meuse_psgp.Rout' to 'meuse_psgp.Rout.save' ...1,36d0
  <
  <
  < > library(psgp)
  <
  < Attaching package: 'lattice'
  <
  < The following object(s) are masked from 'package:evd':
  <
  < qq
  <
  < > set.seed(100)
  < > # set up data:
  < > data(meuse)
  < > coordinates(meuse) = ~x+y
  < > meuse$value = log(meuse$zinc)
  < > data(meuse.grid)
  < > gridded(meuse.grid) = ~x+y
  < > proj4string(meuse) = CRS("+init=epsg:28992")
  < > proj4string(meuse.grid) = CRS("+init=epsg:28992")
  < >
  < > # set up intamap object:
  < > psgpObject = createIntamapObject(
  < + observations = meuse,
  < + formulaString=as.formula(value~1),
  < + predictionLocations = meuse.grid,
  < + class = "psgp"
  < + )
  < rgdal: version: 0.8-5, (SVN revision 449)
  < Geospatial Data Abstraction Library extensions to R successfully loaded
  < Loaded GDAL runtime: GDAL 1.9.0, released 2011/12/29
  < Path to GDAL shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/gdal
  < Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
  < Path to PROJ.4 shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/proj
  < >
  < > # run test:
  < > checkSetup(psgpObject)
  38,40d1
  < >
  < > # do interpolation steps:
  < > psgpObject = estimateParameters(psgpObject)
  390,392d350
  < >
  < > # make prediction
  < > psgpObject = spatialPredict(psgpObject)
  717c675
  < Range (P0) :844.492535
  ---
  > Range (P0) :844.492816
  721c679
  < Length scale (P0) :1752.485290
  ---
  > Length scale (P0) :1752.485482
  726,730d683
  < >
  < > # Plot prediction
  < > # plotIntamap(psgpObject)
  < > # plotIntamap(meuse, pch=1, cex=sqrt(meuse$value)/20, add=TRUE)
  < >
  Running 'psgp.R'
  Comparing 'psgp.Rout' to 'psgp.Rout.save' ...1,28d0
  <
  <
  < > library(psgp) # requires intamap
  <
  < Attaching package: 'lattice'
  <
  < The following object(s) are masked from 'package:evd':
  <
  < qq
  <
  < >
  < > data(meuse)
  < > observations = data.frame(x = meuse$x,y = meuse$y,value = log(meuse$zinc))
  < > coordinates(observations) = ~x+y
  < > set.seed(13531)
  < > predictionLocations = spsample(observations, 50, "regular")
  < >
  < > krigingObject = createIntamapObject(
  < + observations = observations,
  < + predictionLocations = predictionLocations,
  < + formulaString = as.formula(value~1),
  < + params = list(doAnisotropy = TRUE, thresh = quantile(observations$value,0.9)),
  < + outputWhat = list(mean=TRUE, variance=TRUE, excprob = 5.9, cumdistr = 5.9,
  < + quantile = .1)
  < + )
  < > class(krigingObject) = c("psgp")
  < >
  < > checkSetup(krigingObject)
  30,31d1
  < > krigingObject = preProcess(krigingObject)
  < > krigingObject = estimateParameters(krigingObject)
  381d350
  < > krigingObject = spatialPredict(krigingObject)
  700c669
  < Range (P0) :844.492747
  ---
  > Range (P0) :844.492802
  704c673
  < Length scale (P0) :1752.485419
  ---
  > Length scale (P0) :1752.485475
  709,745d677
  < > krigingObject = postProcess(krigingObject)
  < rgdal: version: 0.8-5, (SVN revision 449)
  < Geospatial Data Abstraction Library extensions to R successfully loaded
  < Loaded GDAL runtime: GDAL 1.9.0, released 2011/12/29
  < Path to GDAL shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/gdal
  < Loaded PROJ.4 runtime: Rel. 4.8.0, 6 March 2012, [PJ_VERSION: 480]
  < Path to PROJ.4 shared files: /Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/Rlib/2.15/rgdal/proj
  < >
  < > # Send predictions back to Java. Not sure how to deal with this spatial object though...?
  < > summary(krigingObject$outputTable)
  < x y mean variance
  < Min. :179019 Min. :330013 Min. :4.762 Min. :0.03764
  < 1st Qu.:179485 1st Qu.:330829 1st Qu.:5.314 1st Qu.:0.07613
  < Median :180183 Median :331644 Median :5.874 Median :0.25617
  < Mean :180183 Mean :331644 Mean :6.234 Mean :0.45727
  < 3rd Qu.:180882 3rd Qu.:332459 3rd Qu.:7.409 3rd Qu.:0.64260
  < Max. :181348 Max. :333275 Max. :8.013 Max. :1.81668
  < excprob5.9 cumdistr5.9 quantile0.1
  < Min. :0.0000153 Min. :0.00000 Min. :4.048
  < 1st Qu.:0.0561157 1st Qu.:0.02101 1st Qu.:4.646
  < Median :0.4837435 Median :0.51626 Median :5.177
  < Mean :0.5164719 Mean :0.48353 Mean :5.478
  < 3rd Qu.:0.9789940 3rd Qu.:0.94388 3rd Qu.:6.461
  < Max. :1.0000000 Max. :0.99999 Max. :7.228
  < > summary(krigingObject$observations)
  < Object of class SpatialPointsDataFrame
  < Coordinates:
  < min max
  < x 178605 181390
  < y 329714 333611
  < Is projected: NA
  < proj4string : [NA]
  < Number of points: 155
  < Data attributes:
  < Min. 1st Qu. Median Mean 3rd Qu. Max.
  < 4.727 5.288 5.787 5.886 6.514 7.517
  < > summary(autoKrige(value~1,krigingObject$observations,predictionLocations)$krige_output)
  747,767d678
  < Object of class SpatialPointsDataFrame
  < Coordinates:
  < min max
  < x1 179018.6 181348.1
  < x2 330013.4 333274.7
  < Is projected: NA
  < proj4string : [NA]
  < Number of points: 48
  < Data attributes:
  < var1.pred var1.var var1.stdev
  < Min. :4.929 Min. :0.1153 Min. :0.3395
  < 1st Qu.:5.518 1st Qu.:0.1615 1st Qu.:0.4018
  < Median :6.047 Median :0.3582 Median :0.5963
  < Mean :5.978 Mean :0.3827 Mean :0.5909
  < 3rd Qu.:6.337 3rd Qu.:0.6026 3rd Qu.:0.7762
  < Max. :7.472 Max. :0.6752 Max. :0.8217
  < > autofitVariogram(value~1,krigingObject$observations)$var_model
  < model psill range
  < 1 Nug 0.04847876 0.0000
  < 2 Sph 0.58754476 889.8912
  < >
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  '/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/psgp.Rcheck/00check.log'
  for details.
• elapsed time (check, wall clock): 5:27