• using R Under development (unstable) (2013-04-22 r62639)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• 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 for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘psgp’ can be installed ... [120s/63s] OK
• checking installed package size ... NOTE
  installed size is 6.9Mb
  sub-directories of 1Mb or more:
  libs 6.7Mb
• 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 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 $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running ‘meuse_psgp.R’
  Comparing ‘meuse_psgp.Rout’ to ‘meuse_psgp.Rout.save’ ...1,35d0
  <
  <
  < > library(psgp)
  <
  < Attaching package: 'lattice'
  <
  < The following object is masked from 'package:evd':
  <
  < qq
  <
  < > set.seed(100)
  < > # set up data:
  < > data(meuse)
  < > coordinates(meuse) = ~x+y
  < > meuse$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"
  < + )
  < Warning messages:
  < 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  < there is no package called 'rgdal'
  < 2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  < there is no package called 'rgdal'
  < >
  < > # run test:
  < > checkSetup(psgpObject)
  37,42c2,4
  < >
  < > # do interpolation steps:
  < > psgpObject = estimateParameters(psgpObject)
  < Range: 716.729191
  < Sill: 0.766279
  < Nugget: 0.007457
  ---
  > Range: 727.943976
  > Sill: 0.752485
  > Nugget: 0.005943
  45c7
  < Defaulting to GAUSSIAN with variance 0.000075
  ---
  > Defaulting to GAUSSIAN with variance 0.000059
  359,360c321,322
  < Range (P0) :716.729191
  < Variance (P1) :0.766279
  ---
  > Range (P0) :727.943976
  > Variance (P1) :0.752485
  363,364c325,326
  < Length scale (P0) :716.729191
  < Variance (P1) :0.766279
  ---
  > Length scale (P0) :727.943976
  > Variance (P1) :0.752485
  370,375c332,337
  < Variance (P0) :0.007457
  < Finding optimal parametersCycle 1 Error 101.037136 Scale 1.000000
  < Cycle 2 Error 99.254923 Scale 0.500000
  < Cycle 3 Error 99.086845 Scale 0.250000
  < Cycle 4 Error 98.047846 Scale 0.125000
  < Cycle 5 Error 98.002947 Scale 0.062500
  ---
  > Variance (P0) :0.005943
  > Finding optimal parametersCycle 1 Error 101.557831 Scale 1.000000
  > Cycle 2 Error 99.668320 Scale 0.500000
  > Cycle 3 Error 99.416729 Scale 0.250000
  > Cycle 4 Error 98.418564 Scale 0.125000
  > Cycle 5 Error 98.357160 Scale 0.062500
  377,381c339,343
  < Cycle 1 Error 97.968412 Scale 1.000000
  < Cycle 2 Error 97.507097 Scale 0.500000
  < Cycle 3 Error 97.494582 Scale 0.250000
  < Cycle 4 Error 97.494582 Scale 0.125000
  < Cycle 5 Error 97.167484 Scale 0.500000
  ---
  > Cycle 1 Error 98.328484 Scale 1.000000
  > Cycle 2 Error 97.891931 Scale 0.500000
  > Cycle 3 Error 97.885781 Scale 0.250000
  > Cycle 4 Error 97.493976 Scale 0.125000
  > Cycle 5 Error 97.476106 Scale 0.062500
  383,387c345,349
  < Cycle 1 Error 97.138869 Scale 1.000000
  < Cycle 2 Error 97.044464 Scale 0.500000
  < Cycle 3 Error 97.035699 Scale 0.250000
  < Cycle 4 Error 97.023483 Scale 0.125000
  < Cycle 5 Error 97.021590 Scale 0.062500
  ---
  > Cycle 1 Error 97.472655 Scale 1.000000
  > Cycle 2 Error 97.334270 Scale 0.500000
  > Cycle 3 Error 97.327172 Scale 0.250000
  > Cycle 4 Error 97.310690 Scale 0.125000
  > Cycle 5 Error 97.310470 Scale 0.062500
  389,391d350
  < >
  < > # make prediction
  < > psgpObject = spatialPredict(psgpObject)
  394c353
  < Defaulting to GAUSSIAN with variance 0.000346
  ---
  > Defaulting to GAUSSIAN with variance 0.000302
  716,717c675,676
  < Range (P0) :853.719558
  < Variance (P1) :1.070282
  ---
  > Range (P0) :844.492816
  > Variance (P1) :1.111596
  720,721c679,680
  < Length scale (P0) :1306.632767
  < Variance (P1) :0.881519
  ---
  > Length scale (P0) :1752.485482
  > Variance (P1) :0.793301
  724,729c683
  < Amplitude (P0) :0.023702
  < >
  < > # Plot prediction
  < > # plotIntamap(psgpObject)
  < > # plotIntamap(meuse, pch=1, cex=sqrt(meuse$value)/20, add=TRUE)
  < >
  ---
  > Amplitude (P0) :0.022145
  Running ‘psgp.R’
  Comparing ‘psgp.Rout’ to ‘psgp.Rout.save’ ...1,28d0
  <
  <
  < > library(psgp) # requires intamap
  <
  < Attaching package: 'lattice'
  <
  < The following object is 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)
  30,34c2,4
  < > krigingObject = preProcess(krigingObject)
  < > krigingObject = estimateParameters(krigingObject)
  < Range: 716.729191
  < Sill: 0.766279
  < Nugget: 0.007457
  ---
  > Range: 727.943976
  > Sill: 0.752485
  > Nugget: 0.005943
  37c7
  < Defaulting to GAUSSIAN with variance 0.000075
  ---
  > Defaulting to GAUSSIAN with variance 0.000059
  351,352c321,322
  < Range (P0) :716.729191
  < Variance (P1) :0.766279
  ---
  > Range (P0) :727.943976
  > Variance (P1) :0.752485
  355,356c325,326
  < Length scale (P0) :716.729191
  < Variance (P1) :0.766279
  ---
  > Length scale (P0) :727.943976
  > Variance (P1) :0.752485
  362,367c332,337
  < Variance (P0) :0.007457
  < Finding optimal parametersCycle 1 Error 101.037136 Scale 1.000000
  < Cycle 2 Error 99.254923 Scale 0.500000
  < Cycle 3 Error 99.086845 Scale 0.250000
  < Cycle 4 Error 98.047846 Scale 0.125000
  < Cycle 5 Error 98.002947 Scale 0.062500
  ---
  > Variance (P0) :0.005943
  > Finding optimal parametersCycle 1 Error 101.557831 Scale 1.000000
  > Cycle 2 Error 99.668320 Scale 0.500000
  > Cycle 3 Error 99.416729 Scale 0.250000
  > Cycle 4 Error 98.418564 Scale 0.125000
  > Cycle 5 Error 98.357160 Scale 0.062500
  369,373c339,343
  < Cycle 1 Error 97.968412 Scale 1.000000
  < Cycle 2 Error 97.507098 Scale 0.500000
  < Cycle 3 Error 97.494582 Scale 0.250000
  < Cycle 4 Error 97.494582 Scale 0.125000
  < Cycle 5 Error 97.167483 Scale 0.500000
  ---
  > Cycle 1 Error 98.328484 Scale 1.000000
  > Cycle 2 Error 97.891931 Scale 0.500000
  > Cycle 3 Error 97.885781 Scale 0.250000
  > Cycle 4 Error 97.493976 Scale 0.125000
  > Cycle 5 Error 97.476106 Scale 0.062500
  375,379c345,349
  < Cycle 1 Error 97.138867 Scale 1.000000
  < Cycle 2 Error 97.044464 Scale 0.500000
  < Cycle 3 Error 97.035700 Scale 0.250000
  < Cycle 4 Error 97.023483 Scale 0.125000
  < Cycle 5 Error 97.021590 Scale 0.062500
  ---
  > Cycle 1 Error 97.472655 Scale 1.000000
  > Cycle 2 Error 97.334270 Scale 0.500000
  > Cycle 3 Error 97.327172 Scale 0.250000
  > Cycle 4 Error 97.310690 Scale 0.125000
  > Cycle 5 Error 97.310470 Scale 0.062500
  381d350
  < > krigingObject = spatialPredict(krigingObject)
  384c353
  < Defaulting to GAUSSIAN with variance 0.000346
  ---
  > Defaulting to GAUSSIAN with variance 0.000302
  700,701c669,670
  < Range (P0) :853.720174
  < Variance (P1) :1.070283
  ---
  > Range (P0) :844.492802
  > Variance (P1) :1.111596
  704,705c673,674
  < Length scale (P0) :1306.631925
  < Variance (P1) :0.881520
  ---
  > Length scale (P0) :1752.485475
  > Variance (P1) :0.793301
  708,742c677
  < Amplitude (P0) :0.023702
  < > krigingObject = postProcess(krigingObject)
  < Warning message:
  < In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  < there is no package called 'rgdal'
  < >
  < > # Send predictions back to Java. Not sure how to deal with this spatial object though...?
  < > summary(krigingObject$outputTable)
  < x y mean variance
  < Min. :179019 Min. :330013 Min. :4.764 Min. :0.03598
  < 1st Qu.:179485 1st Qu.:330829 1st Qu.:5.308 1st Qu.:0.07071
  < Median :180183 Median :331644 Median :5.847 Median :0.25432
  < Mean :180183 Mean :331644 Mean :6.257 Mean :0.48081
  < 3rd Qu.:180882 3rd Qu.:332459 3rd Qu.:7.478 3rd Qu.:0.69749
  < Max. :181348 Max. :333275 Max. :8.178 Max. :1.91187
  < excprob5.9 cumdistr5.9 quantile0.1
  < Min. :0.0000083 Min. :0.00000 Min. :3.999
  < 1st Qu.:0.0549936 1st Qu.:0.01972 1st Qu.:4.638
  < Median :0.4629035 Median :0.53710 Median :5.227
  < Mean :0.5165047 Mean :0.48350 Mean :5.491
  < 3rd Qu.:0.9802820 3rd Qu.:0.94501 3rd Qu.:6.480
  < Max. :1.0000000 Max. :0.99999 Max. :7.298
  < > summary(krigingObject$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)
  ---
  > Amplitude (P0) :0.022145
  744,764d678
  < 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
  ‘/data/blackswan/ripley/R/packages/tests-devel/psgp.Rcheck/00check.log’
  for details.