- using R version 2.14.2 RC (2012-02-23 r58468)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘psgp/DESCRIPTION’ ... OK
- this is package ‘psgp’ version ‘0.3-0’
- 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 ... OK
- 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 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 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 $(LAPACK_LIBS) ... OK
- checking compiled code ... NOTE
File ‘/home/hornik/tmp/R.check/r-patched/Work/build/Packages/psgp/libs/psgp.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking examples ... OK
- checking for unstated dependencies in tests ... OK
- checking tests ... OK
Running ‘meuse_psgp.R’
Comparing ‘meuse_psgp.Rout’ to ‘meuse_psgp.Rout.save’ ...1,42d0
<
<
< > library(psgp)
<
< Attaching package: 'zoo'
<
< The following object(s) are masked from 'package:base':
<
< as.Date, as.Date.numeric
<
< Geospatial Data Abstraction Library extensions to R successfully loaded
< Loaded GDAL runtime: GDAL 1.7.3, released 2010/11/10
< Path to GDAL shared files: /usr/share/gdal/1.7
< Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
< Path to PROJ.4 shared files: (autodetected)
<
< Attaching package: 'lattice'
<
< The following object(s) are masked from 'package:evd':
<
< qq
<
< > set.seed(100)
< > # set up data:
< > data(meuse)
< > coordinates(meuse) = ~x+y
< > meuse$value = log(meuse$zinc)
< > data(meuse.grid)
< > gridded(meuse.grid) = ~x+y
< > proj4string(meuse) = CRS("+init=epsg:28992")
< > proj4string(meuse.grid) = CRS("+init=epsg:28992")
< >
< > # set up intamap object:
< > psgpObject = createIntamapObject(
< + observations = meuse,
< + formulaString=as.formula(value~1),
< + predictionLocations = meuse.grid,
< + class = "psgp"
< + )
< >
< > # run test:
< > checkSetup(psgpObject)
44,46d1
< >
< > # do interpolation steps:
< > psgpObject = estimateParameters(psgpObject)
396,398d350
< >
< > # make prediction
< > psgpObject = spatialPredict(psgpObject)
723c675
< Range (P0) :844.492835
---
> Range (P0) :844.492816
727c679
< Length scale (P0) :1752.485493
---
> Length scale (P0) :1752.485482
732,736d683
< >
< > # Plot prediction
< > # plotIntamap(psgpObject)
< > # plotIntamap(meuse, pch=1, cex=sqrt(meuse$value)/20, add=TRUE)
< >
Running ‘psgp.R’
Comparing ‘psgp.Rout’ to ‘psgp.Rout.save’ ...1,40d0
<
<
< > library(psgp) # requires intamap
<
< Attaching package: 'zoo'
<
< The following object(s) are masked from 'package:base':
<
< as.Date, as.Date.numeric
<
< Geospatial Data Abstraction Library extensions to R successfully loaded
< Loaded GDAL runtime: GDAL 1.7.3, released 2010/11/10
< Path to GDAL shared files: /usr/share/gdal/1.7
< Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470]
< Path to PROJ.4 shared files: (autodetected)
<
< 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)
42,43d1
< > krigingObject = preProcess(krigingObject)
< > krigingObject = estimateParameters(krigingObject)
393d350
< > krigingObject = spatialPredict(krigingObject)
712c669
< Range (P0) :844.492804
---
> Range (P0) :844.492802
721,751d677
< > krigingObject = postProcess(krigingObject)
< >
< > # Send predictions back to Java. Not sure how to deal with this spatial object though...?
< > summary(krigingObject$outputTable)
< x y mean variance
< Min. :179019 Min. :330013 Min. :4.762 Min. :0.03764
< 1st Qu.:179485 1st Qu.:330829 1st Qu.:5.314 1st Qu.:0.07613
< Median :180183 Median :331644 Median :5.874 Median :0.25617
< Mean :180183 Mean :331644 Mean :6.234 Mean :0.45727
< 3rd Qu.:180882 3rd Qu.:332459 3rd Qu.:7.409 3rd Qu.:0.64260
< Max. :181348 Max. :333275 Max. :8.013 Max. :1.81668
< excprob5.9 cumdistr5.9 quantile0.1
< Min. :0.0000153 Min. :1.622e-09 Min. :4.048
< 1st Qu.:0.0561158 1st Qu.:2.101e-02 1st Qu.:4.646
< Median :0.4837440 Median :5.163e-01 Median :5.177
< Mean :0.5164720 Mean :4.835e-01 Mean :5.478
< 3rd Qu.:0.9789940 3rd Qu.:9.439e-01 3rd Qu.:6.461
< Max. :1.0000000 Max. :1.000e+00 Max. :7.228
< > summary(krigingObject$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)
753,773d678
< 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