R Development Page

BIOMOD log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2012-09-12-12-07/RF_PKG_CHECK/PKGS/BIOMOD.Rcheck'
* using R version 2.15.1 Patched (2012-09-10 r60659)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'BIOMOD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BIOMOD' version '1.1-7.04'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Wilfried Thuiller '
New submission
* 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 hidden files and directories ... OK
* checking whether package 'BIOMOD' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
* checking package directory ... OK
* checking for portable file names ... WARNING
Found the following file(s) with non-portable file names:
  inst/doc/BIOMOD-R User Functions.R
  inst/doc/Biomod Manual.pdf
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
  'Biomod Manual.pdf'
Please remove or rename the files.
See section 'Package subdirectories' in the 'Writing R Extensions'
manual.
* 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 ... WARNING
'::' or ':::' import not declared from: 'raster'
'library' or 'require' calls not declared from:
  'maptools' 'raster' 'rgdal' 'sp'
package 'methods' is used but not declared
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Biomod.Models: warning in gbm(eval(parse(text = paste(SpNames[i],
  paste(.scopeExpSyst(Biomod.material$VarNames,
  Biomod.material$VarTypes, "GBM"), collapse = "")))), data =
  DataBIOMOD[calib.lines, ], distribution = "bernoulli", var.monotone =
  rep(0, length = NbVar), w = RunWeights[calib.lines],
  interaction.depth = 7, shrinkage = 0.001, bag.fraction = 0.5,
  train.fraction = 1, n.trees = No.trees, verbose = FALSE, cv.folds =
  5): partial argument match of 'w' to 'weights'
Ensemble.Forecasting: warning in matrix(NA, nr = nbrep * NbPA, nc = 9,
  dimnames = list(rep("rep", nbrep * NbPA), Biomod.material$algo)):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting: warning in matrix(NA, nr = nbrep * NbPA, nc = 9,
  dimnames = list(rep("rep", nbrep * NbPA), Biomod.material$algo)):
  partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting: warning in matrix(NA, nr = nbrep * NbPA, nc = 1,
  dimnames = list(rep("rep", nbrep * NbPA), "model.selected")): partial
  argument match of 'nr' to 'nrow'
Ensemble.Forecasting: warning in matrix(NA, nr = nbrep * NbPA, nc = 1,
  dimnames = list(rep("rep", nbrep * NbPA), "model.selected")): partial
  argument match of 'nc' to 'ncol'
Ensemble.Forecasting: warning in matrix(NA, nr = 6, nc = nbrep * NbPA,
  dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), rep("rep", nbrep * NbPA))):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting: warning in matrix(NA, nr = 6, nc = nbrep * NbPA,
  dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), rep("rep", nbrep * NbPA))):
  partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting: warning in matrix(nc = nbrep * NbPA, nr = 6,
  dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), dimnames(ARRAY)[[2]])):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting: warning in matrix(nc = nbrep * NbPA, nr = 6,
  dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), dimnames(ARRAY)[[2]])):
  partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = nbrep * NbPA,
  nc = 9, dimnames = list(rep("rep", nbrep * NbPA),
  Biomod.material$algo)): partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = nbrep * NbPA,
  nc = 9, dimnames = list(rep("rep", nbrep * NbPA),
  Biomod.material$algo)): partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = nbrep * NbPA,
  nc = 1, dimnames = list(rep("rep", nbrep * NbPA), "model.selected")):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = nbrep * NbPA,
  nc = 1, dimnames = list(rep("rep", nbrep * NbPA), "model.selected")):
  partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = 6, nc = nbrep *
  NbPA, dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), rep("rep", nbrep * NbPA))):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting.raster: warning in matrix(NA, nr = 6, nc = nbrep *
  NbPA, dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), rep("rep", nbrep * NbPA))):
  partial argument match of 'nc' to 'ncol'
Ensemble.Forecasting.raster: warning in matrix(nc = nbrep * NbPA, nr =
  6, dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), dimnames(ARRAY)[[2]])):
  partial argument match of 'nr' to 'nrow'
Ensemble.Forecasting.raster: warning in matrix(nc = nbrep * NbPA, nr =
  6, dimnames = list(c("prob.mean", "prob.mean.weighted", "median",
  "Roc.mean", "Kappa.mean", "TSS.mean"), dimnames(ARRAY)[[2]])):
  partial argument match of 'nc' to 'ncol'
Models: warning in matrix(NA, nc = Biomod.material$NbSpecies, nr =
  nrow(DataBIOMOD)): partial argument match of 'nr' to 'nrow'
Models: warning in matrix(NA, nc = Biomod.material$NbSpecies, nr =
  nrow(DataBIOMOD)): partial argument match of 'nc' to 'ncol'
ProbDensFunc: warning in matrix(c(low50, low75, low90, low95, high50,
  high75, high90, high95), nc = 2, nr = 4, dimnames = list(c("50%",
  "75%", "90%", "95%"), c("lower limit", "upper limit"))): partial
  argument match of 'nr' to 'nrow'
ProbDensFunc: warning in matrix(c(low50, low75, low90, low95, high50,
  high75, high90, high95), nc = 2, nr = 4, dimnames = list(c("50%",
  "75%", "90%", "95%"), c("lower limit", "upper limit"))): partial
  argument match of 'nc' to 'ncol'
level.plot: warning in matrix(c(1, 2), nr = 1): partial argument match
  of 'nr' to 'nrow'
.Biomod.Models: no visible binding for global variable 'DataBIOMOD'
.Biomod.Models: no visible binding for global variable 'i'
.Biomod.Models: no visible binding for global variable
  'Biomod.material'
.Biomod.Models: no visible binding for global variable 'pa'
.Biomod.Models: no visible binding for global variable 'DataEvalBIOMOD'
.CV.nnet : : no visible binding for global variable
  'Biomod.material'
.Rescaler4: no visible global function definition for 'layerNames<-'
.check.Ensemble.Forecasting.raster: no visible binding for global
  variable 'Biomod.material'
.check.Ensemble.Forecasting.raster: no visible global function
  definition for 'canProcessInMemory'
.check.Ensemble.Forecasting.raster: no visible binding for global
  variable 'Evaluation.results.Roc'
.check.Ensemble.Forecasting.raster: no visible binding for global
  variable 'Evaluation.results.Kappa'
.check.Ensemble.Forecasting.raster: no visible binding for global
  variable 'Evaluation.results.TSS'
.check.params.sre: no visible global function definition for 'nlayers'
.check.params.sre: no visible global function definition for
  'layerNames'
.somers2: no visible global function definition for 'wtd.mean'
.somers2: no visible global function definition for 'wtd.rank'
.sre.projection: no visible global function definition for 'reclassify'
.sre.projection: no visible global function definition for 'nlayers'
Biomod.RangeSize.raster: no visible global function definition for
  'layerNames'
Biomod.RangeSize.raster: no visible global function definition for
  'addLayer'
Biomod.Turnover.raster: no visible global function definition for
  'layerNames<-'
CreateProjMatrix: no visible binding for global variable
  'Biomod.material'
CurrentPred: no visible binding for global variable 'Biomod.material'
CurrentPred: no visible binding for global variable
  'Evaluation.results.Roc'
CurrentPred: no visible binding for global variable
  'Evaluation.results.Kappa'
CurrentPred: no visible binding for global variable
  'Evaluation.results.TSS'
Ensemble.Forecasting: no visible binding for global variable
  'Biomod.material'
Ensemble.Forecasting: no visible binding for global variable
  'Biomod.PA.sample'
Ensemble.Forecasting: no visible binding for global variable
  'DataBIOMOD'
Ensemble.Forecasting.raster: no visible binding for global variable
  'Biomod.material'
Ensemble.Forecasting.raster: no visible global function definition for
  'addLayer'
Ensemble.Forecasting.raster: no visible global function definition for
  'dropLayer'
Ensemble.Forecasting.raster: no visible global function definition for
  'calc'
Ensemble.Forecasting.raster: no visible global function definition for
  'layerNames'
Ensemble.Forecasting.raster: no visible global function definition for
  'layerNames<-'
Ensemble.Forecasting.raster: no visible binding for global variable
  'ARRAY'
Ensemble.Forecasting.raster: no visible binding for global variable
  'Biomod.PA.sample'
Ensemble.Forecasting.raster: no visible binding for global variable
  'DataBIOMOD'
Ensemble.Forecasting.raster2: no visible binding for global variable
  'Biomod.material'
Ensemble.Forecasting.raster2: no visible binding for global variable
  'Evaluation.results.Roc'
Ensemble.Forecasting.raster2: no visible binding for global variable
  'Evaluation.results.TSS'
Ensemble.Forecasting.raster2: no visible binding for global variable
  'Evaluation.results.Kappa'
Ensemble.Forecasting.raster2: no visible global function definition for
  'layerNames<-'
Ensemble.Forecasting.raster2: no visible global function definition for
  'layerNames'
Ensemble.Forecasting.raster2: no visible global function definition for
  'calc'
Initial.State: no visible binding for global variable 'DataBIOMOD'
LoadModels: no visible binding for global variable 'Biomod.material'
LoadProj: no visible binding for global variable 'Biomod.material'
Models: no visible binding for global variable 'DataBIOMOD'
Models: no visible binding for global variable 'Biomod.PA.data'
Models: no visible binding for global variable 'isnullYweights'
Models: no visible binding for global variable 'DataEvalBIOMOD'
Models: no visible binding for global variable 'predind'
Models: no visible binding for global variable 'GBM.list'
Models: no visible binding for global variable 'Array'
Models: no visible binding for global variable 'calib.lines'
PredictionBestModel: no visible binding for global variable
  'Biomod.material'
PredictionBestModel: no visible binding for global variable
  'DataBIOMOD'
ProbDensFunc: no visible binding for global variable 'low50'
ProbDensFunc: no visible binding for global variable 'low75'
ProbDensFunc: no visible binding for global variable 'low90'
ProbDensFunc: no visible binding for global variable 'low95'
ProbDensFunc: no visible binding for global variable 'high50'
ProbDensFunc: no visible binding for global variable 'high75'
ProbDensFunc: no visible binding for global variable 'high90'
ProbDensFunc: no visible binding for global variable 'high95'
Projection: no visible binding for global variable 'DataBIOMOD'
Projection: no visible binding for global variable 'GBM.perf'
Projection: no visible binding for global variable
  'Evaluation.results.Roc'
Projection: no visible binding for global variable
  'Evaluation.results.Kappa'
Projection: no visible binding for global variable
  'Evaluation.results.TSS'
Projection.raster: no visible global function definition for
  'layerNames'
Projection.raster: no visible binding for global variable 'GBM.perf'
Projection.raster: no visible binding for global variable 'DataBIOMOD'
Projection.raster: no visible global function definition for 'addLayer'
Projection.raster: no visible binding for global variable
  'Evaluation.results.Roc'
Projection.raster: no visible binding for global variable
  'Evaluation.results.Kappa'
Projection.raster: no visible binding for global variable
  'Evaluation.results.TSS'
Projection.raster: no visible global function definition for
  'layerNames<-'
ProjectionBestModel: no visible binding for global variable
  'Biomod.material'
level.plot: no visible binding for global variable 'legendcex'
multiple.plot: no visible binding for global variable 'legendcex'
multiple.plot: no visible binding for global variable 'multiple'
response.plot: no visible global function definition for 'nlayers'
response.plot: no visible global function definition for 'layerNames'
response.plot: no visible global function definition for 'maxValue'
response.plot: no visible global function definition for 'minValue'
sre: no visible global function definition for 'nlayers'
sre: no visible global function definition for 'layerNames'
sre: no visible global function definition for 'mask'
sre: no visible global function definition for 'layerNames<-'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'Ensemble.Forecasting.raster2' 'printcp'
Undocumented data sets:
  'Curr' 'storeC' 'storeF'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'BinaryTransformation':
BinaryTransformation
  Code: function(data, threshold)
  Docs: function(ProbData, CutOffdata)
  Argument names in code not in docs:
    data threshold
  Argument names in docs not in code:
    ProbData CutOffdata
  Mismatches in argument names:
    Position: 1 Code: data Docs: ProbData
    Position: 2 Code: threshold Docs: CutOffdata

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'Biomod.Manual':
  Biomod.Manual(manual="Biomod_Manual"))

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... WARNING
  'gs+qpdf' made some significant size reductions:
     compacted 'BiomodTutorial.pdf' from 3.0Mb to 2.0Mb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 7 warnings.
NOTE: There were 3 notes.
See
  'R:/run/building/build_2012-09-12-12-07/RF_PKG_CHECK/PKGS/BIOMOD.Rcheck/00check.log'
for details.

Run time: 106.66 seconds.