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genpred log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/genpred.Rcheck'
* using R version 2.15.2 Patched (2013-01-31 r61797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'genpred/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genpred' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Nick Sabbe '
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 'genpred' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 examples ... ERROR
Running examples in 'genpred-Ex.R' failed
The error most likely occurred in:

> ### Name: doFormulaCV
> ### Title: Crossvalidate some binary classification
> ### Aliases: doFormulaCV crossPredictBinary fitAndPredictBinary.General
> ### Keywords: ~binary ~classification ~crossvalidation
> 
> ### ** Examples
> 
> #For Gbm, a custom implementation is necessary:
> fitAndPredictBinary.Gbm<-function(trainDfr, valDfr, outcol, lvls, formulaPattern=".", verbosity=0, thres=0,...)
+ {
+ 	require(gbm)
+ 	gf <- basisExpansionFormula(trainDfr, outcol, patternNumericCols=formulaPattern)
+ 	curres=gbm(formula(gf),data=trainDfr,...)
+ 	numToUse<-gbm.perf(curres,method="cv",plot.it=FALSE)
+ 	if(verbosity > 0) cat("numToUse:", numToUse, "\n")
+ 	pred<-predict(curres,newdata=valDfr,type="response",n.trees=numToUse)
+ 	return(lvls[ifelse(pred > thres, 2, 1)])
+ }
> gbmx<-function(thres=0,...){gbm(...)}
> 
> doGbm<-function(dfr, outcol, verbosity=0, thres=0,...)#,distribution="adaboost",cv.folds=5,shrinkage=1,bag.fraction=1
+ {
+ 	require(gbm)
+ 	lvls<-levels(dfr[,outcol])
+ 	dfr[,outcol]<-as.numeric(dfr[,outcol])-1
+ 	rv<-doFormulaCV(dfr, outcol, fitFunc=gbmx, fitAndPredictBinary=fitAndPredictBinary.Gbm,
+ 		verbosity=verbosity, thres=thres, ...)
+ 	rv$cv<-factor(lvls[rv$cv+1], levels=lvls)
+ 	return(rv)
+ }
> iriscopy<-iris
> iriscopy$sthing<-factor(rbinom(dim(iris)[1], 1, 0.5))
> doGbm(iriscopy, outcol="sthing",
+ 	verbosity=5,distribution="adaboost",cv.folds=10,shrinkage=1,bag.fraction=1,
+ 	verbose=FALSE)
Formula used in doFormulaCV:
 sthing ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width + Species 
Error in .Call("gbm", Y = as.double(y), Offset = as.double(offset), X = as.double(x),  : 
  "gbm" not available for .Call() for package "gbm"
Calls: doGbm ... system.time -> eval -> fitFunc -> gbm -> gbm.fit -> .Call
Timing stopped at: 0 0 0 
Execution halted
Run time: 79.91 seconds.