@@ -157,12 +157,12 @@ Documentation for these helper functions will be available in the

 devel version of this package.

 <<constructContainer, eval=FALSE>>=

-path <- system.file("scripts", package="crlmm")

-source(file.path(path, "helperFunctions.R"))

-fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

+##path <- system.file("scripts", package="crlmm")

+##source(file.path(path, "helperFunctions.R"))

+fD <- crlmm:::constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

 new.order <- order(fD$chromosome, fD$position)

 fD <- fD[new.order, ]

-aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

+aD <- crlmm:::constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

 protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))

 container <- new("CNSetLM",

 		 assayData=aD,

@@ -174,12 +174,12 @@ container <- new("CNSetLM",

 <<container2,echo=FALSE>>=

 if(!file.exists(file.path(outdir, "cnSet"))){

-	path <- system.file("scripts", package="crlmm")

-	source(file.path(path, "helperFunctions.R"))

-	fD <- constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

+	##path <- system.file("scripts", package="crlmm")

+	##source(file.path(path, "helperFunctions.R"))

+	fD <- crlmm:::constructFeatureData(c(res$gns, cnAB$gns), cdfName="human370v1c")

 	new.order <- order(fD$chromosome, fD$position)

 	fD <- fD[new.order, ]

-	aD <- constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

+	aD <- crlmm:::constructAssayData(cnAB, res, crlmmResult, order.index=new.order)

 	protocolData(crlmmResult)$batch <- vector("integer", ncol(crlmmResult))

 	container <- new("CNSetLM",

 			 assayData=aD,