@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.13.11

+Version: 1.13.12

 Date: 2010-12-10

 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -10,7 +10,7 @@ License: Artistic-2.0

 Depends: R (>= 2.13.0),

          methods,

          Biobase (>= 2.15.0),

-         oligoClasses (>= 1.17.29)

+         oligoClasses (>= 1.17.34)

 Imports: affyio (>= 1.19.2),

          ellipse,

          genefilter (>= 1.33.0),

@@ -75,4 +75,4 @@ export(crlmm,

        genotype.Illumina,

        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)

 export(genotypes, totalCopynumber, rawCopynumber, xyplot)

-export(ABpanel, constructInf, preprocessInf, genotypeInf, validCEL, celDates)

+export(ABpanel, validCEL, celDates)

@@ -1541,7 +1541,7 @@ shrinkSummary <- function(object,

 	}

 	if(is.lds){

 		##index.list <- splitIndicesByLength(marker.index, ocProbesets())

-		if(!is.null(getCluster()) & isPackageLoaded("snow")){

+		if(parStatus()){

 			index.list <- splitIndicesByNode(marker.index)

 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())

 		ocLapply(seq(along=index.list),

@@ -1595,7 +1595,7 @@ genotypeSummary <- function(object,

 	FUN <- get(myf)

 	if(is.lds){

 		##index.list <- splitIndicesByLength(marker.index, ocProbesets())

-		if(!is.null(getCluster()) & isPackageLoaded("snow")){

+		if(parStatus()){

 			index.list <- splitIndicesByNode(marker.index)

 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())

 		ocLapply(seq(along=index.list),

@@ -2116,7 +2116,7 @@ estimateCnParameters <- function(object,

 	myfun <- lmFxn(type[[1]])

 	FUN <- get(myfun)

 	if(is.lds){

-		if(!is.null(getCluster()) & isPackageLoaded("snow")){

+		if(parStatus()){

 			index.list <- splitIndicesByNode(marker.index)

 		} else index.list <- splitIndicesByLength(marker.index, ocProbesets())

 		ocLapply(seq(along=index.list),

@@ -1267,7 +1267,7 @@ preprocessInf <- function(cnSet,

 	sampleBatches <- splitIndicesByNode(seq(length=ncol(cnSet)))

 	mixtureParams = initializeBigMatrix("crlmmMixt-", 4, narrays, "double")

 	ocLapply(seq_along(sampleBatches),

-		 processIDAT,

+		 crlmm:::processIDAT,

 		 sampleBatches=sampleBatches,

 		 sampleSheet=sampleSheet,

 		 arrayNames=arrayNames,

@@ -99,7 +99,8 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

 				   mIndex=mIndex, params=params,

 				   cIndexes=cIndexes, SMEDIAN=SMEDIAN,

 				   theKnots=theKnots, DF=DF, probs=probs,

-				   batchSize=ocProbesets())

+				   batchSize=ocProbesets(),

+				   neededPkgs="crlmm")

 	newparams <- vector("list", 3)

 	names(newparams) <- c("centers", "scales", "N")

 	newparams[["centers"]] <- do.call("rbind", lapply(newparamsBatch, "[[", 1))

@@ -227,7 +228,8 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL,

 		 A=A, B=B, mixtureParams=mixtureParams, fIndex=fIndex,

 		 mIndex=mIndex, params=params, cIndexes=cIndexes,

 		 SMEDIAN=SMEDIAN, theKnots=theKnots, DF=DF, probs=probs,

-		 regionInfo=regionInfo, batchSize=ocProbesets())

+		 regionInfo=regionInfo, batchSize=ocProbesets(),

+		 neededPkgs="crlmm")

 	##  END MOVE TO C#######

 	## ##################

 	##

@@ -60,6 +60,7 @@ calls.

 <<ldpath,results=hide>>=

 library(ff)

+options(ffcaching="ffeachflush")

 outdir <- paste("/local_data/r00/crlmm/", getRversion(), "/illumina_vignette", sep="")

 ldPath(outdir)

 dir.create(outdir, recursive=TRUE, showWarnings=FALSE)

@@ -102,7 +102,10 @@ library(crlmm)

 ## genotype 50K SNPs at a time

 ocProbesets(50000)

 ## setup cluster - 8 cores on the machine

-setCluster(8, "SOCK")

+library(doSNOW)

+cl <- makeCluster(8, "SOCK")

+registerDoSNOW(cl)

+##setCluster(8, "SOCK")

 path <- system.file("celFiles", package="hapmapsnp6")

 cels <- list.celfiles(path, full.names=TRUE)

@@ -129,8 +129,10 @@ example below indicates.}

 	## to enable paralellization, set to TRUE

 	if(FALSE){

 		library(snow)

-		## 10 workers

-		setCluster(10, "SOCK")

+		library(doSNOW)

+		## with 10 workers

+		cl <- makeCluster(10, type="SOCK")

+		registerDoSNOW(cl)

 	}

 	## path to idat files

 	datadir <- "/thumper/ctsa/snpmicroarray/illumina/IDATS/370k"