@@ -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: 1.9.10

+Version: 1.9.2

 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>

@@ -32,7 +32,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,

 		  "A<-", "B<-", open, close, flags,

 		  batchStatistics, "batchStatistics<-", updateObject)

 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,

-           copyNumber, initializeBigMatrix, initializeBigVector)

+           copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)

 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,

@@ -94,9 +94,6 @@ list2SnpSet <- function(x, returnParams=FALSE){

                           "Center AA", "Center AB", "Center BB",

                           "Scale AA", "Scale AB", "Scale BB",

                           "N AA", "N AB", "N BB"),

-#                          "Shift in parameters AA",

-#                          "Shift in parameters AB",

-#                          "Shift in parameters BB"),

                         row.names=c(

                           "SNPQC",

                           "cAA", "cAB", "cBB",

@@ -142,8 +139,7 @@ loader <- function(theFile, envir, pkgname){

 celDates <- function(celfiles){

 	if(!all(file.exists(celfiles))) stop("1 or more cel file does not exist")

-	celdates <- vector("character", length(celfiles))

-	celtimes <- vector("character", length(celfiles))

+	celdates <- celtimes <- vector("character", length(celfiles))

 	for(i in seq(along=celfiles)){

 		if(i %% 100 == 0) cat(".")

 		tmp <- read.celfile.header(celfiles[i], info="full")$DatHeader

@@ -172,19 +168,12 @@ validCdfNames <- function(){

           "humanimmuno12v1b")

 }

 isValidCdfName <- function(cdfName){

-	chipList <- validCdfNames()

-	result <- cdfName %in% chipList	

-	if(!(result)){

-		warning("cdfName must be one of the following: ",

-			chipList)

-	}

-	return(result)

-}

-

-isPackageLoaded <- function(pkg){

-	stopifnot(is.character(pkg))

-	pkg <- paste("package:", pkg, sep="")

-	pkg %in% search()

+    stopifnot(is.character(cdfName))

+    result <- cdfName %in% validCdfNames()

+    if (!result)

+        warning("cdfName must be one of the following: ",

+                chipList)

+    return(result)

 }

 paramNames <- function(){