@@ -241,4 +241,14 @@ is decoded and scanned

 * fixed malformed DESCRIPTION file

+2009-07-31 B Carvalho - committed version 1.3.16

+* Removed several warnings at the C-level

+

+* Fixed several incorrect links in the documentation

+

+* Removed multiple notes "no visible binding for global variable"

+  by replacing, in crlmmIlluminaWrapper and crlmmWrapper,

+  a) samplesheet5 by get("samplesheet5")

+  b) path by get("path")

+  c) res by get("res")

@@ -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: 1.3.15

+Version: 1.3.16

 Date: 2009-07-22

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

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

@@ -220,21 +220,26 @@ crlmmIlluminaWrapper <- function(sampleSheet, outdir="./", cdfName,

 				 splitByChr=TRUE,...){

 	if(file.exists(file.path(outdir, "RG.rda"))) load(file.path(outdir, "RG.rda"))

 	else {

-		RG <- readIdatFiles(sampleSheet=samplesheet5, arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), saveDate=TRUE,

-				    path=path)

+		RG <- readIdatFiles(sampleSheet=get("samplesheet5"),

+                                    arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"),

+                                    saveDate=TRUE, path=get("path"))

 		J <- match(c("1_A", "3_A", "5_A", "7_A"), sampleNames(RG))

 		RG <- RG[, -J]

 		if(save.intermediate) save(RG, file=file.path(outdir, "RG.rda"))  ##935M for 91 samples...better not to save this

 	}	

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

-		crlmmOut <- crlmmIllumina(RG=RG, cdfName=cdfName, sns=pData(RG)$ID, returnParams=TRUE, save.it=TRUE, intensityFile=file.path(outdir, "res.rda"))

+		crlmmOut <- crlmmIllumina(RG=RG, cdfName=cdfName,

+                                          sns=pData(RG)$ID,

+                                          returnParams=TRUE,

+                                          save.it=TRUE,

+                                          intensityFile=file.path(outdir, "res.rda"))

 		if(save.intermediate) save(crlmmOut, file=file.path(outdir, "crlmmOut.rda"))				

 	} else{

 		message("Loading...")		

 		load(file.path(outdir, "res.rda"))

 		load(file.path(outdir, "crlmmOut.rda"))		

 	}

-	ABset <- combineIntensities(res, NULL, cdfName=cdfName)

+	ABset <- combineIntensities(get("res"), NULL, cdfName=cdfName)

 	protocolData(ABset)[["ScanDate"]] <- as.character(pData(RG)$ScanDate)

 	crlmmResult <- harmonizeSnpSet(crlmmOut, ABset)

 	stopifnot(all.equal(dimnames(crlmmOut), dimnames(ABset)))

@@ -273,7 +278,7 @@ crlmmWrapper <- function(filenames, outdir="./", cdfName="genomewidesnp6",

 		load(file.path(outdir, "cnrmaResult.rda"))

 	}

 	load(file.path(outdir, "intensities.rda"))

-	ABset <- combineIntensities(res, cnrmaResult, cdfName)

+	ABset <- combineIntensities(get("res"), cnrmaResult, cdfName)

 	protocolData(ABset)[["ScanDate"]] <- as.character(celDates(filenames))	

 	crlmmResult <- harmonizeSnpSet(crlmmResult, ABset)

 	stopifnot(all.equal(dimnames(crlmmResult), dimnames(ABset)))

@@ -23,9 +23,9 @@ Objects can be created by calls of the form \code{new("ABset", assayData, phenoD

   }

 }

 \section{Extends}{

-Class \code{"\linkS4class{eSet}"}, directly.

-Class \code{"\linkS4class{VersionedBiobase}"}, by class "eSet", distance 2.

-Class \code{"\linkS4class{Versioned}"}, by class "eSet", distance 3.

+Class \code{\link[Biobase:class.eSet]{eSet}}, directly.

+Class \code{\link[Biobase:class.VersionedBiobase]{VersionedBiobase}}, by class "eSet", distance 2.

+Class \code{\link[Biobase:class.Versioned]{Versioned}}, by class "eSet", distance 3.

 }

 \section{Methods}{

   \describe{

@@ -34,9 +34,9 @@ Objects can be created by calls of the form \code{new("CopyNumberSet", assayData

   }

 }

 \section{Extends}{

-Class \code{"\linkS4class{eSet}"}, directly.

-Class \code{"\linkS4class{VersionedBiobase}"}, by class "eSet", distance 2.

-Class \code{"\linkS4class{Versioned}"}, by class "eSet", distance 3.

+Class \code{\link[Biobase:class.eSet]{eSet}}, directly.

+Class \code{\link[Biobase:class.VersionedBiobase]{VersionedBiobase}}, by class "eSet", distance 2.

+Class \code{\link[Biobase:class.Versioned]{Versioned}}, by class "eSet", distance 3.

 }

 \section{Methods}{

   \describe{

@@ -63,7 +63,7 @@

 \section{Extends}{

   Class \code{"\linkS4class{list}"}, from data part.

   Class \code{"\linkS4class{vector}"}, by class "list", distance 2.

-  Class \code{"\linkS4class{AssayData}"}, by class "list", distance 2.

+  Class \code{\link[Biobase:class.assayData]{assayData}}, by class "list", distance 2.

 }

 \section{Methods}{

   \describe{

@@ -47,7 +47,7 @@ computeCopynumber(object, CHR, bias.adj=FALSE, batch, SNRmin=5, cdfName="genomew

 }

 \seealso{

-  \code{\linkS4class{CopyNumberSet}},   \code{\link{".computeCopynumber"}}

+  \code{\linkS4class{CopyNumberSet}},   \code{.computeCopynumber}

 }

 \author{Rob Scharpf}

 \keyword{manip}

@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   //const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;

+  int intbuffer, ibv1[colsAB], ib2;

   double buffer;

   // All pointers appear here

@@ -303,11 +303,8 @@ SEXP gtypeCallerPart2(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   colsAB = INTEGER(getAttrib(A, R_DimSymbol))[1];

   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];

-  // Constants

-  const int lenLists=3;

-

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

   double buffer;

   ib2 = GET_LENGTH(noTraining);

@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1nm(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   //const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;

+  int intbuffer, ibv1[colsAB], ib2;

   double buffer;

   // All pointers appear here

@@ -304,10 +304,10 @@ SEXP gtypeCallerPart2nm(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];

   // Constants

-  const int lenLists=3;

+  // const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

   double buffer;

   ib2 = GET_LENGTH(noTraining);

@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1NormalNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   //const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;

+  int intbuffer, ibv1[colsAB], ib2;

   double buffer;

   // All pointers appear here

@@ -286,10 +286,10 @@ SEXP gtypeCallerPart2NormalNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];

   // Constants

-  const int lenLists=3;

+  // const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

   double buffer;

   ib2 = GET_LENGTH(noTraining);

@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1TNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   //const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;

+  int intbuffer, ibv1[colsAB], ib2;

   double buffer;

   // All pointers appear here

@@ -286,10 +286,10 @@ SEXP gtypeCallerPart2TNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,

   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];

   // Constants

-  const int lenLists=3;

+  // const int lenLists=3;

   // Buffers

-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;

   double buffer;

   ib2 = GET_LENGTH(noTraining);