Browse code

Fixing several warnings and notes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40930 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/07/2009 04:51:13
Showing11 changed files

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@@ -241,4 +241,14 @@ is decoded and scanned
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 * fixed malformed DESCRIPTION file
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+2009-07-31 B Carvalho - committed version 1.3.16
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+* Removed several warnings at the C-level
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+
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+* Fixed several incorrect links in the documentation
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+
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+* Removed multiple notes "no visible binding for global variable"
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+  by replacing, in crlmmIlluminaWrapper and crlmmWrapper,
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+  a) samplesheet5 by get("samplesheet5")
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+  b) path by get("path")
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+  c) res by get("res")
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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.3.15
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+Version: 1.3.16
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 Date: 2009-07-22
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 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -220,21 +220,26 @@ crlmmIlluminaWrapper <- function(sampleSheet, outdir="./", cdfName,
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 				 splitByChr=TRUE,...){
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 	if(file.exists(file.path(outdir, "RG.rda"))) load(file.path(outdir, "RG.rda"))
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 	else {
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-		RG <- readIdatFiles(sampleSheet=samplesheet5, arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"), saveDate=TRUE,
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-				    path=path)
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+		RG <- readIdatFiles(sampleSheet=get("samplesheet5"),
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+                                    arrayInfoColNames=list(barcode=NULL, position="SentrixPosition"),
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+                                    saveDate=TRUE, path=get("path"))
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 		J <- match(c("1_A", "3_A", "5_A", "7_A"), sampleNames(RG))
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 		RG <- RG[, -J]
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 		if(save.intermediate) save(RG, file=file.path(outdir, "RG.rda"))  ##935M for 91 samples...better not to save this
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 	}	
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 	if(!file.exists(file.path(outdir, "res.rda"))){
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-		crlmmOut <- crlmmIllumina(RG=RG, cdfName=cdfName, sns=pData(RG)$ID, returnParams=TRUE, save.it=TRUE, intensityFile=file.path(outdir, "res.rda"))
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+		crlmmOut <- crlmmIllumina(RG=RG, cdfName=cdfName,
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+                                          sns=pData(RG)$ID,
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+                                          returnParams=TRUE,
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+                                          save.it=TRUE,
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+                                          intensityFile=file.path(outdir, "res.rda"))
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 		if(save.intermediate) save(crlmmOut, file=file.path(outdir, "crlmmOut.rda"))				
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 	} else{
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 		message("Loading...")		
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 		load(file.path(outdir, "res.rda"))
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 		load(file.path(outdir, "crlmmOut.rda"))		
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 	}
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-	ABset <- combineIntensities(res, NULL, cdfName=cdfName)
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+	ABset <- combineIntensities(get("res"), NULL, cdfName=cdfName)
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 	protocolData(ABset)[["ScanDate"]] <- as.character(pData(RG)$ScanDate)
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 	crlmmResult <- harmonizeSnpSet(crlmmOut, ABset)
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 	stopifnot(all.equal(dimnames(crlmmOut), dimnames(ABset)))
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@@ -273,7 +278,7 @@ crlmmWrapper <- function(filenames, outdir="./", cdfName="genomewidesnp6",
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 		load(file.path(outdir, "cnrmaResult.rda"))
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 	}
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 	load(file.path(outdir, "intensities.rda"))
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-	ABset <- combineIntensities(res, cnrmaResult, cdfName)
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+	ABset <- combineIntensities(get("res"), cnrmaResult, cdfName)
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 	protocolData(ABset)[["ScanDate"]] <- as.character(celDates(filenames))	
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 	crlmmResult <- harmonizeSnpSet(crlmmResult, ABset)
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 	stopifnot(all.equal(dimnames(crlmmResult), dimnames(ABset)))
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@@ -23,9 +23,9 @@ Objects can be created by calls of the form \code{new("ABset", assayData, phenoD
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   }
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 }
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 \section{Extends}{
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-Class \code{"\linkS4class{eSet}"}, directly.
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-Class \code{"\linkS4class{VersionedBiobase}"}, by class "eSet", distance 2.
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-Class \code{"\linkS4class{Versioned}"}, by class "eSet", distance 3.
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+Class \code{\link[Biobase:class.eSet]{eSet}}, directly.
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+Class \code{\link[Biobase:class.VersionedBiobase]{VersionedBiobase}}, by class "eSet", distance 2.
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+Class \code{\link[Biobase:class.Versioned]{Versioned}}, by class "eSet", distance 3.
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 }
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 \section{Methods}{
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   \describe{
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@@ -34,9 +34,9 @@ Objects can be created by calls of the form \code{new("CopyNumberSet", assayData
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   }
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 }
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 \section{Extends}{
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-Class \code{"\linkS4class{eSet}"}, directly.
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-Class \code{"\linkS4class{VersionedBiobase}"}, by class "eSet", distance 2.
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-Class \code{"\linkS4class{Versioned}"}, by class "eSet", distance 3.
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+Class \code{\link[Biobase:class.eSet]{eSet}}, directly.
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+Class \code{\link[Biobase:class.VersionedBiobase]{VersionedBiobase}}, by class "eSet", distance 2.
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+Class \code{\link[Biobase:class.Versioned]{Versioned}}, by class "eSet", distance 3.
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 }
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 \section{Methods}{
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   \describe{
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@@ -63,7 +63,7 @@
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 \section{Extends}{
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   Class \code{"\linkS4class{list}"}, from data part.
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   Class \code{"\linkS4class{vector}"}, by class "list", distance 2.
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-  Class \code{"\linkS4class{AssayData}"}, by class "list", distance 2.
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+  Class \code{\link[Biobase:class.assayData]{assayData}}, by class "list", distance 2.
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 }
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 \section{Methods}{
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   \describe{
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@@ -47,7 +47,7 @@ computeCopynumber(object, CHR, bias.adj=FALSE, batch, SNRmin=5, cdfName="genomew
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 }
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 \seealso{
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-  \code{\linkS4class{CopyNumberSet}},   \code{\link{".computeCopynumber"}}
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+  \code{\linkS4class{CopyNumberSet}},   \code{.computeCopynumber}
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 }
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 \author{Rob Scharpf}
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 \keyword{manip}
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@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   //const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;
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+  int intbuffer, ibv1[colsAB], ib2;
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   double buffer;
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   // All pointers appear here
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@@ -303,11 +303,8 @@ SEXP gtypeCallerPart2(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   colsAB = INTEGER(getAttrib(A, R_DimSymbol))[1];
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   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];
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-  // Constants
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-  const int lenLists=3;
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-
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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   double buffer;
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   ib2 = GET_LENGTH(noTraining);
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@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1nm(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   //const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;
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+  int intbuffer, ibv1[colsAB], ib2;
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   double buffer;
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   // All pointers appear here
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@@ -304,10 +304,10 @@ SEXP gtypeCallerPart2nm(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];
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   // Constants
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-  const int lenLists=3;
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+  // const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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   double buffer;
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   ib2 = GET_LENGTH(noTraining);
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@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1NormalNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   //const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;
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+  int intbuffer, ibv1[colsAB], ib2;
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   double buffer;
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   // All pointers appear here
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@@ -286,10 +286,10 @@ SEXP gtypeCallerPart2NormalNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];
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   // Constants
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-  const int lenLists=3;
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+  // const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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   double buffer;
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   ib2 = GET_LENGTH(noTraining);
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@@ -84,7 +84,7 @@ SEXP gtypeCallerPart1TNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   //const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2;
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+  int intbuffer, ibv1[colsAB], ib2;
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   double buffer;
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   // All pointers appear here
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@@ -286,10 +286,10 @@ SEXP gtypeCallerPart2TNoN(SEXP A, SEXP B, SEXP fIndex, SEXP mIndex,
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   double likelihood[colsAB*3], M[colsAB], S[colsAB], f[colsAB];
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   // Constants
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-  const int lenLists=3;
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+  // const int lenLists=3;
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   // Buffers
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-  int intbuffer, ibv1[colsAB], ibv2[colsAB], ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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+  int intbuffer, ib2, ib3, ibSnpLevel1=0, ibSnpLevel2=0;
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   double buffer;
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   ib2 = GET_LENGTH(noTraining);