Package: arrayMagic

Version: 1.11.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check arrayMagic_1.11.0.tar.gz

RetCode: 1

Time: 226.3 seconds

Status: ERROR

CheckDir: arrayMagic.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/arrayMagic.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-07-18 r38641)
* checking for file 'arrayMagic/DESCRIPTION' ... OK
* this is package 'arrayMagic' version '1.11.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'arrayMagic' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating arrayMagic-Ex.R ... OK
* checking examples ... ERROR
Running examples in arrayMagic-Ex.R failed.
The error most likely occurred in:

> ### * exprSetRG-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: exprSetRG-class
> ### Title: Class exprSetRG for two colour DNA microarray data (extension of
> ###   exprSet)
> ### Aliases: exprSetRG-class exprSetRG as.exprSet getExprSetGreen
> ###   getExprSetGreenMinusRed getExprSetRedMinusGreen getExprSetRed
> ###   getExprSetLogRatio getIndGreen getIndRed pDataGreen pDataRed
> ###   pDataSlide phenoDataGreen phenoDataRed phenoDataSlide slideSubset
> ###   [,exprSetRG-method as.exprSet,exprSetRG-method
> ###   as.RGList,exprSetRG-method getExprSetGreen,exprSetRG-method
> ###   getExprSetGreenMinusRed,exprSetRG-method
> ###   getExprSetRedMinusGreen,exprSetRG-method
> ###   getExprSetRed,exprSetRG-method getExprSetLogRatio,exprSetRG-method
> ###   getIndGreen,exprSetRG-method getIndRed,exprSetRG-method
> ###   initialize,exprSetRG-method pDataGreen,exprSetRG-method
> ###   pDataRed,exprSetRG-method pDataSlide,exprSetRG-method
> ###   phenoDataGreen,exprSetRG-method phenoDataRed,exprSetRG-method
> ###   phenoDataSlide,exprSetRG-method show,exprSetRG-method
> ###   slideSubset,exprSetRG-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   indGreen=1:3
>   indRed=4:6
>   channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
>   colnames(channels) <- c("green","red")
>   eSA <- new("exprSetRG", exprs=matrix(1:60, ncol=6, nrow=10), phenoData=
+           new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)),
+               varLabels=list(rep("varLabel1",1))), channels=channels)
>   stopifnot( all(pDataSlide(eSA) ==pData(eSA)[1:3,,drop=FALSE]) )
>   eSAGreen <- getExprSetGreen(eSA)
>   eSARed <- getExprSetRed(eSA)
>   eSALogRatio <- getExprSetLogRatio(eSA)
>   eSALogRatio2 <- getExprSetGreenMinusRed(eSA)
>   eSALogRatio3 <- getExprSetRedMinusGreen(eSA)
>   stopifnot( identical( eSALogRatio, eSALogRatio2 ) )
>   stopifnot( identical( exprs(eSALogRatio), exprs(eSAGreen)-exprs(eSARed)) )
>   stopifnot( all.equal.numeric( as.vector(exprs(eSALogRatio3)), as.vector(exprs(eSARed)-exprs(eSAGreen)) ))
>   eSAPart <- eSA[,c(1,3,1,4,6,4)]
>   eSAInvalid <- eSA[,c(1,3,1,5,6,4),type="invalidExprSetRG"]
>   eSAPart2 <- slideSubset(eSA,j=c(1,3,1))
> 
>   eSAeSA <- cbind(eSA, eSA)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   eSAeSAPart2 <- cbind(eSA, eSAPart2)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   stopifnot( class(as.exprSet(eSA)) == "exprSet" )
> 
>   ## Don't show: 
>   rg <- as.RGList(eSA)
>   stopifnot( identical( exprs(eSAPart), exprs(eSAPart2) ) )
>   ind <- c(1,1,3,2,3,3)
>   stopifnot( identical( exprs(eSALogRatio[,ind]), exprs(eSAGreen[,ind])-exprs(eSARed[,ind])) )
>   stopifnot( dim(exprs(eSALogRatio[,ind]))[2] == length(ind) )
>   eSAPart <- eSA[,1:3, type="invalidExprSetRG"] # not recommended
>   stopifnot(identical(eSAGreen, getExprSetGreen(eSAPart)))
>   #stopifnot(identical(eSAGreen[,c(1,1,1)], getExprSetGreen(eSAPart[,c(1,1,1),type="invalidExprSetRG"])))
>   stopifnot(all.equal.numeric(as.vector(exprs(eSAGreen[,c(1,1,1)])), as.vector(exprs(getExprSetGreen(eSAPart[,c(1,1,1),type="invalidExprSetRG"])))))
>   #stopifnot(identical(eSAGreen[,c(TRUE,TRUE,TRUE)], getExprSetGreen(eSAPart[,c(TRUE,TRUE,TRUE),type="invalidExprSetRG"])))
>   stopifnot(all.equal.numeric(exprs(eSAGreen[,c(TRUE,TRUE,TRUE)]), exprs(getExprSetGreen(eSAPart[,c(TRUE,TRUE,TRUE),type="invalidExprSetRG"]))))
>   #stopifnot(identical(eSAGreen[,c(FALSE,FALSE,FALSE)], getExprSetGreen(eSAPart[,c(FALSE,FALSE,FALSE), type="invalidExprSetRG"])))
>   stopifnot(all.equal.numeric(exprs(eSAGreen[,c(FALSE,FALSE,FALSE)]), exprs(getExprSetGreen(eSAPart[,c(FALSE,FALSE,FALSE), type="invalidExprSetRG"]))))
>   #stopifnot(identical(eSAGreen[,c(FALSE,TRUE,FALSE)], getExprSetGreen(eSAPart[,c(FALSE,TRUE,FALSE), type="invalidExprSetRG"])))
>   stopifnot(all.equal.numeric(exprs(eSAGreen[,c(FALSE,TRUE,FALSE)]), exprs(getExprSetGreen(eSAPart[,c(FALSE,TRUE,FALSE), type="invalidExprSetRG"]))))
>   print(eSA)
exprSetRG with 
	10 genes
	3 slides, i.e. 6 channels 
phenoDataSlide:
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
phenoDataGreen:
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
phenoDataRed:
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
>   print(phenoDataSlide(eSA))
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
>   print(pDataSlide(eSA))
  varLabel1
1         0
2         0
3         0
>   print(phenoDataGreen(eSA))
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
>   print(pDataGreen(eSA))
  varLabel1
1         0
2         0
3         0
>   print(phenoDataRed(eSA))
	phenoData object with 1 variables and 3 cases
	varLabels
		: varLabel1
>   print(pDataRed(eSA))
  varLabel1
4         0
5         0
6         0
> 
>   indGreen <- c(2,4); indRed <- c(1,3)
>   channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
>   colnames(channels) <- c("green","red")
>   myPData <- data.frame(commonOne=c(1,1,2,2), first=c(1,2,3,4))
>   myPDataTwo <- data.frame(commonOne=c(1,1,2,2), second=c("a","b","a","b"))
>   myPDataThree <- data.frame(commonOne=c(1,1,2,2))
>   myPhenoData <- new("phenoData", pData=myPData, varLabels=as.list(colnames(myPData)))
>   myPhenoDataTwo <- new("phenoData", pData=myPDataTwo, varLabels=as.list(colnames(myPDataTwo)))
>   myPhenoDataThree <- new("phenoData", pData=myPDataThree, varLabels=as.list(colnames(myPDataThree)))
>   myMatrix <- cbind(c(1,1,1,1),c(2,2,2,2),c(3,3,3,3),c(4,4,4,4))
>   myExprSetRG <- new("exprSetRG", exprs=myMatrix, se.exprs=myMatrix, phenoData=myPhenoData, channels=channels)
>   myExprSetRGTwo <- new("exprSetRG", exprs=myMatrix, se.exprs=myMatrix, phenoData=myPhenoDataTwo, channels=channels)
>   myExprSetRGThree <- new("exprSetRG", exprs=myMatrix, se.exprs=myMatrix, phenoData=myPhenoDataThree, channels=channels)
>   stopifnot( all.equal.numeric(as.vector(se.exprs(getExprSetGreen(myExprSetRG))), as.vector(cbind(c(2,2,2,2),c(4,4,4,4)))))
>   stopifnot( all.equal.numeric(as.vector(se.exprs(getExprSetRed(myExprSetRG))),as.vector( cbind(c(1,1,1,1),c(3,3,3,3)))))
>   stopifnot( all.equal.numeric(as.vector(se.exprs(getExprSetLogRatio(myExprSetRG, seExprsHandling="mean"))), as.vector(0.5*cbind(c(3,3,3,3),c(7,7,7,7)))))
>   stopifnot( all.equal.numeric(as.vector(se.exprs(myExprSetRG[2,])) , c(1,2,3,4)) )
>   stopifnot( all.equal.numeric(as.vector(se.exprs(myExprSetRG[2,3:4])) , c(3,4)) )
>   stopifnot( all.equal.numeric( as.vector(se.exprs(cbind(myExprSetRG,myExprSetRG))), as.vector(cbind(se.exprs(myExprSetRG),se.exprs(myExprSetRG))) ))
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   stopifnot( all.equal.numeric( as.vector(exprs(getExprSetLogRatio(myExprSetRG))), as.vector(matrix(1,ncol=2,nrow=4)))) 
>   cTwo <- cbind(myExprSetRG, myExprSetRGTwo)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   cThree <- cbind(myExprSetRG, myExprSetRGTwo, myExprSetRGThree)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   cTwob <- cbind(myExprSetRG, myExprSetRGThree)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectOne) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
Warning in is.na(objectTwo) : is.na() applied to non-(list or vector)
>   # match corresponds to %in% , i.e. 
>   stopifnot( all( match(varLabels(cTwo),  c("commonOne", "first", "second")) ) ) 
>   stopifnot( all( match(varLabels(cTwob),c("commonOne", "first")) ) )
>   stopifnot( all( match(varLabels(cThree), c("commonOne", "first", "second")) ) )
>   stopifnot( all( pData(cTwo)[,"commonOne"] ==  pData(cTwob)[,"commonOne"] ) )
> 
>   indGreen <- c(2,4,6); indRed <- c(1,3,5)
>   channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
>   colnames(channels) <- c("green","red")
>   myPData <- data.frame(commonOne=c(1,1,2,2,3,3), commonTwo=c(1,1,1,1,2,2), redOne=c(1,NA,2,NA,3,NA), redTwo=c(1,-1,2,-1,3,-1), greenOne=c(NA,10,NA,20,NA,30), greenTwo=c(-10,10,-10,20,-10,30))
>   myPhenoData <- new("phenoData", pData=myPData, varLabels=as.list(colnames(myPData)))
>   myExprSetRG <- new("exprSetRG", exprs=matrix(1,nrow=10,ncol=6), phenoData=myPhenoData, channels=channels)
>   stopifnot( all.equal( myPData[indRed,] , pDataRed(myExprSetRG) ) )
Error: all.equal(myPData[indRed, ], pDataRed(myExprSetRG)) is not all TRUE
Execution halted

* Installing *source* package 'arrayMagic' ...
** R
** inst
** save image
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: vsn
Loading required package: limma
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
[1] "arrayData"
[1] "initialize"
[1] "weights<-"
[1] "weights<-"
[1] "intensities<-"
[1] "intensities<-"
[1] "spotAttr<-"
[1] "spotAttr<-"
[1] "hybAttrList<-"
[1] "hybAttrList<-"
[1] "getIntensities"
[1] "getIntensities"
[1] "getWeights"
[1] "getWeights"
[1] "getSpotAttr"
[1] "getSpotAttr"
[1] "getHybAttrList"
[1] "getHybAttrList"
[1] "getHybAttr"
[1] "getHybAttr"
[1] "getHybAttrRed"
[1] "getHybAttrRed"
[1] "getHybAttrGreen"
[1] "getHybAttrGreen"
[1] "["
[1] "as.RGList"
[1] "as.RGList"
[1] "show"
[1] "exprSetRG"
[1] "initialize"
[1] "show"
[1] "as.exprSet"
[1] "as.exprSet"
[1] "as.RGList"
[1] "getIndGreen"
[1] "getIndGreen"
[1] "getExprSetGreen"
[1] "getExprSetGreen"
[1] "getIndRed"
[1] "getIndRed"
[1] "getExprSetRed"
[1] "getExprSetRed"
[1] "getExprSetLogRatio"
[1] "getExprSetLogRatio"
[1] "getExprSetGreenMinusRed"
[1] "getExprSetGreenMinusRed"
[1] "getExprSetRedMinusGreen"
[1] "getExprSetRedMinusGreen"
[1] "phenoDataGreen"
[1] "phenoDataGreen"
[1] "pDataGreen"
[1] "pDataGreen"
[1] "phenoDataRed"
[1] "phenoDataRed"
[1] "pDataRed"
[1] "pDataRed"
[1] "phenoDataSlide"
[1] "phenoDataSlide"
[1] "pDataSlide"
[1] "pDataSlide"
[1] "slideSubset"
[1] "slideSubset"
[1] "["
** help
 >>> Building/Updating help pages for package 'arrayMagic'
     Formats: text html latex example 
  arrayData-class                   text    html    latex   example
  cbind.arrayData                   text    html    latex   example
  cbind.exprSetRG                   text    html    latex   example
  colCors                           text    html    latex   example
  controlledApply                   text    html    latex   example
  controlledSubsetting              text    html    latex   example
  detectReplicas                    text    html    latex   example
  exprSetRG-class                   text    html    latex   example
  fdc                               text    html    latex   example
  interweave                        text    html    latex   example
  normalise                         text    html    latex   example
  plot.imageMatrix                  text    html    latex   example
  plotDistributions                 text    html    latex   example
  processArrayData                  text    html    latex   example
  processArrayDataObject            text    html    latex   example
  qualityDiagnostics                text    html    latex   example
  qualityParameters                 text    html    latex   example
  readIntensities                   text    html    latex   example
  readpDataSlides                   text    html    latex   example
  removeSpots                       text    html    latex   example
  simpleApply                       text    html    latex   example
  slideMerge                        text    html    latex   example
  spatialLayout                     text    html    latex   example
  spotMerge                         text    html    latex   example
  visualiseHybridisations           text    html    latex   example
  visualiseQualityParameters        text    html    latex   example
  write.htmltable                   text    html    latex   example
  writeToFile                       text    html    latex   example
** building package indices ...
* DONE (arrayMagic)