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| Package 22/205 | OS | Arch | BUILD | CHECK | BUILD BIN |
arrayMagic1.11.0Andreas Buness | Linux (SUSE 9.2) | x86_64 | OK | ERROR | |
| Linux (SUSE 9.2) | i686 | OK | ERROR | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Linux (SUSE 10.0) | x86_64 | OK | ERROR | ||
| Windows Server 2003 | x86_64 | OK | [ ERROR ] | OK | |
| Windows XP | i686 | OK | ERROR | OK | |
| Mac OS X (10.4.6) | i686 | OK | ERROR |
| Package: arrayMagic |
| Version: 1.11.0 |
| Command: D:\biocbld\1.9d\R\bin\R.exe CMD check arrayMagic_1.11.0.tar.gz |
| RetCode: 1 |
| Time: 96.6 seconds |
| Status: ERROR |
| CheckDir: arrayMagic.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/arrayMagic.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* 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 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 whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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
arrayMagic.Rcheck/00install.out:
installing R.css in D:/biocbld/1.9d/Rpacks/arrayMagic.Rcheck
---------- Making package arrayMagic ------------
adding build stamp to DESCRIPTION
installing R files
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] "["
installing inst files
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'arrayMagic'
Formats: text html latex example chm
arrayData-class text html latex example chm
cbind.arrayData text html latex example chm
cbind.exprSetRG text html latex example chm
colCors text html latex example chm
controlledApply text html latex example chm
controlledSubsetting text html latex example chm
detectReplicas text html latex example chm
exprSetRG-class text html latex example chm
fdc text html latex example chm
interweave text html latex example chm
normalise text html latex example chm
plot.imageMatrix text html latex example chm
plotDistributions text html latex example chm
processArrayData text html latex example chm
processArrayDataObject text html latex example chm
qualityDiagnostics text html latex example chm
qualityParameters text html latex example chm
readIntensities text html latex example chm
readpDataSlides text html latex example chm
removeSpots text html latex example chm
simpleApply text html latex example chm
slideMerge text html latex example chm
spatialLayout text html latex example chm
spotMerge text html latex example chm
visualiseHybridisations text html latex example chm
visualiseQualityParameters text html latex example chm
write.htmltable text html latex example chm
writeToFile text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\1.9d\Rpacks\arrayMagic.Rcheck\00_pkg_src\arrayMagic\chm\arrayMagic.chm
Compile time: 0 minutes, 0 seconds
29 Topics
247 Local links
1 Internet link
1 Graphic
Created d:\biocbld\1.9d\Rpacks\arrayMagic.Rcheck\00_pkg_src\arrayMagic\chm\arrayMagic.chm, 71,631 bytes
Compression decreased file by 99,592 bytes.
adding MD5 sums
* DONE (arrayMagic)