Package: exprExternal

Version: 1.5.0

Command: /loc/biocbuild/2.0d/R/bin/R CMD check exprExternal_1.5.0.tar.gz

RetCode: 1

Time: 78.8 seconds

Status: ERROR

CheckDir: exprExternal.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/2.0d/Rpacks/exprExternal.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'exprExternal/DESCRIPTION' ... OK
* this is package 'exprExternal' version '1.5.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'exprExternal' 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 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 exprExternal-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'exprExternal-Ex.R' failed.
The error most likely occurred in:

> ### * exprExternal-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: exprExternal-class
> ### Title: Class exprExternal, a subclass of exprSet, and methods for
> ###   manipulating objects of class exprExternal
> ### Aliases: exprExternal-class coerce,exprSet,exprExternal-method
> ###   exprs2excel,exprExternal-method exprs,exprExternal-method
> ###   exprs<-,exprExternal,ANY-method
> ###   exprs<-,exprExternal,indirectExternalMatrix-method
> ###   initialize,exprExternal-method
> ###   iter,exprExternal,missing,function-method
> ###   se.exprs,exprExternal-method
> ###   se.exprs<-,exprExternal,indirectExternalMatrix-method
> ###   write.exprs,exprExternal-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
>   ## Run the examples from exprSet manual page
>   library('externalVector')
>   library('Biobase')
>   data(geneData)
>   data(geneCov)
>   covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3")
>   names(covdesc) <- names(geneCov)
>   pdata <- new("phenoData", pData=geneCov, varLabels=covdesc)
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
>   pdata[1,]
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
	phenoData object with 3 variables and 1 cases
	varLabels
		cov1: Covariate 1
		cov2: Covariate 2
		cov3: Covariate 3
>   pdata[,2]
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
	phenoData object with 1 variables and 26 cases
	varLabels
		cov2: Covariate 2
> 
>   eset <- as(new("exprSet", exprs=geneData, phenoData=pdata),
+              "exprExternal")
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
Error in vector(class(x), 1) : vector: cannot make a vector of mode "matrix".
Execution halted

* Installing *source* package 'exprExternal' ...
** R
** help
 >>> Building/Updating help pages for package 'exprExternal'
     Formats: text html latex example 
  exprExternal-class                text    html    latex   example
** building package indices ...
* DONE (exprExternal)