Package: GSEABase

Version: 0.1.9

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check GSEABase_0.1.9.tar.gz

RetCode: 1

Time: 32.5 seconds

Status: ERROR

CheckDir: GSEABase.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/GSEABase.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '0.1.9'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEABase' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  mapIdentifiers mapIdentifiers
See '/home/biocbuild/bbs-2.1-bioc/meat/GSEABase.Rcheck/00install.out' for details.
* 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 non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... 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 ... WARNING
Missing link(s) in documentation object 'GeneSet-class.Rd':
  mapIdentifiers mapIdentifiers

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  bcCategory bcSubCategory collectionType collectionType<- coloring
  coloring<- contributor contributor<- creationDate creationDate<-
  geneColor geneColor<- genes genes<- GeneSetCollection longDescription
  longDescription<- mapIdentifiers organism organism<- phenotype
  phenotype<- phenotypeColor phenotypeColor<- setIdentifier
  setIdentifier<- setName setName<- setType setType<- setVersion
  setVersion<- urls urls<- validIdentifiers
Undocumented S4 classes:
  GeneSetCollection
Undocumented S4 methods:
  generic '[<-' and siglist 'GeneSetCollection,ANY,ANY,ANY'
  generic '[<-' and siglist 'GeneSetCollection,ANY,ANY,GeneSet'
  generic '[<-' and siglist 'GeneSetCollection,character,ANY,GeneSet'
  generic '[' and siglist 'ExpressionSet,GeneSet'
  generic '[' and siglist 'GeneSetCollection,logical'
  generic '[' and siglist 'GeneSetCollection,numeric'
  generic '[' and siglist 'GeneSetCollection,character'
  generic '[[<-' and siglist 'GeneSetCollection,ANY,ANY,ANY'
  generic '[[<-' and siglist 'GeneSetCollection,character,ANY,GeneSet'
  generic '[[' and siglist 'GeneSetCollection,character'
  generic 'GeneSetCollection' and siglist 'GeneSet'
  generic 'GeneSetCollection' and siglist 'list'
  generic 'names' and siglist 'GeneSetCollection'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating GSEABase-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'GSEABase-Ex.R' failed.
The error most likely occurred in:

> ### * GeneIdentifierType-constructors
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: GeneIdentifierType
> ### Title: Gene Identifier Class Constructors
> ### Aliases: GeneIdentifierType NullIdentifier AnnotationIdentifier
> ###   EntrezIdentifier SymbolIdentifier PfamIdentifier
> ### Keywords: manip
> 
> ### ** Examples
> 
> NullIdentifier()
setType: NullIdentifier 
> 
> data(sample.ExpressionSet)
> gs1 <- GeneSet(sample.ExpressionSet[100:109],
+                setName="sample1", setIdentifier="100")
> setType(gs1) # AnnotationIdentifier
setType: Annotation (hgu95av2) 
> 
> genes <- featureNames(sample.ExpressionSet)[100:109]
> gs2 <- GeneSet(genes=genes,
+                setName="sample1", setIdentifier="101")
> setType(gs2) # NullIdentifier, since no info about genes provided
setType: NullIdentifier 
> 
> ## Convert...
> ai <- AnnotationIdentifier(annotation(sample.ExpressionSet))
> setType(gs2) <- ai
Warning: Ambiguous method selection for "mapIdentifiers", target "GeneSet#AnnotationIdentifier#NullIdentifier" (the first of the signatures shown will be used)
    GeneSet#AnnotationIdentifier#GeneIdentifierType
    GeneSet#GeneIdentifierType#NullIdentifier

Warning in value[[3]](cond) :
  direct map failed: map 'hgu95av2NULLIDENTIFIER2PROBE' not found in annotation package 'hgu95av2'
Warning in value[[3]](cond) :
  reverse map failed: map 'hgu95av2NULLIDENTIFIER' not found in annotation package 'hgu95av2'
Error in .toAnnotation(tag, to, what) : 
  unable to map from 'NULLIDENTIFIER' to 'Annotation'
Execution halted

* Installing *source* package 'GSEABase' ...
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: XML
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
** help
 >>> Building/Updating help pages for package 'GSEABase'
     Formats: text html latex example 
  CollectionType-class              text    html    latex   example
  CollectionType-constructors       text    html    latex   example
  GSEABase-package                  text    html    latex   example
  GeneColorSet-class                text    html    latex   example
  GeneColorSet-methods              text    html    latex
  GeneIdentifierType-class          text    html    latex   example
  GeneIdentifierType-constructors   text    html    latex   example
  GeneSet-class                     text    html    latex   example
     missing link(s):  mapIdentifiers mapIdentifiers
  GeneSet-methods                   text    html    latex   example
  getBroadSets                      text    html    latex   example
** building package indices ...
* DONE (GSEABase)