GSEABase 1.2.2
Biocore Team c/o BioC user list
| Snapshot Date: 2008-10-16 00:10:09 -0700 (Thu, 16 Oct 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_2/madman/Rpacks/GSEABase | | Last Changed Rev: 32225 / Revision: 34573 | | Last Changed Date: 2008-06-09 20:20:04 -0700 (Mon, 09 Jun 2008) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | [ ERROR ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.2-bioc/meat/GSEABase.Rcheck'
* using R version 2.7.2 (2008-08-25)
* using session charset: ASCII
* checking for file 'GSEABase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GSEABase' version '1.2.2'
* 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 ... 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 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 ... OK
* checking for missing documentation entries ... OK
* 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:
> ### * GeneSet-class
>
> flush(stderr()); flush(stdout())
>
> ### Name: GeneSet-class
> ### Title: Class "GeneSet"
> ### Aliases: GeneSet-class [,GeneSet,character,ANY-method
> ### [,GeneSet,numeric,ANY-method [,ExpressionSet,GeneSet,ANY-method
> ### [[,GeneSet,character-method [[,GeneSet,numeric-method
> ### Logic,character,GeneSet-method |,GeneSet,GeneSet-method
> ### |,GeneSet,character-method $,GeneSet-method &,GeneSet,GeneSet-method
> ### &,GeneSet,character-method
> ### collectionType<-,GeneSet,CollectionType-method
> ### collectionType,GeneSet-method contributor<-,GeneSet,character-method
> ### contributor,GeneSet-method creationDate<-,GeneSet,character-method
> ### creationDate,GeneSet-method description<-,GeneSet,character-method
> ### description,GeneSet-method geneIds<-,GeneSet,character-method
> ### geneIds,GeneSet-method initialize,GeneSet-method
> ### intersect,GeneSet,GeneSet-method
> ### longDescription<-,GeneSet,character-method
> ### longDescription,GeneSet-method organism<-,GeneSet,character-method
> ### organism,GeneSet-method pubMedIds<-,GeneSet,character-method
> ### pubMedIds,GeneSet-method setdiff,GeneSet,GeneSet-method
> ### setIdentifier<-,GeneSet,character-method setIdentifier,GeneSet-method
> ### setName<-,GeneSet,character-method setName,GeneSet-method
> ### geneIdType<-,GeneSet,character-method
> ### geneIdType<-,GeneSet,GeneIdentifierType-method
> ### geneIdType,GeneSet-method setVersion<-,GeneSet,Versions-method
> ### setVersion,GeneSet-method show,GeneSet-method
> ### union,GeneSet,GeneSet-method urls<-,GeneSet,character-method
> ### urls,GeneSet-method collectionType<- collectionType contributor<-
> ### contributor creationDate<- creationDate geneIds<- geneIds geneIdType
> ### geneIdType<- longDescription<- longDescription organism<- organism
> ### setIdentifier<- setIdentifier setName<- setName setVersion<-
> ### setVersion urls<- urls
> ### Keywords: classes
>
> ### ** Examples
>
> ## Empty gene set
> GeneSet()
setName: NA
geneIds: (total: 0)
geneIdType: Null
collectionType: Null
details: use 'details(object)'
> ## Gene set from ExpressionSet
> data(sample.ExpressionSet)
> gs1 <- GeneSet(sample.ExpressionSet[100:109])
> ## GeneSet from Broad XML; 'fl' could be a url
> fl <- system.file("extdata", "Broad.xml", package="GSEABase")
> gs2 <- getBroadSets(fl)[[1]] # actually, a list of two gene sets
> ## GeneSet from list of geneIds
> geneIds <- geneIds(gs2) # any character vector would do
> gs3 <- GeneSet(geneIds=geneIds)
> ## unspecified set type, so...
> is(geneIdType(gs3), "NullIdentifier") == TRUE
[1] TRUE
> ## update set type to match encoding of identifiers
> geneIdType(gs2)
geneIdType: Symbol
> geneIdType(gs3) <- SymbolIdentifier()
>
> ## Convert between set types; this consults the 'annotation'
> ## information encoded in the 'AnnotationIdentifier' set type and the
> ## corresponding annotation package.
> ## Not run:
> ##D gs4 <- gs1
> ##D geneIdType(gs4) <- EntrezIdentifier()
> ## End(Not run)
>
> ## logical (set) operations
> gs5 <- GeneSet(sample.ExpressionSet[100:109], setName="subset1")
> gs6 <- GeneSet(sample.ExpressionSet[105:114], setName="subset2")
> ## intersection: 5 'genes'; note the set name '(subset1 & subset2)'
> gs5 & gs6
setName: (subset1 & subset2)
geneIds: 31344_at, 31345_at, ..., 31348_at (total: 5)
geneIdType: Annotation (hgu95av2)
collectionType: ExpressionSet
details: use 'details(object)'
> ## union: 15 'genes'; note the set name
> gs5 | gs6
setName: (subset1 | subset2)
geneIds: 31339_at, 31340_at, ..., 31353_f_at (total: 15)
geneIdType: Annotation (hgu95av2)
collectionType: ExpressionSet
details: use 'details(object)'
> ## an identity
> gs7 <- gs5 | gs6
> gs8 <- setdiff(gs5, gs6) | (gs5 & gs6) | setdiff(gs6, gs5)
> identical(geneIds(gs7), geneIds(gs8))
[1] TRUE
> identical(gs7, gs8) == FALSE # gs7 and gs8 setNames differ
[1] TRUE
>
> ## output
> tmp <- tempfile()
> toBroadXML(gs2, tmp)
Error in value[[3]](cond) :
toBroadXML failed to create XML: no method or default for coercing "NULL" to "XMLNamespaceDefinitions"
Calls: toBroadXML ... tryCatchList -> tryCatchOne -> <Anonymous> -> .stopf
Execution halted