[BioC] AnnBuilder subscript out of bounds error

[Ting-Yuan Liu]

Hi Ross,

I believe that this bug had been fixed in the developmental version.  
Please upgrade your AnnBuilder to the developmental version and you won't 
see this error any more.  

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Fri, 17 Mar 2006 ross.chapman at dpi.vic.gov.au wrote:

> Hi All
> 
> I am trying to build an annotation library for some in-house plant
> microarrays using AnnBuilder.
> 
> I have a base file that consists of a column of probe names, and nearest
> matches to NCBI genes.
> 
> I have installed entrex files, unigene files and go files locally to speed
> the process.
> 
> I am trying to map the plant probes on the microarray to rice genes in
> UniGene.
> 
> I run the following script:
> 
> library("AnnBuilder")
> myBase<-("myFile")
> myDir<-tempdir()
> myBaseType="gb";
> mySrcUrls<-c(EG="file:///home/rc69/R/AnnBuilder/gene/DATA",
> LL="file:///home/rc69/R/AnnBuilder/LocusLink/Archive/LL_tmpl.gz",
> UG
> ="file:///home/rc69/R/AnnBuilder/repository/UniGene/Homo_sapiens/Hs.data.gz",
> GO="file:///home/rc69/R/AnnBuilder/Go/Latest")
> date()
> if(.Platform$OS != "windows" && interactive()){
> ABPkgBuilder(baseName=prgBase, srcUrls=mySrcUrls, baseMapType=myBaseType,
> pkgName="myPRG_Pkg", pkgPath=myDir,
> organism="Oryza sativa", version="1.1.0", author=list(author="Ross",
> maintainer="Ross"), fromWeb=FALSE)}
> 
> The code runs well for about 7 minutes, then fails and returns the
> following error:
> 
> Error in all(is.na(annotation[, "GO"])) : subscript out of bounds.
> 
> I am using the latest version of the GO files:
> 
> go_200603-termdb.rdf-xml.gz
> 
> Does anyone have any suggestions of the nature of the problem and how I
> might fix it.
> 
> Many thanks for your help
> 
> Ross
> 
> 
> Dr Ross Chapman
> Bioinformatician
> Senior Research Scientist
> Computational Biology and Discovery Technologies
> Plant Genetics and Genomics Research Platform
> Department of Primary Industries
> Victorian Agribiosciences Centre
> 1 Park Drive, Bundoora, Victoria, 3083
> Australia
> 
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