[BioC] AnnBuilder subscript out of bounds error

[ross.chapman@dpi.vic.gov.au]

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