I am having the following problems with AnnBuilder, using the version of AnnBuilder and the GO annotation package from Bioconductor 1.8 or 1.9 (devel):

I am creating an annotation package for our mouse cDNA arrays.The following commands result in a functional annotation package, but the package contains no GO annotation object, despite the GO related url being returned by getSrcUrl:

library(AnnBuilder)
urls <- getSrcUrl("all", "mus musculus")

#Mm.data.gz seems only intermittently available, so use local copy
urls[[2]] <- "file:///home/erikor/research/mouse/Mm.data.gz"

ABPkgBuilder(baseName="keyp.txt", srcUrls=urls, baseMapType="gb", pkgName="vaimm06", pkgPath="./", organism="Mus musculus", version="0.1", author=list(author="Eric J. Kort", maintainer="Eric J. Kort"))

I get numerous errors along the lines of:

Failed to get data from URL: ftp://ftp.genome.ad.jp/pub/kegg/pathways/mmu/mmu07212.gene

And then:

The following data sets have been added to the database and will be removed:
[1] ".//vaimm06/data/vaimm06ACCNUM.rda"
[2] ".//vaimm06/data/vaimm06CHRLENGTHS.rda"
[3] ".//vaimm06/data/vaimm06CHRLOC.rda"
[4] ".//vaimm06/data/vaimm06ENZYME.rda"
[5] ".//vaimm06/data/vaimm06LOCUSID.rda"
[6] ".//vaimm06/data/vaimm06MAPCOUNTS.rda"
[7] ".//vaimm06/data/vaimm06ORGANISM.rda"
[8] ".//vaimm06/data/vaimm06PATH.rda"
[9] ".//vaimm06/data/vaimm06PFAM.rda"
[10] ".//vaimm06/data/vaimm06PROSITE.rda"
[11] ".//vaimm06/data/vaimm06QCDATA.rda"
[12] ".//vaimm06/data/vaimm06QC.rda"

But what I need is vaimm06GO.rda.How can I get ABPkgBuilder to create the GO annotation object?

Thanks,
Eric



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