[BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error

[TEXTORIS Julien]

I still have the same error with the latest version. 

Julien

Le Lundi 6 Février 2006 19:21, Ting-Yuan Liu a écrit :
> Hi Henrik,
>
> Which version of AnnBuilder you are using?  I believe the "subscript out
> of bounds error" had been fixed.  If you tried the developmental version
> AnnBuilder, you should not get this error again.
>
> HTH,
> Ting-Yuan
> ______________________________________
> Ting-Yuan Liu
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> Seattle, WA, USA
> ______________________________________
>
> On Mon, 6 Feb 2006, Henrik Hornshøj Jensen wrote:
> > Anyone seen this error with ABPkgBuilder (AnnBuilder) and knows how to
> > resolve it?
> >
> >
> > To build a data annotation package, this piece of code usually works for
> > me:
> >
> > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > myBaseType, pkgName = myPkgName, pkgPath = myDir,
> > organism = "Homo sapiens", version = "2.0.0",
> > author = list(author = "Henrik Hornshoj <henrikh.jensen at agrsci.dk
> > <mailto:henrikh.jensen at agrsci.dk> >", maintainer = "Henrik Hornshoj
> > <henrikh.jensen at agrsci.dk <mailto:henrikh.jensen at agrsci.dk> >"), fromWeb
> > = TRUE)
> >
> >
> > But today I suddenly get the following error:
> >
> >
> > Attaching package: 'GO'
> >
> >
> >         The following object(s) are masked from package:AnnBuilder :
> >
> >          GO
> >
> > Warning message:
> > Built for UCSC is not valid! in: getUCSCBuilt(organism)
> > Failed to get data from URL:
> > ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00191.gene
> > <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00191.gene> Failed to
> > get data from URL:
> > ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00192.gene
> > <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa00192.gene> .
> > .
> > Failed to get data from URL:
> > ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99998.gene
> > <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99998.gene> Failed to
> > get data from URL:
> > ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99999.gene
> > <ftp://ftp.genome.ad.jp/pub/kegg/pathways/hsa/hsa99999.gene> [1] "4010 2
> > 2"
> > Error in all(is.na(annotation[, "GO"])) : subscript out of bounds
> >
> >
> > Any suggestions are welcome!!
> >
> > Regards,
> > Henrik Hornshj
> >
> > 	[[alternative HTML version deleted]]