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

[Ting-Yuan Liu]

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
> 
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> 
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