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

[John Zhang]

Perhaps one of the database server was down at the time of building the package. 
Try one more time to see if the problem persists.

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>Thread-Topic: ABPkgBuilder (AnnBuilder) subscript out of bounds error
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>From: Henrik Hornshøj Jensen <HenrikH.Jensen at agrsci.dk>
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>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 Hornshøj
>
>	[[alternative HTML version deleted]]
>

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084