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

[Henrik Hornshøj Jensen]

I am using the latest version, just updated everything.

Did not try the developer version though.

I also tried running my script with days in between, to see if the error is caused by source where it downloads from. But this did not help.

Regards,
Henrik 


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Fra: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] På vegne af TEXTORIS Julien
Sendt: Tuesday, February 07, 2006 8:24 AM
Til: bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] ABPkgBuilder (AnnBuilder) subscript out of bounds error

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]]

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