[BioC] AnnBuilder/ABPkgBuilder URL problem

[Ting-Yuan Liu]

Hi Anja,

If you try again the NCBI link, it should work now.  I just try it and it 
works fine.  I think that's because the NCBI ftp site was unavailable 
temporarily, for some reason, when you were using AnnBuilder.  Let me 
know if you still cannot use it correctly.

One more suggestion:  Please do not use any "space" in the package name.  

HTH,
Ting-Yuan

______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________
We should live by the second, as each second is a critical period to pass 
through. ---Master Cheng Yen

On Wed, 7 Dec 2005, Anja Schiel wrote:

> Hello,
> I am running AnnBuilder 1.8.o and GO 1.10.0 in R 2.2.0 and when trying
> to built an annotation always end up with this error:
> 
> 
>  ABPkgBuilder(baseName=ASBase, srcUrls =ASSrcUrls, baseMapType =
> ASBaseType, pk gName="Sigma Oligo 071205", pkgPath=ASDir, organism="Mus
> musculus", version="1.1 .0", author = list(author = "Anja E. Schiel",
> maintainer ="Anja E. Schiel<a.e.sc hiel at lumc.nl>"))
> 
> Attaching package: 'GO'
> 
> 
>         The following object(s) are masked from package:AnnBuilder :
> 
>          GO
> 
> Warning message:
> Built for UCSC is not valid! in: getUCSCBuilt(organism)
> Error in loadFromUrl(srcUrls[i]) : URL
> ftp://ftp.ncbi.nih.gov/repository/UniGene /Mus_musculus/Mm.data.gz is
> incorrect or the target site is not responding!
> 
> If I try to go directly to the Url it won't work either.
> My list after > getSrcUrl("ALL", organism"Mus musculus") looks like
> this.
> 
> 
> 
> GP
> 
> "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Mus_musculus/database/"
> 
> UG
> 
> "ftp://ftp.ncbi.nih.gov/repository/UniGene/Mus_musculus/Mm.data.gz"
> 
> GO
> "http://www.godatabase.org/dev/database/archive/latest/go_200512-termdb.rdf-xml.gz"
> 
> KEGG
> 
> "ftp://ftp.genome.ad.jp/pub/kegg/pathways"
> 
> YG
> 
> "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/"
> 
> HG
> 
> "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp"
> 
> EG
> 
> "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA"
> 
> IPI
> 
> "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/"
> 
> 
> I can clearly not connect to the ncbi Url, but have I done something
> wrong or has this something to do with a change in the database?
> I searched the archive but didn't find an answer.
> 
> Thanks for you support!
> 
> Anja
> 
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