[BioC] Problem with GOPkgBuilder from AnnBuilder when trying to create an updated GO data package

[Stefan Goetz]

Hi Robert
Thanks for your mail.
I feel there is some misunderstanding here. I am not after a monthly
update of Bioconductor annotation packages at all. I just would like to
use the GO package, because I want to use the gene ontology vocabulary
in R for my research. I would like to be able to have this up to date.
My question is then if I want to do this, then is the GOPkgBuilder
function of the AnnBuilder package the function to use, since this is
what it seems from the documentation.
Best regards, 
S.

> -----Original Message-----
> From: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
> Sent: Thursday, September 27, 2007 4:30 PM
> To: goetz_stefan at gmx.de
> Cc: mcarlson at fhcrc.org; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Problem with GOPkgBuilder from AnnBuilder 
> when trying to create an updated GO data package
> 
> 
> Hi Stefan,
> 
> Stefan Goetz wrote:
> > Dear Marc, 
> > thanks for your reply. Updating my R to beta version 2.6, I 
> managed to
> > download the GO_1.99.1 package of the last Bioconductor 2.1 release
> > with:
> >> source("http://bioconductor.org/biocLite.R")
> >> biocLite("GO")
> > Now I have the GO data package built from Wed Aug 29 09:16:39 2007.
> > Great!
> > Just for the future, dose anybody know how to make monthly 
> GO updates of
> > this package? Would be to use the GOPkgBuilder function of 
> AnnBuilder
> > package the correct way or this a more complex thing?
> > Best regards.
> 
>    There is no intention, and really no way to make monthly 
> updates of 
> this package.  There are about 200 other packages, many built 
> by other 
> people that rely on the contents of this package. Getting them to 
> coordinate their efforts every six months, is about all that is 
> realistically possible.
> 
>    Monthly updates of GO you are pretty much going to have to 
> do on your 
> own, and what every you do, do not build a package and give 
> it the same 
> name as this package.  You could try relying on biomaRt for a more 
> interactive approach.
> 
> 
>     best wishes
>       Robert
> 
> > Stefan
> > 
> > 
> >> -----Original Message-----
> >> From: mcarlson at fhcrc.org [mailto:mcarlson at fhcrc.org] 
> >> Sent: Thursday, September 27, 2007 2:45 AM
> >> To: Stefan Goetz
> >> Cc: bioconductor at stat.math.ethz.ch
> >> Subject: RE: [BioC] Problem with GOPkgBuilder from AnnBuilder 
> >> when trying to create an updated GO data package
> >>
> >>
> >> Quoting Stefan Goetz <goetz_stefan at gmx.de>:
> >>
> >>> Well, I'm new to BioConductor and R and maybe missing some 
> >> details but: 
> >>>> GO() 
> >>> returns: 
> >>> Quality control information for  GO 
> >>> Date built: Created: Tue Sep  5 18:55:54 2006  
> >>> etc.
> >>>
> >>> and
> >>> ?GO return:
> >>>
> >>> GO(GO): Bioconductor annotation data package:
> >>> Description:
> >>> The annotation package was built using a downloadable R package -
> >>> AnnBuilder (download and build your own) etc...
> >>>
> >>> So my question still is how to use GOPkgBuilder from 
> AnnBuilder when
> >>> trying to create an updated GO data package 
> >>> (the one by default on the BioConductor site is from: Tue Sep  5
> >>> 18:55:54 2006 and the Gene Ontology is evolving fast)
> >>> Any ideas/help somebody?
> >>> Many thanks, 
> >>> Stefan
> >>>
> >>> PD.: AnnBuilder is from Bioconductor, you are from CRAN? Is there
> >>> something on CRAN for GO I missed and if so how is this 
> >> package called?
> >>> Thanks!)
> >>
> >> It really sounds like maybe you should download the very 
> >> latest version of the
> >> GO package from our development repository which was made 
> >> only weeks ago.  We
> >> acknowledge that GO is a fast moving target and that is why 
> >> we build entirely
> >> new versions of GO every 6 months.  The very latest version 
> >> can always be found
> >> right here:
> >>
> > http://www.bioconductor.org/packages/2.1/data/annotation/
> > 
> > I hope this helps,
> > 
> >     Marc
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: 
> http://news.gmane.org/gmane.science.biology.in> formatics.conductor
> > 
> 
> -- 
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem at fhcrc.org
>