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

[Robert Gentleman]

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
> 
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-- 
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