[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[Herve Pages]

Hi Jenny,

We've just updated many of our metadata packages and we're now providing
all the Windows binaries (Mac OS X binaries will come later).

Go here for the list of what we have in store

  http://bioconductor.org/packages/2.1/data/annotation/

and install with biocLite() or update with:

  > source("http://bioconductor.org/biocLite.R")
  > update.packages(rep=biocinstallRepos(), ask=FALSE)

Let us know if this solves your problem.

Cheers,
H.


Jenny Drnevich wrote:
> Well, it's good to know that I'm not a _complete_ idiot :)  I didn't 
> realize GO was an annotation/metadata package and not a software 
> package, which is why I couldn't find it on the website. I was able 
> to build from source for the newest versions of GO and GO.db, and the 
> problem with invalid GO terms went away... but then I also built the 
> newest version of the ath1121501 annotation package, and then calling 
> hyperGTest() lead to the following error:
> 
> Error in getUniverseHelper(probes, datPkg, entrezIds) :
>    No Entrez Gene ids left in universe
> 
> 
> ARRRGHH! Anyway, I think I'll wait until Tuesday (I'm off on 
> Monday!!) when the windows binaries are hopefully available, update 
> all my packages again, and then see what happens...
> 
> Thanks for all your help,
> Jenny
> 
> At 01:36 PM 9/14/2007, Robert Gentleman wrote:
>> Hi Jenny,
>>   It seems that the piece that produces windows binaries of the 
>> annotation packages has been broken.  We should be able to push new 
>> versions first thing on Monday.  If you have the ability to build 
>> windows packages, you could do that directly from the source package.
>>
>>   sorry about that
>>    Robert
>>
>>
>> Jenny Drnevich wrote:
>>>> Yes, this is not as desired.  But can you please try updating the GO
>>>> package and see if this remains to be an issue :-)
>>>>
>>>> BTW, I believe this hasn't changed since your last update so I will
>>>> recommend how to update:
>>>>
>>>> library(Biobase)
>>>> update.packages(repos=biocReposList())
>>>>
>>>> + seth
>>> As of 2 minutes ago, these were the only packages that it updated...
>>> package 'affyio' successfully unpacked and MD5 sums checked
>>> package 'annaffy' successfully unpacked and MD5 sums checked
>>> package 'annotate' successfully unpacked and MD5 sums checked
>>> package 'AnnotationDbi' successfully unpacked and MD5 sums checked
>>> package 'biomaRt' successfully unpacked and MD5 sums checked
>>> package 'Category' successfully unpacked and MD5 sums checked
>>> package 'GOstats' successfully unpacked and MD5 sums checked
>>> package 'graph' successfully unpacked and MD5 sums checked
>>> package 'preprocessCore' successfully unpacked and MD5 sums checked
>>> ... and I'm still having the same problem. I also tried using 
>>> biocLite("GO"), but it downloaded the same version I already had: 
>>> 1.17.0.  If there's a newer version, it's not available as a 
>>> Windows binary. BTW, there is no package "GO" on the BioC website 
>>> software listings for either BioC 2.0 or BioC 2.1...
>>> Thanks,
>>> Jenny
>>>
>>>
>>>> --
>>>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>>>> BioC: http://bioconductor.org/
>>>> Blog: http://userprimary.net/user/
>>> Jenny Drnevich, Ph.D.
>>> Functional Genomics Bioinformatics Specialist
>>> W.M. Keck Center for Comparative and Functional Genomics
>>> Roy J. Carver Biotechnology Center
>>> University of Illinois, Urbana-Champaign
>>> 330 ERML
>>> 1201 W. Gregory Dr.
>>> Urbana, IL 61801
>>> USA
>>> ph: 217-244-7355
>>> fax: 217-265-5066
>>> e-mail: drnevich at uiuc.edu
>>> _______________________________________________
>>> 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.informatics.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
> 
> Jenny Drnevich, Ph.D.
> 
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
> 
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
> 
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
> 
> _______________________________________________
> 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.informatics.conductor