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

[Robert Gentleman]

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
> 
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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