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

James W. MacDonald jmacdon at med.umich.edu
Fri Sep 14 20:38:33 CEST 2007


And there is a much newer source version on the website here:

http://www.bioconductor.org/packages/2.1/data/annotation/html/GO.html

Best,

Jim



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
>>
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>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623



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