[BioC] problem with GOstats, developmental version?

[Mark W Kimpel]

Seth and Jenny,

I had the exact same problem last night using code of mine that had been 
working the past year. I updated all packages and the problem persisted. 
I would have reported it but was too busy with something that was due 
today. I am also using R-devel.

Mark

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Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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Seth Falcon wrote:
> Hi Jenny,
> 
> Jenny Drnevich <drnevich at uiuc.edu> writes:
>> Hi Seth and everyone,
>>
>> First, we will all miss you Seth! Good luck in your new career.  But
>> while you're still with Bioconductor, hopefully you can help me with a
>> problem I'm having with GOstats in R-devel 2.6.  I'm copying and
>> pasting directly from the vignette GOstatsHyperG.pdf, Aug 23, 2007,
>> and everything's fine until this point:
>>
>>> hgOver <- hyperGTest(params)
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "edges", for
>> signature "graphNEL"
>>
>> (sessionInfo below)
> 
> You have an old version of AnnotationDbi, can you try updating and
> seeing if that fixes things?  You might want to do an update of all of
> your packages:
> 
>     library("Biobase")
>     update.packages(repos=biocReposList())
> 
> + seth
> 
>