[BioC] problem with GOstats, developmental version?

Seth Falcon sfalcon at fhcrc.org
Wed Sep 5 00:23:52 CEST 2007


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


-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/



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