[BioC] affylmGUI/biocReposList() Problem

[James W. MacDonald]

HI Burkhard,

On 7/5/2012 9:24 AM, Burkhard Heil wrote:
> Hi everybody,
>
> when trying to calculate the Toptable in affylmGUI there pops the following error message up:
>
> Error: The biocReposList() function is defunct. Please use biocLite() to install packages source("http://bioconductor.org/biocLite.R") biocLite("<pkgname>") if you really need to get the list of Bioconductor package repositories (like biocReposList() does), then do: source("http://bioconductor.org/biocLite.R") biocinstallRepos()
>
> The Toptable ist still calculated but without the Gene Symbols. When I call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges' and 'AnnotationDbi'. Sounds to me that the last one is causing the problem. Also, biocLite complains that it can't access "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15". I read the post about that problem and changed the mirror via chooseBioCmirror(). biocLite still looks for the brainarray adress but then install from another mirror. But everytime I call biocLite it installs those 3 packges.
>
> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant packages should have the most recent version.

Should have? That's not very reassuring. Why don't you load affylmGUI, 
run sessionInfo() and then post the output.

Best,

Jim


>
> Any help would be greatly appreciated! Thanks
>
> Burkhard
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099