[R-SIG-Mac] Too many dependencies with BioConductor packages?

[Simon Urbanek]

On Jun 23, 2009, at 8:17 , Gad Abraham wrote:

> Hi,
>
> I've tried to use R.app Package Installer to install the  
> BioConductor package GOstats, with "install dependencies" checked,  
> but R proceeded to download many other packages before I killed it:
>
> (this is the temporary downloaded_packages directory)
> $ ls
> AffymetrixDataTestFiles_0.1.1.tgz R.oo_1.4.8.tgz  
> affxparser_1.16.0.tgz             makePlatformDesign_1.8.0.tgz
> R.methodsS3_1.0.3.tgz             R.utils_1.1.7.tgz  
> hapmap100kxba_1.3.2.tgz           pd.mapping50k.xba240_0.4.1.tgz
>
> These aren't in the Depends of GOstats, http://www.bioconductor.org/packages/release/bioc/html/GOstats.html 
> , which lists:
> Depends  Biobase , Category , graph
>

If A depends on B then installing dependencies means that you also  
have to satisfy all dependencies of B which could be C, D, E, F then  
their dependencies and so on. The dependency tree in BioC can be quite  
big... So R was doing what you told it to do.

Cheers,
Simon



> Without "install dependencies" checked, it installs fine.
>
> I'm using 2.9.0 from CRAN, BioC 2.4.0, OS X 10.5.7.
>
> Thanks,
> Gad
>
> -- 
> Gad Abraham
> MEng Student, Dept. CSSE and NICTA
> The University of Melbourne
> Parkville 3010, Victoria, Australia
> email: gabraham at csse.unimelb.edu.au
> web: http://www.csse.unimelb.edu.au/~gabraham
>
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