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

[Gad Abraham]

On 23/6/09 10:42 PM, Simon Urbanek wrote:
>
> 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.

Does "install dependencies" only install Depends or also Suggests?

The downstream Depends for GOstats are pretty minimal and don't include 
any of the packages I listed:

GOstats: Biobase , Category , graph
Biobase: R , methods , utils
Category: AnnotationDbi , Biobase
graph: R , methods
AnnotationDbi: R , methods , utils , Biobase


-- 
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