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

[Simon Urbanek]

On Jun 23, 2009, at 8:55 , Gad Abraham wrote:

> 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?
>

It's equivalent to install.packages(dependencies=TRUE)

Cheers,
S


> 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
>
>