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

[Gad Abraham]

On 23/6/09 11:12 PM, Simon Urbanek wrote:
>
> 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)
>

OK, so it installs all the Depends, Imports, Suggests, and Enhances.

Maybe this should be mentioned somehow in the GUI (rename "install 
dependencies"?). It's not too much of an issue for CRAN, but in 
BioConductor there are large packages (10s of MB at least) which can get 
downloaded needlessly but are only Suggested.

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