[kepler-users] can I set the default R installation for Kepler to use?

[David LeBauer]

Hi David and Ben,

Thanks for your help and for following up.

Unfortunately, neither of the solutions (changing the PATH or setting
it in environment.txt).

Also, our server administrator ran R CMD javareconf because I thought
that it sounded promising, but it wasn't - he said that Java needs to
know where R is and the command only told R where Java is. He said
that the options are to either to set the path in Kepler (if there is
one, my question to you) or to switch the locations of the two R
installations.

Before doing that, I'd still be interested in other options if
available. In the mean time I'll probably start using Kepler on my
desktop and try to use the ssh and PBS tools.

Thanks.

David

On Wed, Oct 20, 2010 at 8:25 PM, David Welker <david.v.welker at gmail.com> wrote:
> Hi David,
>
> I was wondering whether Ben's reply solved the problem for you. Do you still
> need help with this?
>
> -David Welker
>


From:ben


Hi David,
You can try a couple things:
1. Put your R's bin directory on the PATH environment variable
2. If that doesn't work, there should be an "environment.txt" file in
your Kepler R module directory.
For example:
       Kepler/r-2.0.0/module-info/environment.txt
Contains lines for each OS where you can set R_HOME:
       R_HOME:Mac OS X=/Library/Frameworks/R.framework/Resources
       R_HOME:Windows=C:\Program Files\R\R-2.9.0
       R_HOME:linux=
If I remember correctly, this second option was only for the JNI
implementation of the R actor, so I'd start by doing #1
Thanks,
-ben


>
> On Oct 19, 2010, at 12:36 PM, David LeBauer wrote:
>
>> Hello,
>>
>> Can I tell Kepler to use a specific installation of R? The default on
>> my machine is /usr/lib64/R/bin/R but I would like to use
>> /usr/local/R-2.12.0/bin/R
>>
>> For example, I do this by setting the alias in ~/.bash_profile, e.g.:
>> alias R='/usr/local/R-2.12.0/bin/R'
>>
>> Thanks,
>>
>> David
>> --
>> David LeBauer, PhD
>> Energy Biosciences Institute
>> University of Illinois Urbana-Champaign
>> 1206 W. Gregory Drive
>> Urbana, IL  61801, U.S.A.
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org
>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>



-- 
David LeBauer, PhD
Energy Biosciences Institute
University of Illinois Urbana-Champaign
1206 W. Gregory Drive
Urbana, IL  61801, U.S.A.