R installations

[Daniel Gates]

greetings TreEvoers

I'm attempting to parallelize the particle simulation step and I'm trying it out on the newton cluster but I'm running into problems in that their version of R is 2.11 and the dependency "car" requires 2.14+. Barb I know you've mentioned that you locally installed your own copy of R on the cluster, how did you go about doing this? If anyone has helpful advice it would be greatly appreciated!

Cheers,
-Dan

[B.Banbury]

Hi Dan,

In your main directory on newton, you can install a bin with applications.  Just use wget or curl to download R, then unzip, configure and make.  To use that version of R, instead of calling R, you will call the path to your version of R (~/bin/R-2.15.0/bin/R).  Then you will need to install all the necessary libraries.  

BTW, treevo should load as a library again if you want to check out the main branch I think the doRun_prc function is up and running now.  We are still tweaking some minor things, but hopefully the big changes are behind us.  

Let me know if any of this needs further explanation.

Barb

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville

[Brian O'Meara]

module load R/2.15.0 

will give you R 2.15.0. The other thing you can do is rather than call "R", call the full path the R 2.15: "/data/apps/R/2.15.0/bin/R"

Brian

_______________________________________
Brian O'Meara
Assistant Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://www.brianomeara.info

Students wanted: Applications due Dec. 15, annually
Postdoc collaborators wanted: Check NIMBioS' website
Calendar: http://www.brianomeara.info/calendars/omeara

On Wed, Jun 27, 2012 at 1:51 PM, Daniel Gates <danj...@gmail.com> wrote:

[B.Banbury]

Right!  I always forget that the cluster is set up with modules now.  Good call Brian, that will be much easier.

______________________
Barb Banbury
Postdoctoral Research Associate
Ecology and Evolutionary Biology
University of Tennessee, Knoxville