R

R is a free software environment for statistical computing and graphics.

SGE module files
The following Modules files should be loaded for this package: module load R/R-2.7.2

For other versions, simply replace the version number module load R/R-2.11.1

The following libraries are available
 * /share/apps/R/R- X.X.X /gnu/lib/R/library
 * The default libraries that come with R
 * Rmpi
 * Snow
 * /share/apps/R/R- X.X.X /gnu/lib/R/bioc
 * BioConductor libraries (default package set using getBioC)

Additional libraries should be installed by the user under ~/R_exlibs or follow these instructions:


 * Make a directory on your home page to install packages/libraries to (DEST_DIR)
 * Make a .Rprofile document in your home space (~/) with the following content, i.e. run the following command on your terminal

cat > $HOME/.Rprofile <<\EOF .libPaths(“~/DEST_DIR") cat(".Rprofile: Setting UK repositoryn") r = getOption("repos") # hard code the UK repo for CRAN r["CRAN"] = "http://cran.uk.r-project.org" options(repos = r) rm(r)

EOF

NOTE:Change DEST_DIR to the name of the directory you created.


 * Load R module and open it.
 * Run install.packages(“Package_Name”) at the prompt.
 * This would install Package_Name to DEST_DIR. To use it just use library(Package_Name)

NOTE: If you install a package with one version of R, it might not be compatible with another version. So it would be advisable to pick one version of R and go with it, so that you don’t have to install multiple versions of the same package.

SGE Job script
Sample R Grid Engine Job Script This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM . /etc/profile.d/modules.sh module load R/R-2.7.2
 * 1) !/bin/bash
 * 2) $ -S /bin/bash
 * 3) $ -cwd
 * 4) $ -j y
 * 5) $ -N rtestjob
 * 6) Use '#$ -m n' instead to disable all email for this job
 * 7) $ -m eas
 * 8) $ -M YOUR_EMAIL_ADDRESS
 * 9) $ -l h_rt=2:00:00,s_rt=1:55:00
 * 10) $ -l vf=256M
 * 1) $ -l vf=256M


 * 1) $ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD

R CMD BATCH rscript.R