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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
- The default libraries that come with R
- 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 > $HOME/.Rprofile <<\EOF .libPaths(“~/DEST_DIR") cat(".Rprofile: Setting UK repositoryn") r = getOption("repos") # hard code the UK repo for CRAN r["CRAN"] = "http://cran.uk.r-project.org" options(repos = r) rm(r) EOF NOTE:Change DEST_DIR to the name of the directory you created.
- Load R module and open it.
- Run install.packages(“Package_Name”) at the prompt.
- This would install Package_Name to DEST_DIR. To use it just use library(Package_Name)
NOTE: If you install a package with one version of R, it might not be compatible with another version. So it would be advisable to pick one version of R and go with it, so that you don’t have to install multiple versions of the same package.
SGE Job script
Sample R Grid Engine Job Script This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM
#!/bin/bash #$ -S /bin/bash #$ -cwd # #$ -j y #$ -N rtestjob # Use '#$ -m n' instead to disable all email for this job #$ -m eas #$ -M YOUR_EMAIL_ADDRESS #$ -l h_rt=2:00:00,s_rt=1:55:00 #$ -l vf=256M . /etc/profile.d/modules.sh module load R/R-2.7.2 #$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD R CMD BATCH rscript.R