R
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
This page is a Generic stub.
You can help by expanding this page..
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 > $HOME/.Rprofile <<\EOF
.libPaths(“~/DEST_DIR")
cat(".Rprofile: Setting UK repositoryn")
r = getOption("repos") # hard code the UK repo for CRAN
r["CRAN"] = "http://cran.uk.r-project.org"
options(repos = r)
rm(r)
EOF
NOTE:Change DEST_DIR to the name of the directory you created.
- Load R module and open it.
- Run install.packages(“Package_Name”) at the prompt.
- This would install Package_Name to DEST_DIR. To use it just use library(Package_Name)
NOTE: If you install a package with one version of R, it might not be compatible with another version. So it would be advisable to pick one version of R and go with it, so that you don’t have to install multiple versions of the same package.
SGE Job script
Sample R Grid Engine Job Script This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM
#!/bin/bash #$ -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