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
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R is a free software environment for statistical computing and graphics. Please refer to the following page for additional instructions for running R on Cheaha Running R Jobs on a Rocks Cluster.
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, additional libraries should be installed by the user under ~/R_exlibs
- /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)
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