R is a software environment for statistical computing and graphics.
Category: Bioinformatics/Statistics
Availability: Open access for all academic users
Usage Notes
To show the software versions: module avail R
Loading the module will set the path and any necessary variables: module load R/version
Rmpi, an interface to MPI (Message-Passing Interface), is available with versions of R 2.11.1 and greater. Sample SLURM scripts and examples are in the /util/academic/R directory - subdirectories: Rmpi-example, Rmpi-simple, and Rmpi-julia.
Additional Information
Numerous add-on packages for R have been installed in many of the CCR R installations; however, they may vary by version. A complete list for a given version may be viewed using the following command, after loading your preferred R version using the 'module load' command:
cat $R_DIR/PkgList.txt
To install an R package in user (or projects) space:
Nearly 20,000 packages are available for R. If you want to use a package for R that is not already installed, you can install your own packages by either downloading the package and installing it or pointing to the R package library and installing directly from there. The two options are shown below. To see the full list of R packages available, please visit the R project page:
Option 1: Download and install R packages in your home or project directory
Download the R package you want to install. In this example, we demonstrate the 'readr' package:
wget https://cran.r-project.org/src/contrib/readr_2.0.2.tar.gz
Create your R library directory in your home or project directory, if you don't have one already. For example:
mkdir /user/[username]/rlibs
or
mkdir /projects/[academic/industry]/[groupname]/[username]/rlibs
Then point to that directory when installing the R library you want to use:
R CMD INSTALL -l /user/[username]/rlibs package
For our example, to install the readr package we got with the wget command:
R CMD INSTALL -l /user/[username]/rlibs readr_2.0.2.tar.gz
Option 2: Install directly from the R Project repository from within R:
Load your preferred version of R and launch R:
module load R/version
R
Then install the package by specifying the package name, R project repository, and your R library location in your home or project directory
install.packages("package_name", repos = "http://cran.r-project.org", lib = "/user/[username]/rlibs")
For our example, to install the readr package:
install.packages("readr", repos = "http://cran.r-project.org", lib = "/user/[username]/rlibs")
To load an R package from user (or projects) space:
module load R
R
library(package, lib.loc="/user/[username]/rlibs/")
For our example, this would be:
library(readr, lib.loc="/user/username]/rlibs/")