R is a software environment for statistical computing and graphics.
Availability: Open access for all academic users
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.
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:
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:
Create your R library directory in your home or project directory, if you don't have one already. For example:
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
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
For our example, this would be:
Installing R packages from within the R Studio GUI:
Whether using CCR's R Studio app on OnDemand or launching it from the command line, users can install R packages into their home or project directories. Launch R Studio and navigate to the Tools menu and click on 'Install Packages'
Make sure the installation directory is specifying either your home directory or a subdirectory within your group's shared project directory and check the "Install dependencies" option:
In this example, we've installed ggplot2 which completes the installation but does give an error that not all features are available in this version of R:
Common Installation Error
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
If you are trying to install a R library and see this error, it is trying to create a temporary directory to use during the installation and isn't able to. To resolve this, create a temporary directory in your home or project directory and, after starting R, set the variable before attempting the installation:
The directory will be used during installation and the temporary files removed when the install is complete.