R Libraries

R is a free software environment for statistical computing and graphics. Many commonly used libraries have been preloaded on Roar and can be used with the library() command.

Installing R packages

R packages can be installed from the R console:

> install.packages( <package> )

The first time you run this command in a given version of R, you will be prompted to create a personal library; The default location is the .R directory in your home directory.

After installation, packages can then be loaded with:

> library( <package> )

Custom library paths

To install a package in a custom location, specify a path:

> install.packages( "<package>", lib="<install_path>" )

To load a package installed in a non-standard location, specify the location with lic.loc:

> library( <package>, lib.loc="<install_path>" )

Alternatively, before launching an R session, modify the R_LIBS or R_LIBS_USER environment variable, which tells R where to look for libraries. For command-line use of R, changing R_LIBS suffices; for RStudio, R_LIBS_USER must also be modified.

Dependencies

Some R packages require additional software or changes to the user environment, before the package can be installed.

For example, some R packages use CMake to perform installations; others may require a particular version of a compiler to be loaded. Be sure to use module load to load the necessary dependencies before launching R.

Example: units

For example, to install the R package units, the package documentation lists the C library udunits-2 under "SystemRequirements". So we must download and compile udunits-2:

$ wget https://downloads.unidata.ucar.edu/udunits/2.2.28/udunits-2.2.28.tar.gz
$ tar -xvf udunits-2.2.28.tar.gz
$ cd udunits-2.2.28
$ ./configure prefix=$HOME/.local
$ make
$ make install

Next, we set environmental variables so R can find the udunits-2 library:

$ export UDUNITS2_INCLUDE=$HOME/.local/include
$ export UDUNITS2_LIBS=$HOME/.local/lib
$ export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH

Now we can install the units package:

$ module load r/4.2.1
$ R
> install.packages("units")
> library(units)