R and Rscript
==============

Various versions of the R environment are available on CSD3. The latest
version, R 3.5.2 is available either as ``r-3.5.2-gcc-5.4.0-ordoh5p`` or
``r-3.5.2-gcc-5.4.0-jqs2rxd``. The former is a vanilla R install with no
special options, whereas the latter is linked against the linear algebra
library openblas and may provide substantially better performance.

R can be run interactively by simply calling ``R``, which will give a standard
R shell. This can be used for testing or setting up larger runs. However for
use inside the job scheduler it will generally be more effective to record the
R script in a file ``analysis.R`` and call it from inside a slurm batch script
``Rscript analysis.R``. For more examples of how to use slurm and write an
appropriate batch script please see :ref:`Running`.

Installing R packages
---------------------

While a few R packages have been centrally installed on CSD3 (do ``module avail r-`` to see a list), it is often necessary to install extra R packages into your own environment. For example to install cellranger, one can use::

    $ R
    R version...
    [...]
    > install.packages("cellranger")

which will download and build the package from CRAN.

If you run into build errors, the first fix is to tell R where to find the correct compiler. This can be done by creating the file ``~/.R/Makevars`` in your home directory and adding::

    CC = gcc
    CXX = g++
    CXX11 = g++
    FC = gfortran
    F77 = gfortran
    F90 = gfortran

which tells R to use the system compilers. If you run into problems with the compiler versions being too old, then try loading a more recent compiler before starting R. If you run into problems that refer to the C or C++ standard versions then try adding::

    CFLAGS = -std=c99
    CXXFLAGS = -std=c++11

to ``~/.R/Makevars``.