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 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.