R

Installed versions

Resource	Version
Dardel/cpe23.12	4.4.1, 4.1.2

General information

Instructions for using R at PDC

R is a programming language and software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls, surveys of data miners, and studies of scholarly literature databases show that R's popularity has increased substantially in recent years More information can be found at https://cran.r-project.org/

R Packages

List Packages

To see a list of installed packages, please type

> installed.packages()

How to install local packages

As many packages interfere with each other it is often a good idea to install them locally in your userspace instead. By default, installations of R at PDC automatically sets userpath for user installed packages to ~/.R///library Running are you are able to see the local folder

$ module add R
$ R
> .libPaths()
[1] "/cfs/klemming/home/<FIRST LETTER USERNAME>/<USERNAME>/.R/23.12/4.4.0/library"
[2] "/cfs/klemming/pdc/software/dardel/23.12/other/R/4.4.0-cpeGNU-23.12/lib64/R/library"

If you would like to change this path, you must first define an R folder for the packages

export R_LIBS_USER=<FOLDER NAME>
mkdir -p <FOLDER NAME>

To install packages

> install.packages("package name")

But we aware that if you are changing the local libPaths then you need to define what libPaths you are installing your package. In the example above, beside not adding a libPaths, you could also do to install packages

> install.packages("package name",lib=.libPaths()[1])

Install global packages

Some packages are installed by default by support. You will not have access to install yourself any global packages unless you are a member of the support group. instructions at http://www.bu.edu/tech/support/research/software-and-programming/common-languages/r-basics/r-faq/ In general we can add new packages directly from within R, but to be globally accessible they must be installed in the global repository rather than your home catalogue.

$ module add R
$ R
> .libPaths()
[1] "/cfs/klemming/home/<FIRST LETTER USERNAME>/<USERNAME>/.R/23.12/4.4.0/library"
[2] "/cfs/klemming/pdc/software/dardel/23.12/other/R/4.4.0-cpeGNU-23.12/lib64/R/library"

All the packages installed at PDC where installed in the 2nd path, which is globally accessible. To install packages

> install.packages("package name",lib=.libPaths()[2])

Which will install [package name] in R.

How to use

R on Dardel does not work across nodes but using the cores available on one Dardel node should suffice for all operations. run R it using

$ module add R/4.1.2
$ salloc -A <your-project-ID> -N 1 -t 60 -p <partition> srun -n 8 R --no-save <[myscript]