CSC Computing Environment

R on Puhti and package installations

💬 A pre-installed R environment is available on Puhti.

1. To check available module versions, run:

module spider r-env

1. There are several ways to use R in r-env on Puhti:

• Interactive jobs on a compute node, using either the R console or RStudio
  💡 The easiest way to launch RStudio is to use the Puhti web interface at www.puhti.csc.fi
• Non-interactive batch jobs
• Interactively on the login node, using the R console (only for moving data, checking package availability, installing packages)

For example, to launch the R console in an interactive job, open a shell with sinteractive and then

module load r-env
start-r

💡 See the r-env documentation for further instructions on different ways to launch R on Puhti.

💬 It is also possible to install R packages yourself.

• However, check first if what you need is already available in r-env. The module contains more than 1300 R packages! The easiest way to check if a package is available is trying to load it with the command library(packagename).

How to install an R package on Puhti

• Note that your own package installations are:
  • project specific
  • R version specific
  • located in the /projappl directory of your project

1. Create a folder for your R packages in /projappl (open a login node shell in the Puhti web interface or log in to Puhti with SSH):

# First navigate to /projappl/<project>, then
mkdir project_rpackages_<rversion>

1. Start an R session (launch RStudio in the Puhti web interface or launch the R console in an interactive shell session: start the job with sinteractive -> module load r-env -> start-r). In R, add the folder you created above to the list of directories where R will look for packages:

.libPaths(c("/projappl/<project>/project_rpackages_<rversion>", .libPaths())) 

Assign libpath to point to this directory (not strictly necessary but can make life easier):

libpath <- .libPaths()[1]

1. Install the package (again, defining lib = libpath to specify the installation location is not strictly necessary but recommended)

install.packages("packagename", lib = libpath)

For example, you can try installing a package called beepr with

install.packages("beepr", lib = libpath)

Finished! The R package is now ready to be loaded and used. Try loading beepr with library(beepr).

💡 The package location is defined only for the current R session! R has to be reminded of the location at the start of every R session or script where you want to use the project-specific package by running this command again:

.libPaths(c("/projappl/<project>/project_rpackages_<rversion>", .libPaths())) 

💡 Instead of installing a missing package for your own project, you can ask for a module-wide installation for all users by contacting servicedesk\@csc.fi

More information

💡 Read more about using R on Puhti in r-env documentation in Docs CSC.

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