💬 A pre-installed R environment is available on Puhti.
module spider r-env
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.
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
/projappldirectory of your project
/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>
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:
libpath to point to this directory (not strictly necessary but can make life easier):
libpath <- .libPaths()
lib = libpathto specify the installation location is not strictly necessary but recommended)
install.packages("packagename", lib = libpath)
For example, you can try installing a package called
install.packages("beepr", lib = libpath)
Finished! The R package is now ready to be loaded and used. Try loading
💡 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:
💡 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
💡 Read more about using R on Puhti in r-env documentation in Docs CSC.