💬 A pre-installed R environment is available on Puhti.
module spider r-env
r-env
on Puhti: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 library(packagename)
./projappl
directory 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>
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]
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
💡 Read more about using R on Puhti in r-env documentation in Docs CSC.