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Installing R Packages

Installing R packages

Users should install R packages for themselves locally. This documentation shows you how to install R packages locally (without root access) on Oscar.
If the package you want to install has operating-system-level dependencies (i.e. the package depends on core libraries), then we can install it as a module.

Installing an R package

First load the R version that you want to use the package with:
module load R/3.4.3_mkl
Start an R session
R
Note some packages will require code to be compiled so it is best to do R packages installs on the login node.
To install the package 'wordcloud':
> install.packages("wordcloud", repos="http://cran.r-project.org")
You will see a warning:
Warning in install.packages("wordcloud", repos = "http://cran.r-project.org") :
'lib = "/gpfs/runtime/opt/R/3.4.2/lib64/R/library"' is not writable
Would you like to use a personal library instead? (y/n)
Answer y . If you have not installed any R packages before you will see the following message:
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.4
to install packages into? (y/n)
Answer y . The package will then be installed. If the install is successful you will see a message like:
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (wordcloud)
If the installation was not successful you will see a message like:
Warning message:
In install.packages("wordcloud", repos = "http://cran.r-project.org") :
installation of package ‘wordcloud’ had non-zero exit status
​
There is normally information in the message that gives the reason why the install failed. Look for the word ERROR in the message.
Possible reasons for an installation failing include:
  • Other software is needed to build the R package, e.g. the R package rgdal needs gdal so you have to do module load gdal
  • A directory needs deleting from a previous failed installation.

Removing an R package

Start an R session:
R
To remove the 'wordcloud' package:
> remove.packages("wordcloud")