Installing R packages with devtools

Introduction

The installation of some R packages may require the use of devtools. Devtools is an R package that facilitates the installation of other R packages from github, gitlab, bitbucket or other repositories. In what follows github will be used as an example. Please consult the devtools documentation for examples of other repositories.

Depending on how your R library is managed, you will need a slightly different approach to use and install devtools.

Note

When consulting the devtools documentation, make sure that it is the correct version! It should match the devtools version included in the R module. To check which devtools version is installed:

library(devtools)
sessioninfo::session_info()

Installing in a local R library

If you manage your R packages in a local R library under $VSC_DATA/R while using a centrally installed R module, you can use the devtools package included in the module. You will need to execute the following commands in the R console:

> # First check that the R library path points to your local R library:
> .libPaths()
> # Set the R library path if this is not the case.
> .libPaths("/data/leuven/XXX/vscXXXXX/R/")
> # Load devtools and e.g. install your package from github:
> library(devtools)
> devtools::install_github("Developer/Package")

Note

The devtools package is not included in “-bare” R modules, e.g. R/4.0.2-foss-2018a-bare.

Installing in a conda environment

If you are using conda to manage your R packages, you should first install devtools in your conda environment. The following steps assume that you already have a conda environment named “science”. If you do not yet have a conda environment, First create a conda environment. In the following example, it is assumed that your miniconda environment is installed in $VSC_DATA/miniconda3.

$ # Activate your conda environment and install devtools
$ source activate science
$ conda install -c conda-forge r-devtools
$ # Launch R
$ R

> # Check that the R library path points to your conda R library
> .libPaths()
> # Set the R library path if this was not the case.
> .libPaths("/data/leuven/XXX/vscXXXXX/miniconda3/envs/science/lib/R/library")
> # Load devtools and e.g. install your package from github:
> library(devtools)
> devtools::install_github("Developer/Package")