R packages with devtools

The installation of some R packages may require the use of devtools. The devtools package facilitates the development of your own R packages as well as the installation of R packages from Git repositories such as GitHub, Gitlab or Bitbucket.

In the following we will use GitHub as example. Please consult the devtools documentation for examples with other repositories.

The devtools package is already available in all software modules of R found in the central libraries of VSC clusters.

$ module load R/4.5.1-gfbf-2025a
$ R
> library(devtools)
> sessioninfo::session_info()
## ─ Session info ────────────────────
##  setting  value
##  version  R version 4.5.1 (2025-06-13)
##  [...]
## ─ Packages ────────────────────────
##  package     * version date (UTC) lib source
##  cachem        1.1.0   2024-05-16 [2] CRAN (R 4.5.1)
##  cli           3.6.5   2025-04-23 [2] CRAN (R 4.5.1)
##  devtools    * 2.4.6   2025-10-03 [2] CRAN (R 4.5.1)
##  [...]

Installs in local R library

Installations with devtools in a local R library follow the same location rules as for the default package manager in R.

You can check and control the list of library paths with .libPaths() as usual:

# 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. e.g.
.libPaths("/data/leuven/XXX/vscXXXXX/Rlibs/rocky9/icelake/R-4.2.2")

Once the target location is set, then you can install a package from GitHub with devtools as follows:

library(devtools)
install_github("Developer/Package")

Devtools 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 working Conda environment with R named science. If you do not yet have such an environment, you can create one by following the instructions in R packages using Conda.

In the following example, it is assumed that your miniconda environment is installed in $VSC_DATA/miniconda3.

1. Activate your conda environment and install devtools

   $ source activate science
   $ conda install -c conda-forge r-devtools
   

2. Launch R and load devtools

   ## 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/<vsc-site>/xxx/vscxxxxx/miniconda3/envs/science/lib/R/library")
   ## Load devtools and e.g. install your package from github:
   library(devtools)
   

3. Install some R package with devtools

   devtools::install_github("Developer/Package")