Feature/r devtools

source/software/r_devtools.rst

@@ -0,0 +1,71 @@
+.. _r_devtools:
+
+R installing 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 or install devtools.
+
+.. note::
+
+  When consulting the devtools documentation, make sure that it is the correct version!
+  It should match the module devtools version. To check what devtools version is installed:
+
+  .. code-block:: r
+
+    library(devtools)
+    sessioninfo::session_info()
+
+Installing in a local R library
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you manage your R packages in a :ref:`local R library<r_package_management_standard_lib>` 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:
+
+.. code-block:: r
+
+   > # First check that the R library path points to your personal R library:
+   > .libPaths()
+   > # Set the R library path if this was is 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")
+
+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 :ref:`conda environment<r_package_management_conda>`. 
+
+.. code-block:: bash
+
+   $ # Activate your conda environment and install devtools
+   $ source activate science
+   $ conda install -c conda-forge r-devtools
+   $ # Launch R
+   $ R
+
+.. code-block:: 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")
+
+.. _devtools: https://www.rdocumentation.org/packages/devtools

source/software/r_package_management.rst

@@ -1,3 +1,5 @@
+.. _R_package_management:
+
 R package management
 ====================
 
@@ -12,6 +14,8 @@ very easy for a user to install them just for himself, or for his
 research group, that is not a problem though. Do not hesitate to contact
 support whenever you encounter trouble doing so.
 
+.. _r_package_management_standard_lib:
+
 Standard R package installation
 -------------------------------
 
@@ -48,6 +52,8 @@ library, .e.g., ::
 Note that R packages often depend on the specific R version they were installed
 for, so you may need to reinstall them for other versions of R.
 
+.. _r_package_management_conda:
+
 Installing R packages using conda
 ---------------------------------
 
@@ -177,3 +183,5 @@ More information
 ~~~~~~~~~~~~~~~~
 
 Additional information about conda can be found on its `documentation site <https://conda.readthedocs.io/en/latest/>`__.
+
+For installing R packages from github or other repositories see also :ref:`R devtools<r_devtools>`:

source/software/using_software.rst

@@ -55,6 +55,7 @@ R
 .. toctree::
    :maxdepth: 2
 
+   r_devtools
    r_command_line_arguments_in_scripts
    r_integrating_c_functions