This week, I used pkgdown, rhub, and GitHub Action via the usethis package to allow web-based documentation, checking, and continuous integration and delivery (CI/CD) for the ribiosUtils package. Here are my learning notes.


Why do I do this? Mainly for three reasons:

  1. To create web-accessible documentations so that I can point users to them.
  2. To test the package on systems that I am not working in to make sure that it works everywhere.
  3. To automatically notify me if the latest pushes in GitHub breaks any tests or make the package stop working in some environment.

It is hoped that, with these efforts, I can make ribiosUtils towards a better piece of scientific software.

Convert package documentations to a website with pkgdown

pkgdown builds a website form the package using Rd files (which can come from, for instance, roxygen documentations).

It is fairly easy to use. If we run it locally, we need first to configure the package to use pkgdown with usethis::use_pkgdown(), and then to generate the website with pkddown::build_site(). The site will be stored in the docs directory of the package.

On my first try, I found pkgdown had problems with functions whose examples attempt to write to the standard output or other connections (for instance registerLog and writerLog in ribiosUtils). These commands will trap pkgdown in a dead, permanent loop complaining connections are not closed. By wrapping such examples inside \dontrun{}, I got rid of the problem.

There are two ways to make the website available on GitHub. We can set the GitHub pages’ source to ‘master branch /docs folder’. If we do this, we can build website locally, commit any changes to GitHub, and pushing the changes to the GitHub repository.

Alternatively, We can also set the source of GitHub pages to the gh-pages branch of the repository, and setup a GitHub Action (see also below) to automatically generate and update the website when we push changes. This is the variant that I used. Below I document the steps that I took to setup this up (which I discovered from here).

A step-by-step guide to setup pkgdown and gh-pages

First, create an empty gh-pages branch in the package directory (the package has already been in GitHub).

git checkout --orphan gh-pages
git rm -rf .
git commit --allow-empty -m 'Initial gh-pages commit'
git push origin gh-pages
git checkout master

Next, configure the package to use pkgdown by running the following command in R console.


Finally, we add the GitHub Action for pkg to automatically add documentation. There is an existing yaml template example in the actions package available on GitHub r-lib/actions.

usethis::use_github_action(url = "")

By using this template (see the yaml file for details), we will make pkgdown generate or update the site anytime there is a push event in the master branch.

As soon as we add, commit, and push the yaml file, we have setup the CI/CD of pkgdown.

Test R package building with r-hub

The R-hub builder is a website which can be used to build a source R package into binaries on many different platforms including Mac, Linux, and Windows. Its R client, rhub, can used to check R code on platforms other than the one the developer is working on.

For instance, you can run the following commands to test the package residing in the current directory, even if you are not working on the systems in which the package will be tested.

myCheck<- check() ## you can choose on which R-hub platforms it will be checked
## the following commands let you examine the results, retrieve URLs, etc.
## useful shortcuts
## prior to submission to CRAN
check_for_cran() ## very useful for packages need to be submitted to CRAN
check_with_valgrind() ## checking in valgrind to find memory leaks and pointer errors
## retrieve previous checks
previousChecks <- rhub::list_package_checks("PATH",email="",howmany=4)

When you use rhub for the first time, you need to validate the E-mail address. From then one, an email of checking results will also be sent to that address.

My impression is that R-hub and its client rhub are useful to check the package and to make sure that the package can be built also on other systems (especially if it contains compiled code). I find the only drawback is that it can be slow, especially when the dependent packages need to be first installed.

Setup GitHub Actions to test R packages and to render pkgdown automatically

The GitHub repository r-lib/actions lists commonly used GitHub Actions for the R language. I used to copy and paste action definition files from there to my packages.

Recently, thanks to this tutorial on GitHub Actions with R from Brown et al. (ropenscilabs), I found that the usethis package can be used to automate this process.

usethis::use_github_action_check_standard() ## or _check_release

More about usethis

usethis is a workflow package which automates repetitive tasks during project setup and development. Its main functionalities include

  • Creating a package or project
  • Managing an active project
  • Adding or modifying files found in R packages
  • Setting up packages
  • Releasing packages
  • CI/CD functionalities
  • Conventions specific to tidyverse
  • Configuration
  • Interfacing with Git and GitHub
  • etc.

For more details, see Reference of the package.


By using pkgdown, and rhub, and usethis, it is possible to setup web-based documentation, checking, and continuous integration and delivery (CI/CD) in short time (less than a few hours) for a R package such as ribiosUtils that needs compilation of source code and thus extensive testing in multiple operating systems.

Adopting such tools can be time-consuming, especially at the beginning, because one needs to invest time in learning them and adapting existing packages to use these tools. Making the hurdle of learning higher, the tools themselves are under fast development and therefore unexpected problems may appear from time to time. It is hoped, however, that the long-term payment is worth the investment, especially when the code can run anywhere and when bugs are found early enough.

There are still a few small problems that I wish I can dive deeper. For instance, why the devel branch of Mac fails the test while other versions of R are doing well (as of July 22nd, 2020)? Currently, I cannot afford that and will just proceed. Nevertheless, the overall experience of adopting these tools was positive. I will continue updating other ribios packages as well as several CRAN/Bioconductor R packages of mine, so that they are up to the standards that I described above. Clearly, some hard work lies ahead.