Adding Exectutable Code

You can add executable code chunks to your pages. See quarto Using R documentation for more information.

Example Code Chunk

# Generate some sample data
x <- 1:10
y <- x^2

# Create a basic scatter plot
plot(x, y, type = "b", col = "blue",
     main = "Base R Plot",
     xlab = "X values", ylab = "Y = X squared")

Adding Packages & Common Errors

If you are working on some code that has additional package dependencies, you may need to add them to your GitHub Actions workflow so those code chunks can be rendered and executed properly.

This template includes a basic render-and-publish.yml workflow that should work for most applications.

Package Errors

If you are encountering errors in your GitHub actions which are not allowing you to publish your pages, you will need to change your workflow.

On your GitHub repository, click on the ‘Actions’ tab and look for failed workflows. You can click on the failed workflow to identify where the action failed. Below is an example fail-point where a required package cannot be found

Edit Basic Workflow

One solution to this error is to include your additional packages in the basic render-and-publish.yml workflow.

  1. Open your render-and-publish.yml workflow file

  2. Identify the following lines (should be around line 17 & 18)

      - name: Install packages (needed for Rmd)
    run: Rscript -e 'install.packages(c("rmarkdown", "knitr", "jsonlite"))'

  3. Add packages to the list on the second line

    • Example:

          run: Rscript -e 'install.packages(c("rmarkdown", "knitr", "jsonlite", "dplyr"))'

  4. Commit the changes and your workflow should re-run without errors

Using renv Workflow

If you are still encountering package errors you may need to set up a renv workflow in your R project. This will manage the package dependencies and ensure the proper packages are installed and loaded for rendered GitHub pages.

  1. Make sure you have an R project open for your repository and initialize renv in the project by running the following code renv::init() (you may need to install the renv package). This will create a locale renv folder and a renv.lock file with the packages you loaded
  2. Install and load any additional packages, every time you add a new package you will need to add them to your project’s renv.lock file by running the following code renv::snapshot()
  3. Use .github/workflows/render-and-publish-with-code.yml as your default GitHub pages actions workflow