Bookdown Document Not Rendering Outputs Correctly

Question

I have a bookdown document that renders fine on my local machine, but when I have it run as an automated process using GitHub Actions the outputs from the individual code chunks show up all jumbled up:

This is the GitHub repository for the book: https://github.com/ries9112/cryptocurrencyresearch-org

And here are where the automated runs through GitHub Actions are running: https://github.com/ries9112/cryptocurrencyresearch-org/actions

In order to help troubleshoot the problem, I created a separate repository as a much more barebones example, and I am running into the exact same issue. Here is the repository for the simpler example: https://github.com/ries9112/bookdown-test

I deployed the results from that simpler test and you can find them here: https://brave-leakey-37b898.netlify.app/intro.html#here-adding-new-test

The documents format totally fine locally, so looks like there may be something else that I need to install, but I am currently installing pandoc and tinytex, and I can't figure out what else may be missing. Here is the YAML file that defines the GitHub Action:

jobs:
  build:
    runs-on: macOS-10.15
    steps:
      - uses: actions/checkout@v2
      - uses: r-lib/actions/setup-r@v1
      - name: Install pandoc and pandoc citeproc
        run: |
          brew install pandoc
          brew install pandoc-citeproc
      - name: Install Packages
        run: |-
          Rscript -e "install.packages(c('pins','bookdown','tidyverse','DT'))"
      - name: Refresh book
        run: |-
          Rscript -e "bookdown::render_book('index.Rmd', 'bookdown::gitbook')"

Any thoughts on any anything that may be missing in those installation steps to get this to render correctly? I have tried on Ubuntu and Windows as well and ran into the same problems.

I also tried these steps for pandoc and tinytex install and ran into the same exact problem:

      - uses: r-lib/actions/setup-pandoc@v1
      - uses: r-lib/actions/setup-tinytex@v1

Would really appreciate any thoughts on how to fix this issue!

Also posted to RStudio Community and will update both with the answer if one is found.

Answer 1

I think you need to deactivate coloring enabled by the crayon package, which is used by the tidyverse.

By default, it is activated on Github Action when you are using setup-r https://github.com/r-lib/actions/blob/9598b8eeb6d88de7d76d580d84443542bbfdffce/setup-r/action.yml#L14-L16

So you need to change it to FALSE

      - uses: r-lib/actions/setup-r@v1
        with:
          crayon.enabled: 'FALSE'

in you actions yaml file.

You can also deactivate it as an option in your bookdown project

options(crayon.enabled = FALSE)

You have to do that on Github Action because crayon is not disable automatically when used in GHA. Don't know why