Update R.gitignore

[promicrobial]

Reasons for making this change

I've noticed that the current version has not taken the use of Quarto or renv ignore rules into consideration. The file is also missing the RStudio project file .Rbuildignore.

Both Quarto and renv create cache and/or library directories that should not be checked in to git.

Links to documentation supporting these rule changes

If enabled, Quarto creates a _freeze directory that stores computations to reduce the need to re-compute code. Users may or may not want to add this to their .gitignore files depending on if you need others to reproduce your computational environment (source).

• Quarto should automatically add .local to your .gitignore to ensure that .local files are not committed (source), but to be better safe than sorry I have added a pattern for this.
• Output directories can be ignored (source).
• renv and .renvignore but not renv/activate.R (source)
• .Rbuildignore is missing from the RStudio patterns

Merge and Approval Steps

• [x] Confirm that you've read the contribution guidelines and ensured your PR aligns
• [x] Ensure CI is passing
• [ ] Get a review and Approval from one of the maintainers

[wirecat]

@promicrobial Everything but .Rbuildignore makes sense and docs help a lot with the review, thank you!

For .Rbuildignore it's listed as a project setting file and when I look into it, I can't tell whether it should be ignored or not 🤔. I do see people ignoring it a bit on GitHub though. Is this maybe a situation where it should be commented out with a comment explaining why some people may want to ignore the file?

[github-actions[bot]]

This PR is stale because there have been no updates in 90 days. It will close after 180 days of inactivity. Leave a comment if you want to keep it open :smile:

[doriangurazdowski0-prog]

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Dorian Gurazdowski - Chat @ Spike [3dciry]

On November 7, 2025 at 16:41 GMT, github actions bot @.***> wrote:

github-actions[bot] left a comment (github/gitignore#4672)

This PR is stale because there have been no updates in 90 days. It will close after 180 days of inactivity. Leave a comment if you want to keep it open 😄

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