Disable multienrichjam install code, exclude it from workshop.R - #39
Merged
Conversation
Comments out the install.packages/remotes/library/help lines in the optional multienrichjam install chunk so they can't be accidentally run, and wraps the whole chunk in <!--omit-begin/end--> so it's excluded from the generated workshop.R entirely while remaining visible in the rendered book chapter.
hosseinvk
had a problem deploying
to
github-pages
August 10, 2026 12:41 — with
GitHub Actions
Failure
2 tasks
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
install.packages("remotes")/library(remotes)/remotes::install_github(...)/library(multienrichjam)/?enrichDF2enrichResultlines in the optional multienrichjam install chunk in10-clusterprofiler.Rmd, so they can't be run accidentally (chunk already hadeval = FALSE, but that only affects knitting, not manual execution).<!--omit-begin-->/<!--omit-end-->so it's excluded entirely from the generatedworkshop.R, while remaining visible (as before) in the rendered book chapter.Test plan
bookdown::render_book()completes cleanly; confirmed the chunk still renders indocs/clusterprofiler-and-enrichplot.html.workshop.Rand confirmed none of the install/library/help lines appear anywhere in it.bookdown-renderjob to be confirmed green before merge.