Bug: pkgdown site fails to build after merging PRs into `main`

Summary

After merging a pull request into main, the GitHub Actions pkgdown workflow fails and the package website is not rebuilt or deployed.

The failure occurs during the vignette rendering stage when pkgdown::build_site_github_pages() attempts to build the site.

Expected behavior

• A PR is merged into main.
• The pkgdown GitHub Action runs successfully.
• The package website is rebuilt.
• Updated documentation is deployed automatically to GitHub Pages.

Actual behavior

The pkgdown workflow fails during the Build site step, preventing the website from being generated and deployed.

Workflow error:

Error in `.f()`:
! Failed to render 'vignettes/capstoneanalysis_clare.rmd'.

Caused by error:
! Duplicate chunk label 'significant-taxa-plot'

Error log

Reading vignettes/capstoneanalysis_clare.rmd

Error in `.f()`:
! Failed to render 'vignettes/capstoneanalysis_clare.rmd'.

Caused by error:
! Duplicate chunk label 'significant-taxa-plot', which has been used for the chunk:

sig_df <- significantTaxa(
  sigs      = gut.sigs.increased,
  cn_result = cn_res,
  n         = 20,
  plot      = FALSE,
  plot_type = "lollipop",
  title     = "Taxon frequency vs. Monte Carlo threshold\n(gut, COVID-19 increased)"
)

Execution halted
Error: Process completed with exit code 1.

Additional warnings reported by pkgdown

Bootstrap 3 is deprecated; please switch to Bootstrap 5.

URLs not ok.

In DESCRIPTION, URL is missing package url
(http://waldronlab.io/bugSigSimple).

These warnings do not appear to be responsible for the workflow failure, but they may also need attention.

Reproduction

1. Merge a pull request into main.
2. Allow the pkgdown GitHub Action to run.
3. Observe that the workflow fails during the vignette build stage.
4. The package website is not rebuilt or deployed.

Possible cause

The vignette vignettes/capstoneanalysis_clare.rmd contains at least two code chunks with the same label:

{r significant-taxa-plot}

knitr requires every chunk label within an .Rmd file to be unique.

Suggested fix that i propose

• I think we need to rename duplicate chunk labels in vignettes/capstoneanalysis_clare.rmd. OR

• Re-run the pkgdown workflow. (But I doubt this one)

• Optionally:

  • Migrate from Bootstrap 3 to Bootstrap 5. (Not sure about this one but we can read about it and see) OR MAY BE
  • Add the missing package URL to DESCRIPTION.

Could you be having a different approach here @lwaldron @cmirzayi

Start in vignettes/capstoneanalysis_clare.rmd and locate all chunks labeled significant-taxa-plot, then review the pkgdown GitHub Actions workflow that runs the site build. Rename duplicate labels as needed and rerun the pkgdown workflow; done means the vignette renders, the workflow succeeds, and the website is rebuilt and deployed.