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Declare openxlsx so the pkgdown build can render all vignettes - #54
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capstoneanalysis_BearklandM.Rmd loads openxlsx in an evaluated chunk, but openxlsx was not listed in DESCRIPTION and is not a dependency of anything that is, so the pkgdown workflow (which only installs declared dependencies) could not render it. Add it to Suggests. Also build the site on pull requests to main (deploy and Codecov steps are skipped on PRs) so vignette failures surface before merge. Refs #50 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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openxlsx is now declared, but capstoneanalysis_BearklandM.Rmd (line 33) also evaluates library(boot), and boot is still undeclared. It is a recommended package that usually ships with R, so it is probably installed on CI, but R CMD check and Bioconductor will still flag it. Add boot to Suggests. Also consider bumping Date: (still 2026-06-01) along with the version.
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The new PR trigger runs build_site_github_pages() and the full vignette build on every PR. That step is slow because it pulls curatedMetagenomicData and bugsigdb data. It also makes GITHUB_PAT: secrets.GITHUB_TOKEN a read-only token on fork PRs, which can hit API rate limits or fail the build. Consider adding a paths: filter (vignettes/**, DESCRIPTION, _pkgdown.yml, R/**) so unrelated PRs don't pay for it.
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Review notes, most important first:
No exported-function documentation or test changes are involved in this PR. |
- fieldworkanalysis_samara: use createTaxonTable()'s current column names (increased_signatures / decreased_signatures). - WomensHealth_Pregnancy: replace hard-coded 3-colour fill scales with scale_fill_brewer(), since the data now has 4 sequencing types. - healthysig: BugSigDB Study 562 (the healthy reference signatures this analysis relies on) no longer exists, so every chunk failed. Show the code without evaluating it and add a note explaining why. Refs #50 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
capstoneanalysis_BearklandM.Rmd loads openxlsx in an evaluated chunk, but openxlsx was not listed in DESCRIPTION and is not a dependency of anything that is, so the pkgdown workflow (which only installs declared dependencies) could not render it. Add it to Suggests.
Also build the site on pull requests to main (deploy and Codecov steps are skipped on PRs) so vignette failures surface before merge.
Refs #50