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Install pkgdown before pkgdown::build_site() - #4
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The reusable workflow installs remotes/rcmdcheck/BiocCheck/covr plus the package's declared dependencies, but nothing installs pkgdown, so the Build pkgdown step (release-branch pushes with enable_pkgdown) fails unless a calling package happens to Suggest it. Install it just before use. Flagged by Copilot review on waldronlab/curatedCRCData#5. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Copilot review overview
🟡 Changes recommended
The installation does not honor the workflow’s configured CRAN repository.
Review effort: Balanced
Findings: 1
What changed in this PR
Installs pkgdown before building package documentation.
Changes:
- Adds conditional
pkgdowninstallation beforebuild_site().
| File | Description |
|---|---|
.github/workflows/bioc-pr-cmdcheck-pkgdown.yml |
Installs pkgdown before site generation. |
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Set options(repos) from the CRAN env var before BiocManager::install, matching the workflow's other install steps. Flagged by Copilot. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Good catch — now sets options(repos) from the CRAN env var before installing, matching the other install steps. 🤖 Drafted with Claude Code |
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The dependency setup installs remotes/rcmdcheck/BiocCheck/covr plus each calling package's declared dependencies, but nothing installs pkgdown itself, so the
Build pkgdownstep (release-branch pushes withenable_pkgdown, the default) fails unless the calling package happens to list pkgdown in Suggests — which none of the curated*Data packages do, and adding it there risks "suggested but not available" notes on the Bioconductor builders. Install it just before use instead.Flagged by Copilot review on waldronlab/curatedCRCData#5.
🤖 Generated with Claude Code