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Drop BiocStyle vignette dep so webR build resolves - #79

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vcjdeboer merged 1 commit into
develfrom
webr-drop-biocstyle
Sep 5, 2026
Merged

vcjdeboer merged 1 commit into
develfrom
webr-drop-biocstyle

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Problem

After #78 removed Remotes: bioc::BiocStyle (required by BiocCheck), the manual webr.yml build failed deterministically at rwasm dependency resolution:

Error in res_one_row_df(entries) : nrow(out) must equal 1

rwasm pulls Suggests, which included the Bioconductor-only BiocStyle. Without the Remotes hint and without a Bioconductor repo, rwasm's environment can't resolve it. (The R-CMD-check CI passes because those runners have Bioconductor; the webR/rwasm environment does not.)

Fix

  • Vignette output: switched from BiocStyle::html_document → rmarkdown::html_document (same toc/numbering/float options).
  • BiocStyle removed from Suggests.

This removes the only Bioconductor dependency, so the webR build resolves — and it keeps DESCRIPTION clean for Bioconductor (no Remotes needed).

Verification

  • R CMD build: vignette renders OK with the new format.
  • R CMD check --as-cran: 0 WARNINGs / 0 ERRORs, 3 NOTEs (URL 404 + style, non-blocking).
  • Dependency resolution of this branch: BiocStyle no longer present (85 deps, none Bioconductor) — the resolution error is gone.

After merge, re-run webr.yml to rebuild the book's gh-pages build.

🤖 Generated with Claude Code

Switch the vignette output from BiocStyle::html_document to
rmarkdown::html_document and remove BiocStyle from Suggests. rwasm
cannot resolve the Bioconductor-only BiocStyle without a Remotes hint
(which BiocCheck disallows), which broke the webR/gh-pages build.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01WRiaazotsabW2TZ499LLr4
@vcjdeboer
vcjdeboer merged commit c2b17b1 into devel Sep 5, 2026
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