General Development Requirements

Covers: Chapter 3 - General guidelines, and Chapter 4 - Important Bioconductor package development features.

Development environment

  • Develop against the devel version of Bioconductor and use devel Bioconductor packages.
  • Use a recent R-devel matching the current Bioconductor devel branch.

Pre-submission gate (build and check)

  • Must pass R CMD build and R CMD check with NO errors and NO warnings on recent R-devel.
  • Must pass BiocCheck::BiocCheckGitClone() with no errors/warnings.
  • Must pass BiocCheck::BiocCheck('new-package' = TRUE) with no errors/warnings.
  • All ERRORs, WARNINGs, and NOTEs must be addressed or explicitly justified.

Numeric thresholds (note the modality - only one of these is a “must”)

  • Individual files (software packages): <= 5 MB each. Upstream: “individual files must be <= 5MB”.
  • Source package produced by R CMD build: < 10 MB. Upstream: “should occupy less than 10 MB on disk”.
  • R CMD check --no-build-vignettes runtime: < 10 minutes. Upstream: “should require less than 10 minutes to run R CMD check –no-build-vignettes”.
  • Memory across vignettes, examples, and tests: < 8 GB. Upstream: “it is recommended that the vignettes, man page examples, and unit tests do not require more than 8 GB of memory”.
  • Use lossy compression (e.g., pngquant) to shrink large images/screenshots.

Treat the three “should” items as strong expectations: the build system enforces them in practice and a reviewer will ask. But do not tell a submitter they are blocked from submitting by them.

File hygiene

  • Do not include filenames that differ only in case (cross-platform safety).
  • Exclude unnecessary files: .DS_Store, .project, .git, cache files, logs, *.Rproj, *.so.
  • Use .gitignore to keep undesirable files out of the repository.
  • Application-specific tooling (GitHub Actions, devtools config) “should be in a different branch” than the default one holding package code. A recommendation upstream, not a rule.
  • R CMD check options are customized by Bioconductor via flags configurable through the R_CHECK_ENVIRON environment variable.

biocViews (required feature)

  • The DESCRIPTION file MUST contain a biocViews: field (case-sensitive, lowercase ‘b’).
  • Choose terms from only ONE category: Software, Annotation Data, Experiment Data, or Workflow.
  • Use leaf-level terms rather than broad parent categories.
  • Terms must match the official hierarchy exactly (spelling and capitalization); consult the devel branch biocViews list.
  • Submission validation checks that biocViews are present, valid, and from a single category.

Vignettes (required feature)

  • Every submitted package must have at least one Rmd (preferred) or Rnw vignette.
  • Render with BiocStyle::html_document.
  • Vignettes must contain evaluated (non-trivial, runnable) R code.
  • Include a detailed introduction motivating inclusion in Bioconductor and, where relevant, compare against existing similar packages.

Reuse existing infrastructure

  • Reuse established Bioconductor classes and methods where appropriate (see the Common Bioconductor Methods and Classes guidance / methods-classes.md).

Source: General package development and Important Bioconductor package development features Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).

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