Documentation

Covers: Chapter 13 - Documentation (man pages and vignettes).

Man pages (Rd files)

Every exported function and class must have a man page.
Class documentation must be very detailed about the structure and type of information stored in the object.
Data man pages must include provenance information and data structure information.
A package-level man page is encouraged, accessible via ?<package name>.
Documentation may be authored with roxygen2 (comments compiled to Rd) or written directly as Rd.

All man pages should have runnable examples.
The enforced threshold is 80%: BiocCheck counts man pages that document an exported object, and raises an ERROR - “At least 80% of man pages documenting exported objects must have runnable examples” - when fewer than 80% of them have one. Verified in checkExportsAreDocumented(), BiocCheck devel, 2026-08-14.
A page whose examples sit entirely inside \dontrun or \donttest counts as having no example: BiocCheck runs tools::Rd2ex(commentDontrun = TRUE, commentDonttest = TRUE) and then parses what is left. Wrapping an example to silence a check therefore moves the package toward the ERROR, not away from it.
\donttest and \dontrun are generally not allowed except with proper justification.
If wrapping is unavoidable, prefer \donttest over \dontrun.

At least one vignette is required, in Rmd (recommended), qmd (Quarto), or Rnw (Sweave) format.
Code must be executable and demonstrate actual functionality: “Non-trivial executable code is a must!!! Static vignettes are not acceptable.”
Each vignette should include an Introduction, Installation instructions, a Table of Contents (when appropriate), and a sessionInfo() call.
Installation instruction chunks must use eval = FALSE.
R Markdown vignettes should use the BiocStyle package for rendering.
Quarto vignettes require the Quarto command-line tool to be listed in DESCRIPTION.

Source: Documentation Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).