R Package Development — From Zero to CRAN & Bioconductor

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name: r-package-dev description: Build, check, and submit R packages to CRAN or Bioconductor. Use when creating a new R package from scratch, fixing R CMD check errors/warnings, preparing for CRAN or Bioconductor submission, setting up GitHub Actions CI for R packages, writing S4 classes extending Bioconductor containers (SummarizedExperiment, GRanges), adding roxygen2 documentation with @references and DOIs, or debugging BiocCheck issues. Covers both CRAN and Bioconductor workflows with real submission experience.

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R Package Development — CRAN & Bioconductor

Package Skeleton

usethis::create_package("~/mypkg")
usethis::use_mit_license("Author Name")   # CRAN
OR: License: Artistic-2.0              # Bioconductor standard
usethis::use_testthat()
usethis::use_vignette("introduction")
usethis::use_readme_md()
usethis::use_news_md()

Required: DESCRIPTION, NAMESPACE, LICENSE, NEWS.md, README.md, .Rbuildignore, .gitignore

DESCRIPTION

CRAN rules

Title: title case, ≤65 chars, no period

Description: ≥2 sentences, ends with period

Software names in quotes: 'CmdStan', 'OpenSSL'

Authors@R: use person() with aut, cre roles + ORCID

Imports: only packages actually called via :: or importFrom

Suggests: must have requireNamespace() guard in code

Bioconductor additions

Version: 0.99.0 for new submissions

biocViews: required (e.g., Genetics, Sequencing, QualityControl)

LazyData: false (Bioconductor requirement)

≥2 Bioconductor packages in Imports

VignetteBuilder: knitr

Collate field listing all R/*.R files in dependency order

R/ Code Standards

Never use in R/ files:

| Forbidden | Use instead | |-----------|-------------| | library() / require() | :: or @importFrom | | T / F | TRUE / FALSE | | sapply() | vapply() (type-safe) | | 1:length(x) | seq_along(x) / seq_len(n) | | cat() / print() | message() (except in show methods) | | options() / par() | Never modify global state | | @slot direct access | Use accessor generics | | <<<- | Never use global assignment | | set.seed() / browser() | Remove before submission |

Documentation (roxygen2)

Every @export function must have:

@param for all arguments

@return describing the return value

@examples that run in <5 seconds

@references with DOIs for methods: \doi{10.xxxx/yyyy}

Use \donttest{} for slow examples. Never \dontrun{}.

S4 Classes (Bioconductor)

For infrastructure packages extending Bioconductor classes:

# Define generic — this is the extension point
setGeneric("myFunction", function(x, ...)
    standardGeneric("myFunction"))
Define method for your class
setMethod("myFunction", "MyClass", function(x, ...) {
    # implementation
})

Key principle: analytical operations should be generics, not plain functions. This lets downstream packages specialize behavior for their own classes. See references/bioconductor.md.

Testing

devtools::test()                    # all tests
covr::package_coverage()            # target ≥80%

Test error paths with expect_error(), not just happy paths.

R CMD check

rcmdcheck::rcmdcheck(
    args = c("--no-manual", "--as-cran"),
    error_on = "warning"
)

For Bioconductor, also run:

BiocCheck::BiocCheck("pkg_0.99.0.tar.gz", new-package = TRUE)
BiocCheck::BiocCheckGitClone(".")

GitHub Actions CI

See references/github-actions.md for platform-specific configs.

CRAN packages: use r-lib/actions standard workflow. Bioconductor packages: use r-lib/actions/setup-r-dependencies which auto-resolves Bioc deps from DESCRIPTION.

Visualization (publication grade)

See references/visualization.md for Nature/Science style standards.

Key rules:

Colorblind-safe palette: Wong (2011) *Nat Methods* 8:441

theme_classic(), no gridlines, 8pt base font

No titles on figures (titles go in captions)

Panel labels: bold lowercase a, b, c

Paired dot plots > bar charts for before/after comparisons

Submission

CRAN

Upload tarball to https://xmpalantir.wu.ac.at/cransubmit/ Include cran-comments.md. See references/cran.md.

Bioconductor

1. Register at https://support.bioconductor.org (same email as DESCRIPTION) 2. Subscribe to bioc-devel mailing list 3. Add SSH key to GitHub 4. Make repo Public 5. Open issue at https://github.com/Bioconductor/Contributions/issues/new See references/bioconductor.md for the submission template.

Common Issues

See references/troubleshooting.md for solutions to frequent R CMD check and BiocCheck problems.