R Package Development — From Zero to CRAN & Bioconductor

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.

R Package Development — CRAN & Bioconductor

Package Skeleton

r

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:

r

# 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

r

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

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

R CMD check

r

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

For Bioconductor, also run:

r

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.