- 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.
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: useperson()with aut, cre roles + ORCID- Imports: only packages actually called via
::orimportFrom - Suggests: must have
requireNamespace()guard in code
Bioconductor additions
- Version:
0.99.0for 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:
@paramfor all arguments@returndescribing the return value@examplesthat run in <5 seconds@referenceswith 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
- Register at https://support.bioconductor.org (same email as DESCRIPTION)
- Subscribe to bioc-devel mailing list
- Add SSH key to GitHub
- Make repo Public
- 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.