Covers: Chapter 14 - Including data in a package

Package Data

Size limits and where large data goes

• Keep the whole package small. Source tarballs should stay under roughly 5 MB for software packages; do not bloat a software package with data.
• Large data sets must NOT be committed to the package. There is no Git-LFS support. Distribute large data through ExperimentHub or AnnotationHub.
• Traditional (self-contained) experiment data packages need pre-approval on the bioc-devel mailing list. Prefer Hub-based distribution instead.

Directory conventions

Location	Purpose	Access
data/	Exported R datasets	data("mydata")
inst/extdata/	Raw files parsed by workflows	system.file()
R/sysdata.rda	Internal, non-exported data	package-internal

• Small data used by examples, vignettes, and tests may ship directly in the package (data/ or inst/extdata/).
• Store scripts that generated the data in inst/scripts/ (or data-raw/).

Formats and compression

• Preferred format for data/: .RData created with save(). Other formats allowed (see ?data).
• Compress all data files.
• Avoid LazyData: true. Despite general R advice, Bioconductor recommends against it because it slows package loading when data is large.

Documentation requirements

• Every dataset must be documented: creation method, source, and intended use.
• Raw files in inst/extdata/ need metadata describing derivation and format.

Caching and file-writing restrictions

• Forbidden: downloading or writing files to the user home directory, working directory, or the installed package directory.
• For persistent caching use BiocFileCache (preferred) or tools::R_user_dir(package, which = "cache").
• For non-persistent scratch files use tempdir() / tempfile().

ExperimentHub / AnnotationHub

• ExperimentHub: curated experiment data stored externally, retrieved on demand.
• AnnotationHub: annotation resources (genomic identifiers, mappings) served externally.
• Both give a lightweight package: metadata + man pages + vignette, with the heavy data hosted remotely. See the HubPub CreateAHubPackage vignette.

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