Covers: Chapter 17 - Code other than R (compiled and third-party)

Compiled Code and Third-Party Code

General rules

Compiled code must follow the “System and foreign language interfaces” section of the Writing R Extensions (R-exts) manual.
Use Makevars/Makefile sparingly; they are often unnecessary. See the “Configure and cleanup” section of R-exts.
Code must be portable and build across all supported platforms (Linux, macOS, Windows). Test on all before submission.
Place compiled sources in src/.

C++: use Rcpp for cross-platform C++ integration (see the Rcpp Gallery).
Fortran: consider dotCall64 for modern Fortran integration.
Python: use basilisk to configure Python environments automatically so users need no manual install. reticulate is at developer discretion.
CMake-based builds: use the biocmake package.

Do not bundle external libraries that duplicate functionality already provided by supported R/Bioconductor packages.
Maintainers take full responsibility for any bundled third-party code: keep it updated with upstream bug fixes and releases.
Complex external libraries may require you to provide pre-built binaries for some platforms.
Ensure the license of any bundled third-party code is compatible with, and redistributable under, the package license.

Source: Code other than R Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).