Bioconductor GitHub Actions Workflows

This repository (bioconductor/workflows) hosts reusable GitHub Actions workflows for R/Bioconductor package development.

NOTE: This is pre-release. Please try it and file issues, but some things may not work yet. The first stable release will be tagged v1.

Quick Start

To run the Linux version of the "official" Bioconductor R CMD check and BiocCheck, just copy ci.yml template to .github/workflows/ci.yml in your package repository on GitHub. It should "just work".

To customize options (add Codecov, pkgdown, cyclocomp, or change check sensitivity from the default "warning") use the web-based Bioconductor GitHub Actions Workflow Generator and see the BiocCheck Usage Guide.

r-universe-org/workflows for Multi-platform Testing

For Multi-OS (Linux, macOS, Windows, WebAssembly) checks, use the r-universe-org build.yml workflow. Specify that BiocCheck should be run during the build by adding organization: bioconductor to the workflow with: parameters; indented the same as the last line in the r-universe README.md workflow example. For packages already in Bioconductor, search the r-universe package landing pages for current build status.

Documentation

The documentation for these workflows has been separated into distinct files for clarity:

• BiocCheck Usage: Comprehensive instructions for using the bioccheck.yml reusable workflow, including test coverage and pkgdown setup.
• Workflow Comparison: A detailed comparison of the two workflows to help you choose the right one for your needs.
• Technical Notes: Software architecture, ADRs, internal test flows (canary.yml, actionlint.yml), and guidelines for contributors.