Github Actions for Bioconductor

This repository holds some GitHub actions that may be useful for those developing or maintaining R packages that will be hosted by the Bioconductor project. Actions can be considered as tasks that form the building blocks of larger workflows. The development of an R package often benefits from the deployment of workflows for testing the code in a variety of conditions e.g. a variety of operating systems and specific versions of software.

The acceptance of a package to Bioconductor project, as well as continued inclusion and deployment by passing tests on it's nightly build system, involves accommodating a number of specific requirements and features that make developing for it subtly different to a CRAN package. The actions provided here aim to simplify deploying a Github Workflow that closely matches the Bioconductor requirements.

These actions are built upon the GitHub Actions for the R language and should be considered complementary to them. It's also recommended to take a look at the biocthis package, which provides templates and functions for setting up GitHub Actions workflows for Bioconductor packages.

Actions

The actions currently hosted here are:

• bioc-actions/setup-bioc - Given a version of Bioconductor, this action installs the appropriate version of R and initialises the BiocManager package.
• bioc-actions/build-install-check - Build, install, and check a package emulating the process used by the Bioconductor Build System.
• bioc-actions/run-BiocCheck - Runs BiocCheck::BiocCheck() on a given package directory.
• bioc-actions/use-bioc-caches - Create and use a directory for caching files downloaded by Bioconductor packages between workflow runs.

Examples

Example workflows for using these actions on both a package repository and a repository where a package is stored in a subdirectory can be found in the biocActionsExamples repository.