neurogenomics/rworkflows
rworkflows: Full workflow to test, document, and deploy R packages.
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- Scorecard 4–6scored Jul 6, 2026
- Maintenance Recency
- Activelast commit May 6, 2026
- License
- None
Pinned Snippet
uses: neurogenomics/rworkflows@6aaf49348859a96eea744b1907b1fe850e3ead5e # v1.0.12tags can be moved; commit SHAs can't. why a SHA?
Inputs
| name | description | required | default |
|---|---|---|---|
| run_bioccheck | Run Bioconductor checks. Must pass in order to continue workflow. | — | true |
| run_rcmdcheck | Run R CMD checks. Must pass in order to continue workflow. | — | true |
| as_cran | When running R CMD checks, use the '--as-cran' flag to apply CRAN standards. | — | — |
| run_vignettes | Build and check R package vignettes. | — | true |
| run_covr | Run code coverage tests and publish results to Codecov. | — | true |
| run_pkgdown | Knit the README.Rmd (if available), build documentation website, and deploy to gh-pages branch. | — | true |
| has_testthat | Run unit tests with the `testthat` package and report the results. Requires a subdirectory named 'tests'. | — | true |
| run_lintr | Run `lintr::lint_package()` and emit GitHub annotations for each lint. Does not fail the workflow by default. | — | true |
| run_spelling | Run `spelling::spell_check_package()` and surface any misspellings via GitHub annotations. Does not fail the workflow by default. | — | true |
| has_runit | Run unit tests with the `RUnit` package. Requires a subdirectory named 'unitTests'. | — | false |
| has_latex | Install a suite of LaTeX dependencies used for rendering Sweave (.rnw) and other documentation files. | — | false |
| tinytex_installer | Which release of tinytex (bundles of LaTeX packages) to use. All options can be found here: https://github.com/rstudio/tinytex-releases/ Note, 'TinyTeX-2' is only available for 'tinytex_version: daily'. | — | TinyTeX-1 |
| tinytex_version | Which version of tinytext to use. When set to '', uses the latest daily build. All versions can be found here: https://github.com/rstudio/tinytex-releases/releases | — | "" |
| pandoc_version | Which version of pandoc to use. For details see here: https://github.com/r-lib/actions/tree/v2-branch/setup-pandoc | — | 2.19 |
| run_docker | Whether to build and push a Docker container to DockerHub. | — | false |
| docker_registry | Docker container registry to push to. Options include: - ghcr.io : GitHub Container Registry (https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) - docker.io : DockerHub (https://hub.docker.com/) | — | ghcr.io |
| docker_user | Docker registry username. Not used when `docker_registry="ghcr.io"`. | — | — |
| docker_org | Docker registry organization name. Can be the same as `docker_user`. Not used when `docker_registry="ghcr.io"`. | — | — |
| DOCKER_TOKEN | Docker registry authentication token. Not used when `docker_registry="ghcr.io"`. | — | — |
| GITHUB_TOKEN | GitHub authentication token with permissions to push to the R package's GitHub repository. Also used to bypass GitHub download limits. By default, uses {{ secrets.GITHUB_TOKEN }} which is automatically set up by GitHub. However users can also choose to pass a custom GitHub secret variable (e.g. {{ secrets.PAT_GITHUB }}) which allows access to private repositories. Read here for more details: https://docs.github.com/en/actions/security-guides/automatic-token-authentication. | — | — |
| CODECOV_TOKEN | Codecov repository token needed to upload coverage reports. Providing this token helps prevent report upload failures by bypassing Codecov's GitHub API rate limits. Read here for more details: https://docs.codecov.com/docs/adding-the-codecov-token | — | — |
| cache_version | Which cache version to use. Change this when trying to avoid using previous caches. | — | cache-v1 |
| runner_os | The Operating System (OS) that the workflow is running on. | — | Linux |
| timeout | The maximum time to wait for long R processes like dependency installations, downloads, and code checks. | — | 2000 |
| miniforge_variant | If provided, this variant of Miniforge will be downloaded and installed. If `miniforge_variant=false`, Miniforge will not be installed at all. If `miniforge_variant=""`, the "Miniforge3" variant will be installed. If `miniforge_version` is not provided, the `latest` version will be used. Currently-known values: - "Miniforge3" (default) - "Miniforge-pypy3". Note: "Mambaforge" and "Mambaforge-pypy3" are discontinued and will 404. Visit https://github.com/conda-forge/miniforge/releases/ for more information on available variants. | — | false |
| miniforge_version | If provided, this version of the given Miniforge variant will be downloaded and installed. If `miniforge_variant` is not provided, `Miniforge3` will be used. Visit https://github.com/conda-forge/miniforge/releases/ for more information on available versions. | — | latest |
| activate_environment | Environment name (or path) to activate on all shells. Default is `test` which will be created in `$CONDA/envs/test`. If an empty string is used, no environment is activated by default (For `base` activation see the `auto-activate-base` option). If the environment does not exist, it will be created and activated. If `environment-file` is used and you want that to be the environment used, you need to explicitely provide the name of that environment on `activate-environment`. If using sh/bash/cmd.exe shells please read the IMPORTANT! section on the README.md! to properly activate conda environments on these shells. | — | test |
| environment_file | Path or URL to a .yml file to build the conda environment with. For more information see: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file | — | "" |
| channels | Conda configuration. Comma separated list of channels to use in order of priority. See https://docs.conda.io/projects/conda/en/latest/user-guide/configuration/ for more information. | — | "" |
| free_diskspace | Free up additional disk space by deleting non-essential sofwares. | — | false |
| run_telemetry | Whether to run the workflow telemetry action: https://github.com/catchpoint/workflow-telemetry-action | — | true |
| force_install | Whether to force install packages. If `true`, all packages will be reinstalled, bypassing the cache. Recommended to set to `true` when pushing changes without updating R package version, such as during pre-release phase of developement. | — | false |
| ncpus | Number of CPUs to use for R package installation. Higher values can speed up the dependency installation process but may result in spurious errors. Default is 2. | — | 2 |
Outputs
no outputs