https://github.com/insightsengineering/staged-dependencies-action
Github Action to implement R development stages for package development
https://github.com/insightsengineering/staged-dependencies-action
github-actions r renv staged-dependencies system-dependencies
Last synced: 4 months ago
JSON representation
Github Action to implement R development stages for package development
- Host: GitHub
- URL: https://github.com/insightsengineering/staged-dependencies-action
- Owner: insightsengineering
- License: apache-2.0
- Created: 2021-10-18T12:13:07.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-10-21T10:05:11.000Z (7 months ago)
- Last Synced: 2026-02-10T23:40:56.308Z (4 months ago)
- Topics: github-actions, r, renv, staged-dependencies, system-dependencies
- Language: R
- Homepage: https://github.com/marketplace/actions/staged-dependencies-action
- Size: 102 KB
- Stars: 4
- Watchers: 1
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
⚠️ **This GitHub Action is deprecated and will receive no further updates.** ⚠️
Please consider using [`insightsengineering/setup-r-dependencies`](https://github.com/insightsengineering/setup-r-dependencies) instead.
# Staged Dependencies Action
Github Action to install R package and system dependencies, based on the [`{staged.dependencies}`](https://github.com/openpharma/staged.dependencies) R package.
**NOTE**: For the time being, this action only supports installation of _system dependencies_ for Ubuntu OS. Other OSes will be supported upon request.
The [staged.dependencies] package simplifies the development process for developing a set of
interdependent R packages. In each repository of the set of R packages you are co-developing you should
specify a `staged_dependencies.yaml` file containing _upstream_ (i.e. those packages your current repo depends on) and
_downstream_ (i.e. those packages which depend on your current repo's package)
dependency packages within your development set of packages.
An example of the output of the action can be seen below:
## Table of Contents
- [Staged Dependencies Action](#staged-dependencies-action)
- [Table of Contents](#table-of-contents)
- [Getting Started](#getting-started)
- [Usage Options](#usage-options)
- [Inputs](#inputs)
- [Outputs](#outputs)
## Getting Started
To get started, follow these instructions:
1. (Optional) Create `staged_dependencies.yaml` file with [this guide][structure-of-yaml-file].
2. Create a new file in your repository called `.github/workflows/r-check.yml`.
3. Copy the example workflow from below into that new file. Add additional configurations as needed.
4. Commit and push the `.github/workflows/r-check.yml` file to a new branch.
5. Open up a pull request and witness dependencies being installed during the workflow run.
```yml
---
name: Check R package
on:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
check:
runs-on: ubuntu-latest
name: Check
container:
image: rocker/verse:4.1.0
steps:
- name: Checkout repo
uses: actions/checkout@v3
- name: Run Staged dependencies
uses: insightsengineering/staged-dependencies-action@v1
with:
run-system-dependencies: true
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- name: Build R package
run: |
R CMD build ${{ github.event.repository.name }}
echo "PKGBUILD=$(echo *.tar.gz)" >> $GITHUB_ENV
shell: bash
- name: Check R package
run: R CMD check --no-manual ${{ env.PKGBUILD }}
shell: bash
- name: Install R package
run: R CMD INSTALL ${{ env.PKGBUILD }}
shell: bash
```
## Usage Options
The following options are available are available for this action:
### Inputs
* `run-system-dependencies`:
_Description_: Check for and install system dependencies
_Required_: `false`
_Default_: `False`
* `git-user-name`:
_Description_: Git user.name configuration for fetching remote staged dependencies
_Required_: `false`
_Default_: `github-actions[bot]`
* `git-user-email`:
_Description_: Git user.email configuration for fetching remote staged dependencies
_Required_: `false`
_Default_: `27856297+dependabot-preview[bot]@users.noreply.github.com`
* `path`:
_Description_: Path to the R package
_Required_: `false`
_Default_: `.`
* `version`:
_Description_: Version of {staged.dependencies} to use. This action is compatilble with `>=v0.2.2`
_Required_: `false`
_Default_: `v0.3.1`
* `threads`:
_Description_: Number of threads to use. Set to 'auto' to use max available threads
_Required_: `false`
_Default_: `auto`
* `cran-repos`:
_Description_: Map of CRAN repositories delimited by comma
_Required_: `false`
_Default_: `CRAN=https://cloud.r-project.org`
* `enable-bioc-repos`:
_Description_: Add `BiocManager::repositories()` to option repos
_Required_: `false`
_Default_: `False`
* `token-mapping`:
_Description_: Token mapping that is used in `staged.dependencies.token_mapping` delimited by comma. Note that you will need to set these tokens with their respective values as environment variables while using this action.
_Required_: `false`
_Default_: `https://github.com=GITHUB_PAT,https://gitlab.com=GITLAB_PAT`
* `enable-check`:
_Description_: Run `check_yamls_consistent` before installation of dependencies
_Required_: `false`
_Default_: `False`
* `git-ref`:
_Description_: Git reference to use as a reference stage for installing dependencies
_Required_: `false`
_Default_: `${{ github.ref }}`
* `renv-restore`:
_Description_: Restore dependencies from `renv.lock`, if it exists
_Required_: `false`
_Default_: `True`
* `quiet`:
_Description_: If TRUE, suppress output
_Required_: `false`
_Default_: `True`
* `direction`:
_Description_: The direction to use to install dependencies. Choose between 'upstream', 'downstream' and 'all'
_Required_: `false`
_Default_: `all`
### Outputs
None
[staged.dependencies]: https://github.com/openpharma/staged.dependencies
[structure-of-yaml-file]: https://github.com/openpharma/staged.dependencies#structure-of-staged_dependenciesyaml-file