GitHub Actions for R Package Development

GitHub Actions for R Package Development

This skill covers setting up comprehensive GitHub Actions workflows for R package development, including cross-platform testing, continuous integration, automated documentation deployment, and test coverage reporting.

Rules

1. Use r-lib/actions v2 for all R-related workflow steps
2. Test on multiple platforms: macOS, Windows, Ubuntu (latest + devel + oldrel)
3. Always include permissions blocks with minimal required scopes
4. Use concurrency groups to cancel outdated workflow runs
5. Cache dependencies for faster builds (handled by setup-r-dependencies)
6. Set GITHUB_PAT environment variable for private repos or rate limits
7. Use checkout@v4 (not v2 or v3) for repository checkout
8. Deploy pkgdown only on push to main/master, not on PRs
9. Report test coverage to Codecov on successful test runs
10. Use workflow_dispatch for manual workflow triggering

Essential Workflows

Every R package should have these three workflows:

1. R-CMD-check.yaml - Cross-platform package checking
2. pkgdown.yaml - Documentation website deployment
3. test-coverage.yaml - Code coverage reporting

1. R CMD Check Workflow

Complete R-CMD-check.yaml

Create .github/workflows/R-CMD-check.yaml:

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

permissions: read-all

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
          - {os: ubuntu-latest,  r: 'release'}
          - {os: ubuntu-latest,  r: 'oldrel-1'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - name: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update -y
          sudo apt-get install -y libcurl4-openssl-dev

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - name: Check package
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

Minimal R-CMD-check.yaml

For simpler packages, you can use fewer test configurations:

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

permissions: read-all

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,  r: 'release'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/setup-pandoc@v2
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          use-public-rspm: true
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check
      - uses: r-lib/actions/check-r-package@v2

With System Dependencies

For packages with system dependencies (e.g., gdal, jags, gsl):

      - name: Install system dependencies on macOS
        if: runner.os == 'macOS'
        run: |
          brew install gdal proj geos

      - name: Install system dependencies on Linux
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libgdal-dev \
            libproj-dev \
            libgeos-dev \
            libudunits2-dev

      - name: Install system dependencies on Windows
        if: runner.os == 'Windows'
        run: |
          # Usually handled by rtools or binary packages

Build Arguments Explained

- uses: r-lib/actions/check-r-package@v2
  with:
    upload-snapshots: true
    build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
    error-on: '"error"'  # Can be "warning", "note", or "error"

build_args options:

• --no-manual: Skip PDF manual creation (faster, requires less LaTeX)
• --compact-vignettes=gs+qpdf: Compress vignettes with Ghostscript and qpdf
• --no-build-vignettes: Skip vignette building entirely
• --resave-data: Optimize data file compression

2. pkgdown Deployment Workflow

Complete pkgdown.yaml

Create .github/workflows/pkgdown.yaml:

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  release:
    types: [published]
  workflow_dispatch:

name: pkgdown

# Limit concurrency: cancel in-progress runs when new ones are triggered
concurrency:
  group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}

permissions:
  contents: write

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    # Only restrict concurrency for non-PR jobs
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website

      - name: Build site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub Pages
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: docs
          branch: gh-pages
          clean: true
          single-commit: false

Using deploy_to_branch Alternative

      - name: Build and deploy
        if: github.event_name != 'pull_request'
        run: |
          git config --local user.name "$GITHUB_ACTOR"
          git config --local user.email "[email protected]"
          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

Build on PR (Preview Only)

      - name: Build site for preview
        if: github.event_name == 'pull_request'
        run: |
          pkgdown::build_site(preview = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Upload preview
        if: github.event_name == 'pull_request'
        uses: actions/upload-artifact@v3
        with:
          name: pkgdown-preview
          path: docs/

3. Test Coverage Workflow

Complete test-coverage.yaml

Create .github/workflows/test-coverage.yaml:

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: test-coverage

permissions: read-all

jobs:
  test-coverage:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::covr, any::xml2
          needs: coverage

      - name: Test coverage
        run: |
          cov <- covr::package_coverage(
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4
        with:
          fail_ci_if_error: true
          files: ./cobertura.xml
          token: ${{ secrets.CODECOV_TOKEN }}
          verbose: true

      - name: Show testthat output
        if: always()
        run: |
          ## --------------------------------------------------------------------
          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

Codecov Setup

1. Sign up at https://codecov.io with your GitHub account
2. Add your repository
3. Add CODECOV_TOKEN to GitHub secrets (Settings > Secrets and variables > Actions)
4. Add badge to README.md:

[![codecov](https://codecov.io/gh/username/packagename/branch/main/graph/badge.svg)](https://codecov.io/gh/username/packagename)

Alternative: Coveralls

      - name: Upload coverage to Coveralls
        uses: coverallsapp/github-action@v2
        with:
          github-token: ${{ secrets.GITHUB_TOKEN }}
          path-to-lcov: ./coverage.lcov

Additional Useful Workflows

4. PR Commands Workflow

Respond to comments like /document or /style:

Create .github/workflows/pr-commands.yaml:

on:
  issue_comment:
    types: [created]

name: Commands

jobs:
  document:
    if: startsWith(github.event.comment.body, '/document')
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/pr-fetch@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}
      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::roxygen2
      - name: Document
        run: roxygen2::roxygenise()
        shell: Rscript {0}
      - name: Commit
        run: |
          git config --local user.name "$GITHUB_ACTOR"
          git config --local user.email "[email protected]"
          git add man/\* NAMESPACE
          git commit -m 'Document' || echo "No changes to commit"
      - uses: r-lib/actions/pr-push@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}

  style:
    if: startsWith(github.event.comment.body, '/style')
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/pr-fetch@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}
      - uses: r-lib/actions/setup-r@v2
      - name: Install styler
        run: install.packages("styler")
        shell: Rscript {0}
      - name: Style
        run: styler::style_pkg()
        shell: Rscript {0}
      - name: Commit
        run: |
          git config --local user.name "$GITHUB_ACTOR"
          git config --local user.email "[email protected]"
          git add \*.R
          git commit -m 'Style' || echo "No changes to commit"
      - uses: r-lib/actions/pr-push@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}

5. Lint Workflow

Create .github/workflows/lint.yaml:

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: lint

permissions: read-all

jobs:
  lint:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::lintr, local::.
          needs: lint
      - name: Lint
        run: lintr::lint_package()
        shell: Rscript {0}
        env:
          LINTR_ERROR_ON_LINT: true

Workflow Management Commands

Setup with usethis

# Add R-CMD-check workflow
usethis::use_github_action("check-standard")

# Add pkgdown workflow
usethis::use_github_action("pkgdown")

# Add test-coverage workflow
usethis::use_github_action("test-coverage")

# Add lint workflow
usethis::use_github_action("lint")

# List available workflows
usethis::use_github_actions()

# Browse workflow files
usethis::use_github_action()

Manual Workflow Files

Place workflows in .github/workflows/ directory:

.github/
  workflows/
    R-CMD-check.yaml
    pkgdown.yaml
    test-coverage.yaml
    lint.yaml

Common Pitfalls

1. Permissions Errors

Problem: Workflow can't push to gh-pages or create releases

Solution: Add permissions block:

permissions:
  contents: write  # For pushing to gh-pages
  # Or for fine-grained control:
  # contents: read
  # pages: write
  # id-token: write

2. GITHUB_PAT Not Set

Problem: Rate limited or can't access private repos

Solution: Set environment variable:

env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

For private dependencies, create a Personal Access Token:

1. GitHub Settings > Developer settings > Personal access tokens
2. Generate token with repo scope
3. Add to repo secrets as GH_PAT
4. Use: GITHUB_PAT: ${{ secrets.GH_PAT }}

3. Vignette Build Failures

Problem: vignettes fail on Ubuntu devel

Solution: Skip vignettes on devel:

- uses: r-lib/actions/check-r-package@v2
  with:
    build_args: 'c("--no-manual", if (Sys.getenv("R_VERSION") != "devel") "--compact-vignettes=gs+qpdf")'

Or add system dependencies:

- name: Install system dependencies
  if: runner.os == 'Linux'
  run: |
    sudo apt-get update
    sudo apt-get install -y \
      texlive-latex-base \
      texlive-fonts-recommended \
      texlive-fonts-extra \
      texlive-latex-extra

4. macOS Binary Issues

Problem: macOS builds fail with missing system libraries

Solution: Use Homebrew:

- name: Install system dependencies
  if: runner.os == 'macOS'
  run: |
    brew install pkg-config
    brew install openssl
    brew install libgit2

5. Concurrent Builds Conflict

Problem: Multiple pushes create conflicting deployments

Solution: Use concurrency groups:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

For pkgdown specifically:

concurrency:
  group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}

6. Cached Dependencies Out of Date

Problem: Old package versions used despite new releases

Solution: Dependencies are cached by setup-r-dependencies. To force refresh:

• Update your DESCRIPTION file
• Or manually clear cache in GitHub Actions settings
• Or increment cache version:

- uses: r-lib/actions/setup-r-dependencies@v2
  with:
    cache-version: 2  # Increment this to bust cache

7. Windows LaTeX Issues

Problem: PDF manual fails on Windows

Solution: Skip manual on Windows:

- uses: r-lib/actions/check-r-package@v2
  with:
    build_args: 'c(if (.Platform$OS.type != "windows") "--no-manual", "--compact-vignettes=gs+qpdf")'

Or install TinyTeX:

- name: Install TinyTeX
  if: runner.os == 'Windows'
  run: |
    install.packages("tinytex")
    tinytex::install_tinytex()
  shell: Rscript {0}

8. Test Snapshots Don't Update

Problem: Snapshot tests fail but snapshots aren't committed

Solution: Use upload-snapshots: true:

- uses: r-lib/actions/check-r-package@v2
  with:
    upload-snapshots: true

Then download artifacts and commit manually, or use pr-commands workflow.

9. Workflow Doesn't Trigger

Problem: Push to main but workflow doesn't run

Solution: Check:

• Branch name matches trigger (main vs master)
• Workflow file is in .github/workflows/
• YAML is valid (use yamllint)
• File has .yaml or .yml extension
• You have Actions enabled in repo settings

10. Badge Shows "unknown"

Problem: README badge doesn't show status

Solution: Ensure badge URL matches workflow name:

<!-- Workflow name: R-CMD-check -->
[![R-CMD-check](https://github.com/username/repo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/username/repo/actions/workflows/R-CMD-check.yaml)

Get badge from GitHub: Repository > Actions > Select workflow > ... > Create status badge

Badge Examples

R-CMD-check Badge

[![R-CMD-check](https://github.com/username/packagename/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/username/packagename/actions/workflows/R-CMD-check.yaml)

Test Coverage Badge

[![codecov](https://codecov.io/gh/username/packagename/branch/main/graph/badge.svg)](https://codecov.io/gh/username/packagename)

Lifecycle Badge

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

CRAN Badge

[![CRAN status](https://www.r-pkg.org/badges/version/packagename)](https://CRAN.R-project.org/package=packagename)

Advanced Configuration

Matrix Strategy Customization

strategy:
  fail-fast: false  # Don't cancel all if one fails
  matrix:
    config:
      - {os: macos-latest,   r: 'release'}
      - {os: windows-latest, r: 'release'}
      - {os: ubuntu-latest,  r: 'devel'}
      - {os: ubuntu-latest,  r: 'release'}
      - {os: ubuntu-latest,  r: 'oldrel-1'}
    exclude:  # Skip specific combinations
      - os: windows-latest
        r: 'devel'

Conditional Steps

- name: Install LaTeX
  if: runner.os == 'Linux' && matrix.config.r == 'release'
  run: sudo apt-get install texlive

- name: Build PDF manual
  if: matrix.config.r != 'devel'
  run: R CMD Rd2pdf .

Environment Variables

env:
  # Global (all jobs)
  GLOBAL_VAR: value

jobs:
  check:
    env:
      # Job-level
      JOB_VAR: value
    steps:
      - name: Step with env
        env:
          # Step-level
          STEP_VAR: value
        run: echo $STEP_VAR

Scheduled Workflows

Run checks daily to catch upstream breakage:

on:
  schedule:
    - cron: '0 8 * * *'  # 8 AM UTC daily
  workflow_dispatch:  # Allow manual trigger

This comprehensive setup ensures robust CI/CD for your R package.