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Automated CI/CD workflows for R packages including R CMD check across platforms, test coverage reporting, and pkgdown deployment

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SKILL.md

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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

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Use concurrency groups to cancel outdated workflow runs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

Essential Workflows

Every R package should have these three workflows:

R-CMD-check.yaml - Cross-platform package checking
pkgdown.yaml - Documentation website deployment
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 "$GITHUB_ACTOR"
          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
          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

Sign up at https://codecov.io with your GitHub account
Add your repository
Add CODECOV_TOKEN to GitHub secrets (Settings > Secrets and variables > Actions)
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 "$GITHUB_ACTOR@users.noreply.github.com"
          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 "$GITHUB_ACTOR@users.noreply.github.com"
          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:

GitHub Settings > Developer settings > Personal access tokens
Generate token with repo scope
Add to repo secrets as GH_PAT
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.

name	github-actions
description	Automated CI/CD workflows for R packages including R CMD check across platforms, test coverage reporting, and pkgdown deployment

github-actions

More from this repository

More from this repository

GitHub Actions for R Package Development

Rules

Essential Workflows

1. R CMD Check Workflow

Complete R-CMD-check.yaml

Minimal R-CMD-check.yaml

With System Dependencies

Build Arguments Explained

2. pkgdown Deployment Workflow

Complete pkgdown.yaml

Using deploy_to_branch Alternative

Build on PR (Preview Only)

3. Test Coverage Workflow

Complete test-coverage.yaml

Codecov Setup

Alternative: Coveralls

Additional Useful Workflows

4. PR Commands Workflow

5. Lint Workflow

Workflow Management Commands

Setup with usethis

Manual Workflow Files

Common Pitfalls

1. Permissions Errors

2. GITHUB_PAT Not Set

3. Vignette Build Failures

4. macOS Binary Issues

5. Concurrent Builds Conflict

6. Cached Dependencies Out of Date

7. Windows LaTeX Issues

8. Test Snapshots Don't Update

9. Workflow Doesn't Trigger

10. Badge Shows "unknown"

Badge Examples

R-CMD-check Badge

Test Coverage Badge

Lifecycle Badge

CRAN Badge

Advanced Configuration

Matrix Strategy Customization

Conditional Steps

Environment Variables

Scheduled Workflows

GitHub Actions for R Package Development

Rules

Essential Workflows

1. R CMD Check Workflow

Complete R-CMD-check.yaml

Minimal R-CMD-check.yaml

With System Dependencies

Build Arguments Explained

2. pkgdown Deployment Workflow

Complete pkgdown.yaml

Using deploy_to_branch Alternative

Build on PR (Preview Only)

3. Test Coverage Workflow

Complete test-coverage.yaml

Codecov Setup

Alternative: Coveralls

Additional Useful Workflows

4. PR Commands Workflow

5. Lint Workflow

Workflow Management Commands

Setup with usethis

Manual Workflow Files

Common Pitfalls

1. Permissions Errors

2. GITHUB_PAT Not Set

3. Vignette Build Failures

4. macOS Binary Issues

5. Concurrent Builds Conflict

6. Cached Dependencies Out of Date

7. Windows LaTeX Issues

8. Test Snapshots Don't Update

9. Workflow Doesn't Trigger

10. Badge Shows "unknown"

Badge Examples