build-pkgdown-site

Build pkgdown Site

Configure and deploy a pkgdown documentation website for an R package.

When to Use

• Creating a documentation site for an R package
• Customizing pkgdown layout, theme, or navigation
• Fixing 404 errors on a deployed pkgdown site
• Migrating between deployment methods

Inputs

• Required: R package with roxygen2 documentation
• Required: GitHub repository
• Optional: Custom theme or branding
• Optional: Vignettes to include as articles

Procedure

Step 1: Initialize pkgdown

usethis::use_pkgdown()

This creates _pkgdown.yml and adds pkgdown to .Rbuildignore.

Expected: _pkgdown.yml exists in the project root. .Rbuildignore contains pkgdown-related entries.

On failure: Install pkgdown with install.packages("pkgdown"). If _pkgdown.yml already exists, the function will update .Rbuildignore without overwriting the config.

Step 2: Configure _pkgdown.yml

url: https://username.github.io/packagename/

development:
  mode: release

template:
  bootstrap: 5
  bootswatch: flatly

navbar:
  structure:
    left: [intro, reference, articles, news]
    right: [search, github]
  components:
    github:
      icon: fa-github
      href: https://github.com/username/packagename

reference:
  - title: Core Functions
    desc: Primary package functionality
    contents:
      - main_function
      - helper_function
  - title: Utilities
    desc: Helper and utility functions
    contents:
      - starts_with("util_")

articles:
  - title: Getting Started
    contents:
      - getting-started
  - title: Advanced Usage
    contents:
      - advanced-features
      - customization

Critical: Set development: mode: release. The default mode: auto causes 404 errors on GitHub Pages because it appends /dev/ to URLs.

Expected: _pkgdown.yml contains valid YAML with url, template, navbar, reference, and articles sections appropriate for the package.

On failure: Validate YAML syntax with an online YAML linter. Ensure all function names in reference.contents match actual exported functions.

Step 3: Build Locally

pkgdown::build_site()

Expected: docs/ directory created with a complete site including index.html, function reference pages, and articles.

On failure: Common issues: missing pandoc (set RSTUDIO_PANDOC in .Renviron), missing vignette dependencies (install suggested packages), or broken examples (fix or wrap in \dontrun{}).

Step 4: Preview Site

pkgdown::preview_site()

Verify navigation, function reference, articles, and search work correctly.

Expected: Site opens in the browser at localhost. All navigation links work, function reference pages render, and search returns results.

On failure: If the preview does not open, manually open docs/index.html in a browser. If pages are missing, check that devtools::document() was run before building the site.

Step 5: Deploy to GitHub Pages

Method A: GitHub Actions (Recommended)

See setup-github-actions-ci skill for the pkgdown workflow.

Method B: Manual Branch Deployment

# Build site
Rscript -e "pkgdown::build_site()"

# Create gh-pages branch if it doesn't exist
git checkout --orphan gh-pages
git rm -rf .
cp -r docs/* .
git add .
git commit -m "Deploy pkgdown site"
git push origin gh-pages

# Switch back to main
git checkout main

Expected: The gh-pages branch exists on the remote with the site files at the root level.

On failure: If the push is rejected, ensure you have write access to the repository. If using GitHub Actions deployment instead, skip this step and follow the setup-github-actions-ci skill.

Step 6: Configure GitHub Pages

1. Go to repository Settings > Pages
2. Set Source to "Deploy from a branch"
3. Select gh-pages branch, / (root) folder
4. Save

Expected: Site available at https://username.github.io/packagename/ within a few minutes.

On failure: If the site returns 404, verify the Pages source matches the deployment method (branch deployment requires "Deploy from a branch"). Check that development: mode: release is set in _pkgdown.yml.

Step 7: Add URL to DESCRIPTION

URL: https://username.github.io/packagename/, https://github.com/username/packagename

Expected: DESCRIPTION URL field contains both the pkgdown site URL and the GitHub repository URL, separated by a comma.

On failure: If R CMD check warns about invalid URLs, verify the pkgdown site is actually deployed and accessible before adding the URL.

Validation

• Site builds locally without errors
• All function reference pages render correctly
• Articles/vignettes are accessible and render properly
• Search functionality works
• Navigation links are correct
• Site deploys successfully to GitHub Pages
• No 404 errors on the deployed site
• development: mode: release is set in _pkgdown.yml

Common Pitfalls

• 404 errors after deployment: Almost always caused by development: mode: auto (the default). Change to mode: release.
• Missing reference pages: Functions must be exported and documented. Run devtools::document() first.
• Broken vignette links: Use vignette("name") syntax in cross-references, not file paths.
• Logo not showing: Place logo at man/figures/logo.png and reference in _pkgdown.yml.
• Search not working: Requires url field in _pkgdown.yml to be set correctly.
• Wrong R binary on hybrid systems: On WSL or Docker, Rscript may resolve to a cross-platform wrapper instead of native R. Check with which Rscript && Rscript --version. Prefer the native R binary (e.g., /usr/local/bin/Rscript on Linux/WSL) for reliability. See Setting Up Your Environment for R path configuration.

Related Skills

• setup-github-actions-ci - automated pkgdown deployment workflow
• write-roxygen-docs - function documentation that appears on the site
• write-vignette - articles that appear in the site navigation
• release-package-version - trigger site rebuild on release