Build pkgdown Site

Configure and deploy pkgdown documentation website for R package.

When Use

• Creating documentation site for R package
• Customizing pkgdown layout, theme, navigation
• Fixing 404 errors on 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

Steps

Step 1: Initialize pkgdown

usethis::use_pkgdown()

Creates _pkgdown.yml, adds pkgdown to .Rbuildignore.

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

If fail: Install pkgdown with install.packages("pkgdown"). _pkgdown.yml already exists? Function updates .Rbuildignore without overwriting 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. Default mode: auto causes 404 errors on GitHub Pages — appends /dev/ to URLs.

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

If fail: Validate YAML syntax with online YAML linter. Ensure all function names in reference.contents match actual exported functions.

Step 3: Build Locally

pkgdown::build_site()

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

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

Step 4: Preview Site

pkgdown::preview_site()

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

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

If fail: Preview doesn't open? Manually open docs/index.html in browser. Pages missing? Check devtools::document() was run before building site.

Step 5: Deploy to GitHub Pages

Method A: GitHub Actions (Recommended)

See setup-github-actions-ci skill for 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

Got: gh-pages branch exists on remote with site files at root level.

If fail: Push rejected? Ensure you have write access to repository. Using GitHub Actions deployment instead? Skip this step, follow 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

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

If fail: Site returns 404? Verify Pages source matches deployment method (branch deployment requires "Deploy from a branch"). Check development: mode: release set in _pkgdown.yml.

Step 7: Add URL to DESCRIPTION

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

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

If fail: R CMD check warns about invalid URLs? Verify pkgdown site actually deployed and accessible before adding URL.

Checks

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

Pitfalls

• 404 errors after deployment: Almost always caused by development: mode: auto (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, reference in _pkgdown.yml.
• Search not working: Requires url field in _pkgdown.yml set correctly.
• Wrong R binary on hybrid systems: On WSL or Docker, Rscript may resolve to cross-platform wrapper instead of native R. Check with which Rscript && Rscript --version. Prefer native R binary (e.g., /usr/local/bin/Rscript on Linux/WSL) for reliability. See Setting Up Your Environment for R path configuration.

See Also

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