Build pkgdown Site

Config + deploy pkgdown doc site for R pkg.

Use When

• Doc site for R pkg
• Customize pkgdown layout, theme, nav
• Fix 404s on deployed pkgdown site
• Migrate between deploy methods

In

• Required: R pkg w/ roxygen2 docs
• Required: GitHub repo
• Optional: Custom theme/branding
• Optional: Vignettes to include as articles

Do

Step 1: Init pkgdown

usethis::use_pkgdown()

Creates _pkgdown.yml + adds pkgdown to .Rbuildignore.

→ _pkgdown.yml in project root. .Rbuildignore has pkgdown entries.

If err: Install pkgdown via install.packages("pkgdown"). _pkgdown.yml already exists → fn updates .Rbuildignore w/o 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 404s on GitHub Pages (appends /dev/ to URLs).

→ _pkgdown.yml valid YAML w/ url, template, navbar, reference, articles appropriate for pkg.

If err: Validate YAML syntax w/ online linter. All fn names in reference.contents match actual exported fns.

Step 3: Build Locally

pkgdown::build_site()

→ docs/ dir created w/ complete site incl index.html, fn ref pages, articles.

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

Step 4: Preview

pkgdown::preview_site()

Verify nav, fn ref, articles, search work.

→ Site opens in browser at localhost. Nav links work, ref pages render, search returns results.

If err: Preview doesn't open → manually open docs/index.html. Pages missing → check devtools::document() ran before build.

Step 5: Deploy to GitHub Pages

Method A: GitHub Actions (Recommended)

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

Method B: Manual Branch Deploy

# 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

→ gh-pages branch on remote w/ site files at root.

If err: Push rejected → ensure write access. Using GitHub Actions instead → skip + follow setup-github-actions-ci.

Step 6: Configure GitHub Pages

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

→ Site available at https://username.github.io/packagename/ within min.

If err: 404 → verify Pages source matches deploy method (branch deploy needs "Deploy from a branch"). Check development: mode: release in _pkgdown.yml.

Step 7: Add URL to DESCRIPTION

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

→ DESCRIPTION URL has pkgdown site URL + GitHub repo URL, comma-separated.

If err: R CMD check warns invalid URLs → verify pkgdown site actually deployed + accessible before adding.

Check

• Builds locally w/o errs
• All fn ref pages render
• Articles/vignettes accessible + render
• Search works
• Nav links correct
• Deploys to GitHub Pages
• No 404s
• development: mode: release set

Traps

• 404 after deploy: Almost always development: mode: auto (default). → mode: release
• Missing ref pages: Fns must be exported + documented. Run devtools::document() first
• Broken vignette links: Use vignette("name") syntax for cross-refs, not file paths
• Logo not showing: Place at man/figures/logo.png, ref in _pkgdown.yml
• Search not working: Needs url field in _pkgdown.yml set correctly
• Wrong R binary hybrid sys: WSL/Docker → Rscript may resolve to cross-platform wrapper vs native. Check which Rscript && Rscript --version. Prefer native (e.g., /usr/local/bin/Rscript on Linux/WSL). See Setting Up Your Environment

→

• setup-github-actions-ci — automated pkgdown deploy workflow
• write-roxygen-docs — fn docs that appear on site
• write-vignette — articles in site nav
• release-package-version — trigger rebuild on release