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