R Build and Checks #856

	# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
	# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
	on:
	workflow_dispatch:
	push:
	branches: [ master, dev ]
	pull_request:
	schedule:
	- cron: "0 6 10 * *"

	name: R Build and Checks

	jobs:
	R-CMD-check:
	runs-on: ubuntu-${{ matrix.config.os }}

	name: ubuntu-${{ matrix.config.os }} (${{ matrix.config.r }} / ${{ matrix.config.bioc }})

	strategy:
	fail-fast: false
	matrix:
	config:
	- { os: 24.04, r: '4.5', bioc: '3.21', pkgdown: "true" }

	env:
	R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	- uses: actions/checkout@v4

	- name: Free Disk Space (Ubuntu)
	uses: jlumbroso/free-disk-space@main
	with:
	tool-cache: false
	docker-images: false

	- uses: bimberlabinternal/DevOps/githubActions/r-gh-setup@master
	with:
	r_version: ${{ matrix.config.r }}
	bioc_version: ${{ matrix.config.bioc }}
	cache_version: ${{ secrets.CACHE_VERSION }}
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	- uses: r-lib/actions/check-r-package@v2
	with:
	args: 'c("--no-manual")'
	env:
	_R_CHECK_CRAN_INCOMING_: false

	- name: Install package
	if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true'
	run: R CMD INSTALL .

	- name: Deploy package
	if: github.ref == 'refs/heads/master' && matrix.config.pkgdown == 'true'
	run: \|
	git config --local user.email "actions@github.com"
	git config --local user.name "GitHub Actions"
	Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE)'

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