pkgdown #1043

	name: pkgdown
	on:
	pull_request:
	push:
	workflow_dispatch:
	schedule:
	- cron: '0 5 * * *'
	jobs:
	job1:
	runs-on: ubuntu-latest
	container: bioconductor/bioconductor_docker:RELEASE_3_19
	env:
	R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	steps:
	- uses: actions/checkout@v3

	# System dependencies
	- name: Install apt dependencies
	run: \|
	apt-get update
	apt-get -y upgrade
	apt-get -y install rsync #for deploy

	- name: Query dependencies and update old packages
	run: \|
	repos = install.packages('remotes')
	saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
	shell: Rscript {0}

	- name: Cache R packages
	if: runner.os == 'Linux'
	uses: actions/cache@v3
	with:
	path: /usr/local/lib/R/site-library
	key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
	restore-keys: ${{ runner.os }}-r-1-

	# This lets us augment with additional dependencies

	- name: Install dependencies
	run: \|
	options(repos = BiocManager::repositories())
	remotes::install_deps(dependencies = TRUE)
	remotes::install_cran("rcmdcheck")
	shell: Rscript {0}

	- name: Check
	env:
	_R_CHECK_CRAN_INCOMING_REMOTE_: false
	run: \|
	rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
	shell: Rscript {0}


	- name: Build pkgdown
	run: \|
	PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'

	- name: Deploy ð
	uses: JamesIves/[email protected]
	with:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	BRANCH: gh-pages # The branch the action should deploy to.
	FOLDER: docs # The folder the action should deploy.

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