Merge changes from development branch #172

	name: 'rcmdcheck'

	on: [push, pull_request]

	env:
	cache-version: v1

	# source: https://github.com/seandavi/BuildABiocWorkshop

	jobs:
	r-check:
	runs-on: ubuntu-latest
	container: bioconductor/bioconductor_docker:devel
	env:
	R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	steps:
	- uses: actions/checkout@v2

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

	- name: Cache R packages
	if: runner.os != 'Windows'
	uses: actions/cache@v1
	with:
	path: /usr/local/lib/R/site-library
	key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
	restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-

	# This lets us augment with additional dependencies
	- name: Install system dependencies
	run: \|
	remotes::install_cran('Seurat')
	shell: Rscript {0}

	- name: Install dependencies
	run: \|
	options(repos = c(CRAN = "https://cran.r-project.org"))
	BiocManager::repositories()
	remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
	remotes::install_cran("rcmdcheck")
	remotes::install_bioc("BiocCheck")
	shell: Rscript {0}

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

	- name: BiocCheck
	run: BiocCheck::BiocCheck()
	shell: Rscript {0}

Provide feedback