Bump version: 0.48.3 → 0.49.0 #60

	# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
	# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
	on:
	push:
	branches: [main, master]
	pull_request:
	branches: [main, master]

	name: R-CMD-check

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

	name: ${{ matrix.config.os }} (${{ matrix.config.r }})

	strategy:
	fail-fast: false
	matrix:
	config:
	- {os: ubuntu-latest, r: 'release'}

	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
	R_KEEP_PKG_SOURCE: yes

	steps:
	- uses: actions/checkout@v2

	- uses: r-lib/actions/setup-pandoc@v2

	- uses: r-lib/actions/setup-r@v2
	with:
	r-version: ${{ matrix.config.r }}
	http-user-agent: ${{ matrix.config.http-user-agent }}
	use-public-rspm: true

	- name: "Install libraries"
	run: \|
	sudo apt-get update
	sudo apt-get install -y git bzip2 \
	cmake autoconf automake make gcc perl zlib1g-dev libbz2-dev samtools

	- name: "Install aligners and SLIMM"
	run: \|
	rm -rf vignettes
	curl -L https://github.com/lh3/minimap2/releases/download/v2.13/minimap2-2.13_x64-linux.tar.bz2 \| tar -jxf -
	sudo cp ./minimap2-2.13_x64-linux/minimap2 /usr/bin/ && rm -rf ./minimap2-*
	git clone --recursive https://github.com/seqan/slimm
	(cd slimm && mkdir build && cd build && cmake .. && make && sudo cp bin/slimm /usr/bin/)
	rm -rf slimm

	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	extra-packages: any::rcmdcheck, any::XML
	needs: check

	- uses: r-lib/actions/check-r-package@v2

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