Don't skip tests in R CMD check. #104

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	R-CMD-check:
	name: R CMD check (${{ matrix.os }})
	runs-on: ${{ matrix.os }}

	strategy:
	fail-fast: false
	matrix:
	os: ['ubuntu-latest']

	steps:
	- uses: actions/checkout@v4
	- name: Set up Conda env
	uses: mamba-org/provision-with-micromamba@e2b397b12d0a38069451664382b769c9456e3d6d
	with:
	cache-env: true
	- name: Install TinyTex
	shell: bash -l {0}
	run: \|
	Rscript -e 'tinytex::install_tinytex()'
	- name: Install demo datasets
	shell: bash -l {0}
	run: \|
	Rscript -e 'install.packages("eicu.demo", repos="https://eth-mds.github.io/physionet-demo")'
	- name: Run R CMD check
	shell: bash -l {0}
	run: \|
	R CMD build . && R CMD check --no-manual --as-cran $(ls -t . \| head -n1)
	env:
	_R_CHECK_CRAN_INCOMING_: false
	_R_CHECK_FORCE_SUGGESTS_: false
	# R CMD check raises a warning by qpdf that the generated docs PDF is large and
	# should be compressed. Currently we ignore this warning via the grep below.
	- name: Check for warnings
	shell: bash -l {0}
	run: \|
	CHECK_LOG_FILE=ricu.Rcheck/00check.log
	CHECK_INSTALL_FILE=ricu.Rcheck/00install.out
	if ! [[ -f "$CHECK_LOG_FILE" ]]; then
	echo "Log-file not found."
	exit 1
	fi
	if cat $CHECK_LOG_FILE \| grep -q "ERROR"; then
	cat $CHECK_INSTALL_FILE
	cat $CHECK_LOG_FILE
	exit 1
	fi
	if cat $CHECK_LOG_FILE \| grep -q "WARNING" \| grep -q -v -e "checking sizes of PDF files under ‘inst/doc’ ... WARNING"; then
	echo "Found warnings, treated as errors."
	cat $CHECK_LOG_FILE
	exit 1
	fi

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