[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown' #7752

Workflow file for this run

.github/workflows/r_package.yml at 813f8bc

	name: R-package

	on:
	push:
	branches:
	- master
	pull_request:
	branches:
	- master
	- release/*

	# automatically cancel in-progress builds if another commit is pushed
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	env:
	# hack to get around this:
	# https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html
	_R_CHECK_SYSTEM_CLOCK_: 0
	# ignore R CMD CHECK NOTE checking how long it has
	# been since the last submission
	_R_CHECK_CRAN_INCOMING_REMOTE_: 0
	# CRAN ignores the "installed size is too large" NOTE,
	# so our CI can too. Setting to a large value here just
	# to catch extreme problems
	_R_CHECK_PKG_SIZES_THRESHOLD_: 100

	jobs:
	test:
	name: ${{ matrix.task }} (${{ matrix.os }}, ${{ matrix.compiler }}, R ${{ matrix.r_version }}, ${{ matrix.build_type }})
	runs-on: ${{ matrix.os }}
	container: ${{ matrix.container }}
	timeout-minutes: 60
	strategy:
	fail-fast: false
	matrix:
	include:
	################
	# CMake builds #
	################
	- os: ubuntu-latest
	task: r-package
	compiler: gcc
	r_version: 3.6
	build_type: cmake
	container: 'ubuntu:18.04'
	- os: ubuntu-latest
	task: r-package
	compiler: gcc
	r_version: 4.3
	build_type: cmake
	container: 'ubuntu:22.04'
	- os: ubuntu-latest
	task: r-package
	compiler: clang
	r_version: 3.6
	build_type: cmake
	container: 'ubuntu:18.04'
	- os: ubuntu-latest
	task: r-package
	compiler: clang
	r_version: 4.3
	build_type: cmake
	container: 'ubuntu:22.04'
	- os: macOS-latest
	task: r-package
	compiler: gcc
	r_version: 4.3
	build_type: cmake
	container: null
	- os: macOS-latest
	task: r-package
	compiler: clang
	r_version: 4.3
	build_type: cmake
	container: null
	- os: windows-latest
	task: r-package
	compiler: MINGW
	toolchain: MINGW
	r_version: 3.6
	build_type: cmake
	container: null
	- os: windows-latest
	task: r-package
	compiler: MINGW
	toolchain: MSYS
	r_version: 4.3
	build_type: cmake
	container: null
	# Visual Studio 2019
	- os: windows-2019
	task: r-package
	compiler: MSVC
	toolchain: MSVC
	r_version: 3.6
	build_type: cmake
	container: null
	# Visual Studio 2022
	- os: windows-2022
	task: r-package
	compiler: MSVC
	toolchain: MSVC
	r_version: 4.3
	build_type: cmake
	container: null
	###############
	# CRAN builds #
	###############
	- os: windows-latest
	task: r-package
	compiler: MINGW
	toolchain: MINGW
	r_version: 3.6
	build_type: cran
	container: null
	- os: windows-latest
	task: r-package
	compiler: MINGW
	toolchain: MSYS
	r_version: 4.3
	build_type: cran
	container: null
	- os: ubuntu-latest
	task: r-package
	compiler: gcc
	r_version: 4.3
	build_type: cran
	container: 'ubuntu:22.04'
	- os: macOS-latest
	task: r-package
	compiler: clang
	r_version: 4.3
	build_type: cran
	container: null
	################
	# Other checks #
	################
	- os: ubuntu-latest
	task: r-rchk
	compiler: gcc
	r_version: 4.3
	build_type: cran
	container: 'ubuntu:22.04'
	steps:
	- name: Prevent conversion of line endings on Windows
	if: startsWith(matrix.os, 'windows')
	shell: pwsh
	run: git config --global core.autocrlf false
	- name: Install packages used by third-party actions
	if: startsWith(matrix.os, 'ubuntu')
	shell: bash
	run: \|
	apt-get update -y
	apt-get install --no-install-recommends -y \
	ca-certificates \
	dirmngr \
	gpg \
	gpg-agent \
	software-properties-common \
	sudo
	# install newest version of git
	# ref:
	# - https://unix.stackexchange.com/a/170831/550004
	# - https://git-scm.com/download/linux
	add-apt-repository ppa:git-core/ppa -y
	apt-get update -y
	apt-get install --no-install-recommends -y \
	git
	- name: Trust git cloning LightGBM
	if: startsWith(matrix.os, 'ubuntu')
	run: \|
	git config --global --add safe.directory "${GITHUB_WORKSPACE}"
	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 5
	submodules: true
	- name: Install pandoc
	uses: r-lib/actions/setup-pandoc@v2
	- name: install tinytex
	if: startsWith(matrix.os, 'windows')
	uses: r-lib/actions/setup-tinytex@v2
	env:
	CTAN_MIRROR: https://ctan.math.illinois.edu/systems/win32/miktex
	TINYTEX_INSTALLER: TinyTeX
	- name: Setup and run tests on Linux and macOS
	if: matrix.os == 'macOS-latest' \|\| matrix.os == 'ubuntu-latest'
	shell: bash
	run: \|
	export TASK="${{ matrix.task }}"
	export COMPILER="${{ matrix.compiler }}"
	export GITHUB_ACTIONS="true"
	if [[ "${{ matrix.os }}" == "macOS-latest" ]]; then
	export OS_NAME="macos"
	elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
	export OS_NAME="linux"
	export IN_UBUNTU_BASE_CONTAINER="true"
	# the default version of cmake provided on Ubuntu 18.04 (v3.10.2), is not supported by LightGBM
	# see https://github.com/microsoft/LightGBM/issues/5642
	if [[ "${{ matrix.container }}" == "ubuntu:18.04" ]]; then
	export INSTALL_CMAKE_FROM_RELEASES="true"
	fi
	fi
	export BUILD_DIRECTORY="$GITHUB_WORKSPACE"
	export R_VERSION="${{ matrix.r_version }}"
	export R_BUILD_TYPE="${{ matrix.build_type }}"
	$GITHUB_WORKSPACE/.ci/setup.sh
	$GITHUB_WORKSPACE/.ci/test.sh
	- name: Setup and run tests on Windows
	if: startsWith(matrix.os, 'windows')
	shell: pwsh -command ". {0}"
	run: \|
	$env:BUILD_SOURCESDIRECTORY = $env:GITHUB_WORKSPACE
	$env:LGB_VER = (Get-Content -TotalCount 1 $env:BUILD_SOURCESDIRECTORY\VERSION.txt).trim().replace('rc', '-')
	$env:TOOLCHAIN = "${{ matrix.toolchain }}"
	$env:R_VERSION = "${{ matrix.r_version }}"
	$env:R_BUILD_TYPE = "${{ matrix.build_type }}"
	$env:COMPILER = "${{ matrix.compiler }}"
	$env:GITHUB_ACTIONS = "true"
	$env:TASK = "${{ matrix.task }}"
	& "$env:GITHUB_WORKSPACE/.ci/test_windows.ps1"
	test-r-sanitizers:
	name: r-sanitizers (ubuntu-latest, R-devel, ${{ matrix.compiler }} ASAN/UBSAN)
	timeout-minutes: 60
	runs-on: ubuntu-latest
	container: wch1/r-debug
	strategy:
	fail-fast: false
	matrix:
	include:
	- r_customization: san
	compiler: gcc
	- r_customization: csan
	compiler: clang
	steps:
	- name: Trust git cloning LightGBM
	run: \|
	git config --global --add safe.directory "${GITHUB_WORKSPACE}"
	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 5
	submodules: true
	- name: Install packages
	shell: bash
	run: \|
	RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
	sh build-cran-package.sh --r-executable=RD${{ matrix.r_customization }}
	RD${{ matrix.r_customization }} CMD INSTALL lightgbm_*.tar.gz \|\| exit -1
	- name: Run tests with sanitizers
	shell: bash
	run: \|
	cd R-package/tests
	exit_code=0
	RDscript${{ matrix.r_customization }} testthat.R >> tests.log 2>&1 \|\| exit_code=-1
	cat ./tests.log
	exit ${exit_code}
	test-r-debian-clang:
	name: r-package (debian, R-devel, clang)
	timeout-minutes: 60
	runs-on: ubuntu-latest
	container: rhub/debian-clang-devel
	steps:
	- name: Install Git before checkout
	shell: bash
	run: \|
	apt-get update --allow-releaseinfo-change
	apt-get install --no-install-recommends -y git
	- name: Trust git cloning LightGBM
	run: \|
	git config --global --add safe.directory "${GITHUB_WORKSPACE}"
	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 5
	submodules: true
	- name: update to clang 15
	shell: bash
	run: \|
	# remove clang stuff that comes installed in the image
	apt-get autoremove -y --purge \
	clang-* \
	libclang-* \
	libunwind-* \
	llvm-*
	#
	# replace it all with clang-15
	apt-get update -y
	apt-get install --no-install-recommends -y \
	gnupg \
	lsb-release \
	software-properties-common \
	wget
	#
	wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key \| apt-key add -
	#
	add-apt-repository "deb http://apt.llvm.org/unstable/ llvm-toolchain main"
	apt-get install -y --no-install-recommends \
	clang-15 \
	clangd-15 \
	clang-format-15 \
	clang-tidy-15 \
	clang-tools-15 \
	lldb-15 \
	lld-15 \
	llvm-15-dev \
	llvm-15-tools \
	libomp-15-dev \
	libc++-15-dev \
	libc++abi-15-dev \
	libclang-common-15-dev \
	libclang-15-dev \
	libclang-cpp15-dev \
	libunwind-15-dev
	# overwrite everything in /usr/bin with the new v15 versions
	cp --remove-destination /usr/lib/llvm-15/bin/* /usr/bin/
	- name: Install packages and run tests
	shell: bash
	run: \|
	export PATH=/opt/R-devel/bin/:${PATH}
	Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
	sh build-cran-package.sh
	R CMD check --as-cran --run-donttest lightgbm_*.tar.gz \|\| exit -1
	if grep -q -E "NOTE\|WARNING\|ERROR" lightgbm.Rcheck/00check.log; then
	echo "NOTEs, WARNINGs, or ERRORs have been found by R CMD check"
	exit -1
	fi
	all-r-package-jobs-successful:
	if: always()
	runs-on: ubuntu-latest
	needs: [test, test-r-sanitizers, test-r-debian-clang]
	steps:
	- name: Note that all tests succeeded
	uses: re-actors/[email protected]
	with:
	jobs: ${{ toJSON(needs) }}

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[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown' #7752

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[R-package] [ci] switch vignettes from 'rmarkdown' to 'markdown' #7752

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Workflow file for this run