R-CMD-check.yaml

on:
  push:
    paths-ignore:
      - 'appveyor.yml'
      - 'developmentBuild.sh'
      - 'docs/**'
      - 'Doxyfile'
      - 'etc/**'
      - 'lhs.Rproj'
      - 'logo.svg'
      - 'pkgdown/**'
      - 'README.md'
      - 'README.Rmd'
      - 'refs/**'
      - 'SECURITY.md'
      - '.github/workflows/docker-builds.yml'
      - '.github/workflows/rev-dep-check.yaml'
      - '.github/workflows/rhub-check.yml'
      - '.github/workflows/pkgdown.yml'
      - '.github/workflows/build_readme.yaml'
      - '.github/workflows/rhub.yaml'
    branches:
      - master
    tags:
      - none
  pull_request:
    branches:
      - master
  workflow_dispatch:

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: windows-latest, r: 'release'}
          - {os: windows-latest, r: 'devel'}
          - {os: macOS-latest, r: 'release'}
          - {os: macOS-latest, r: 'devel'}
          - {os: ubuntu-latest, r: 'release'}
          - {os: ubuntu-latest, r: 'devel'}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.MY_PAT }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: R setup-pandoc@master
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - name: Pandoc setup-pandoc@master
        uses: r-lib/actions/setup-pandoc@v2

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v3
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          Rscript -e "remotes::install_github('r-hub/sysreqs')"
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
          sudo -s eval "$sysreqs"
          sudo apt-get install libcurl4-openssl-dev

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

      - name: Check Standard
        if: ( matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'devel' ) == false
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          _R_CHECK_LENGTH_1_CONDITION_: true
          _R_CHECK_LENGTH_0_LOGIC2_: true
        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Install Valgrind (Linux-rdevel only)
        if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'devel'
        run: sudo apt-get install valgrind

      - name: Check Valgrind (Linux-rdevel only)
        if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'devel'
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          # https://www.valgrind.org/docs/manual/manual-core.html
          VALGRIND_OPTS: "--leak-check=full --track-origins=yes"
          # https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt
          RJAVA_JVM_STACK_WORKAROUND: 0
          R_DONT_USE_TK: true
        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--use-valgrind"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Code Coverage
        if: matrix.config.os == 'windows-latest' && matrix.config.r == 'release'
        run: |
          install.packages("covr")
          covr::codecov(line_exclusions=list("src/COrthogonalArray.cpp", "src/COrthogonalArray.h", "src/CRandom.h", "src/RStandardUniform.h", "src/ak3.cpp", "src/akconst.cpp", "src/akn.cpp", "src/construct.cpp", "src/GaloisField.h", "src/GaloisField.cpp", "src/geneticLHS.cpp", "src/improvedLHS.cpp", "src/matrix.h", "src/maximinLHS.cpp", "src/oa.cpp", "src/oaLHS.cpp", "src/oaLHSUtility.h", "src/optSeededLHS.cpp", "src/optimumLHS.cpp", "src/order.h", "src/primes.cpp", "src/randomLHS.cpp", "src/runif.cpp", "src/runif.h", "src/rutils.cpp", "src/rutils.h", "src/utilityLHS.cpp", "src/utilityLHS.h", "src/xtn.h", "src/bclibVersion.h", "src/oalibVersion.h", "src/lhslibVersion.h", "src/OACommonDefines.h"))
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check