mac_r.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.
name: R Package CI for macOS

on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master" ]

permissions:
  contents: read 

jobs:
  build:
    runs-on: macos-latest
    strategy:
      matrix:
        os: [macos-latest]
        r-version: ['4.1.1']

    steps:
      - uses: actions/checkout@v4

      - name: Install system dependencies on macOS
        run: |
          brew install jags
          brew install --cask mactex-no-gui
          brew install gfortran
        shell: bash

      - name: Create symbolic link for gfortran
        run: |
          sudo mkdir -p /opt/R/arm64/bin
          sudo ln -s $(which gfortran) /opt/R/arm64/bin/gfortran
        shell: bash

      - name: Set up R ${{ matrix.r-version }}
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r-version }}

      - name: Install remotes package
        run: |
          Rscript -e "install.packages('remotes')"
        shell: Rscript {0}

      - name: Install package dependencies
        run: |
          Rscript -e "install.packages(c('smacof', 'ellipse', 'plyr', 'vegan'))"
        shell: Rscript {0}

      - name: Install basicspace from GitHub
        env:
          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
        run: |
          Rscript -e "remotes::install_github('cran/basicspace', force = TRUE)"
        shell: Rscript {0}

      - name: Set CRAN mirror and install other R package dependencies
        env:
          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
        run: |
          Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org/')); install.packages(c('rjags', 'ggplot2', 'knitr'));"
        shell: Rscript {0}

      - name: Install rcmdcheck package
        run: |
          Rscript -e "install.packages('rcmdcheck')"
        shell: Rscript {0}

      - name: Run R CMD check
        env:
          PATH: /opt/homebrew/opt/gcc/bin:/opt/homebrew/bin:$PATH
        run: |
          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"
        shell: Rscript {0}

      - name: Test (optional)
        run: |
          Rscript -e "devtools::test()"
        shell: Rscript {0}

    env:
      TZ: UTC
      _R_CHECK_SYSTEM_CLOCK_: false
      NOT_CRAN: true

  build-windows:
    runs-on: windows-latest
    strategy:
      matrix:
        os: [windows-latest]
        r-version: ['4.1.1']

    steps:
      - uses: actions/checkout@v4

      - name: Download and install JAGS
        run: |
          Invoke-WebRequest -Uri "https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.0.exe/download" -OutFile "JAGS-4.3.0.exe"
          if (Test-Path -Path ".\JAGS-4.3.0.exe") {
            Start-Process -FilePath ".\JAGS-4.3.0.exe" -ArgumentList '/S' -NoNewWindow -Wait
          } else {
            Write-Error "Failed to download JAGS installer."
          }
        shell: powershell

      - name: Add JAGS to PATH
        run: |
          echo "C:\Program Files\JAGS\JAGS-4.3.0\bin" >> $GITHUB_PATH
        shell: cmd

      - name: Verify JAGS installation
        run: jags --version
        shell: cmd

      - name: Set up R ${{ matrix.r-version }}
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r-version }}

      - name: Install remotes package
        run: Rscript -e 'install.packages("remotes")'
        shell: /bin/bash -e {0}


      - name: Install CRAN packages including rjags
        run: |
          Rscript -e "options(repos = 'https://cloud.r-project.org/')"
          Rscript -e "install.packages('rjags')"
          Rscript -e "install.packages(c('smacof', 'ellipse', 'plyr', 'vegan'), dependencies=TRUE)"
        shell: cmd

      - name: Install basicspace from GitHub
        env:
          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
        run: |
          Rscript -e "remotes::install_github('cran/basicspace', force = TRUE)"
        shell: cmd

      - name: Set CRAN mirror and install other R package dependencies
        env:
          GITHUB_PAT: ${{ secrets.MY_GITHUB_PAT }}
        run: |
          Rscript -e "options(repos = c(CRAN = 'https://cloud.r-project.org/')); install.packages(c('ggplot2', 'knitr'));"
        shell: cmd

      - name: Install rcmdcheck package
        run: |
          Rscript -e "install.packages('rcmdcheck')"
        shell: cmd

      - name: Check
        run: |
          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'error')"
        shell: cmd

      - name: Test (optional)
        run: |
          Rscript -e "devtools::test()"
        shell: cmd

    env:
      TZ: UTC
      _R_CHECK_SYSTEM_CLOCK_: false
      NOT_CRAN: true