R-CMD-check.yaml

# 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:
  pull_request:
    branches:
      - master

name: R-CMD-check

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref }}
  cancel-in-progress: true

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

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

    strategy:
      fail-fast: false
      matrix:
        config:
          ##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          ##                              IMPORTANT                                   ##
          ##                                                                          ##
          ##             Checks are deliberately not run on R-devel.                  ##
          ##  This is because they are already run in `R-CMD-check-strict` workflow.  ##
          ##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

          - { os: macOS-latest, r: "release" }

          - { os: windows-latest, r: "devel" }
          - { os: windows-latest, r: "release" }

          - { os: ubuntu-latest, r: "devel" }
          - { os: ubuntu-latest, r: "release" }

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      _R_CHECK_CRAN_INCOMING_: false
      _R_CHECK_FORCE_SUGGESTS_: false

    steps:
      # - name: Set locale
      #   if: matrix.config.locale == 'zh_CN.UTF-8'
      #   run: |
      #     sudo locale-gen zh_CN.UTF-8
      #     echo "LC_ALL=zh_CN.UTF-8" >> $GITHUB_ENV

      - name: Set locale
        if: matrix.config.locale == 'en_US'
        run: |
          sudo locale-gen en_US
          echo "LC_ALL=en_US" >> $GITHUB_ENV
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-pandoc@v2
        with:
          pandoc-version: "3.1"

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

      - name: Install packages from source
        run: |
          install.packages(c("Matrix", "TMB"), type = "source")
        shell: Rscript {0}

      # TODO: Check which of the ignore conditions are still relevant given the
      # current suggested dependencies and the minimum supported R version.
      # Update if anything out of date or not needed anymore.
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          pak-version: devel
          extra-packages: |
            any::rcmdcheck
            any::BH
            TMB=?ignore-before-r=100.0.0
            Matrix=?ignore-before-r=100.0.0
            glmmTMB=?ignore-before-r=100.0.0
            epiR=?ignore-before-r=4.0.0
            gam=?ignore-before-r=4.0.0
            gdtools=?ignore-before-r=4.0.0
            fastICA=?ignore-before-r=4.0.0
            metafor=?ignore-before-r=4.0.0
            panelr=?ignore-before-r=4.0.0
            jtools=?ignore-before-r=4.0.0
            mmrm=?ignore-before-r=4.0.0
            rsvd=?ignore-before-r=4.0.0
            sparsepca=?ignore-before-r=4.0.0
            qqconf=?ignore-before-r=4.0.0
            qqplotr=?ignore-before-r=4.0.0
            ape=?ignore-before-r=4.1.0
            car=?ignore-before-r=4.1.0
            drc=?ignore-before-r=4.1.0
            EGAnet=?ignore-before-r=4.1.0
            ggpubr=?ignore-before-r=4.1.0
            rstatix=?ignore-before-r=4.1.0
            PROreg=?ignore-before-r=4.1.0
            FactoMineR=?ignore-before-r=4.3.0
            factoextra=?ignore-before-r=4.3.0
            sjstats=?ignore-before-r=4.3.0
            nestedLogit=?ignore-before-r=4.3.0
            estimability=?ignore-before-r=4.3.0
            emmeans=?ignore-before-r=4.3.0
            effects=?ignore-before-r=4.3.0
            rmcorr=?ignore-before-r=4.1.0
            randomForest=?ignore-before-r=4.1.0
            MuMIn=?ignore-before-r=4.2.0
            pbkrtest=?ignore-before-r=4.1.0
            afex=?ignore-before-r=4.1.0
            car=?ignore-before-r=4.1.0
            ivreg=?ignore-before-r=4.1.0
            AER=?ignore-before-r=4.1.0
          needs: check

      # install *after* other deps to avoid FreeADFunObject error
      - name: Install glmmTMB from source
        run: |
          install.packages(c("MatrixModels", "glmmTMB"), type = "source")
        shell: Rscript {0}

      # Don't error on "note" because if any of the suggested packages are not available
      # for a given R version, this generates a NOTE causing unnecessary build failure
      - uses: r-lib/actions/check-r-package@v2
        with:
          error-on: '"warning"'
          upload-snapshots: true