R-CMD-check-fedora.yaml

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  schedule:
    - cron: 0 0 * * 1 # schedule to run at midnight on Monday each week
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master
name: Fedora

env:
  OMP_THREAD_LIMIT: 2
  KMP_DEVICE_THREAD_LIMIT: 2
  _R_CHECK_SUGGESTS_ONLY_: true
  _R_CHECK_NO_RECOMMENDED_: true
  _R_CHECK_DOC_SIZES2_: true
  _R_CHECK_DEPRECATED_DEFUNCT_: true
  _R_CHECK_SCREEN_DEVICE_: warn
  _R_CHECK_REPLACING_IMPORTS_: true
  _R_CHECK_TOPLEVEL_FILES_: true
  _R_CHECK_DOT_FIRSTLIB_: true
  _R_CHECK_RD_LINE_WIDTHS_: true
  _R_CHECK_S3_METHODS_NOT_REGISTERED_: true
  _R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_: true
  _R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_: true
  _R_CHECK_NATIVE_ROUTINE_REGISTRATION_: true
  _R_CHECK_FF_CALLS_: registration
  _R_CHECK_PRAGMAS_: true
  _R_CHECK_COMPILATION_FLAGS_: true
  _R_CHECK_R_DEPENDS_: true
  _R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_: true
  _R_CHECK_SHLIB_OPENMP_FLAGS_: true
  _R_CHECK_BROWSER_NONINTERACTIVE_: true
  _R_CHECK_CODE_ASSIGN_TO_GLOBALENV_: true
  _R_CHECK_CODE_DATA_INTO_GLOBALENV_: true
  _R_CHECK_PKG_SIZES_: true
  _R_CHECK_LIMIT_CORES_: true
  _R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_: true
  _R_CHECK_AUTOCONF_: true
  _R_CHECK_THINGS_IN_CHECK_DIR_: true
  _R_CHECK_THINGS_IN_TEMP_DIR_: true
  _R_CHECK_THINGS_IN_TEMP_DIR_EXCLUDE_: "^ompi"
  _R_CHECK_BASHISMS_: true
  _R_CHECK_ORPHANED_: true
  _R_CHECK_DEPENDS_ONLY_DATA_: true
  _R_CHECK_XREFS_PKGS_ARE_DECLARED_: true
  _R_CHECK_MATRIX_DATA_: true
  _R_CHECK_RD_VALIDATE_RD2HTML_: true
  _R_CHECK_RD_MATH_RENDERING_: true

jobs:
  R-CMD-check:
    name: Fedora (devel)

    runs-on: ubuntu-latest

    container:
      image: docker://rhub/fedora-clang-devel:latest
      options: --user root
      env:
        _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
        _R_CHECK_FORCE_SUGGESTS_: false
        _R_CHECK_TIMINGS_: 10
        _R_CHECK_CRAN_INCOMING_REMOTE_: false
        _R_CHECK_LIMIT_CORES_: true
        _R_CHECK_LICENSE_: true
        OMP_THREAD_LIMIT: 2
        KMP_DEVICE_THREAD_LIMIT: 2
        KMP_TEAMS_THREAD_LIMIT: 2
        KMP_ALL_THREADS: 2
        NOT_CRAN: true
        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
        CI: true

    steps:
      - uses: actions/checkout@v2

      - name: Setup path
        run: |
          echo "/opt/R-devel/bin" >> $GITHUB_PATH

      - name: Install system dependencies
        run: |
          echo $PATH
          dnf install -y \
            mpfr-devel \
            automake \
            fftw-devel \
            gmp-devel \
            openssl-devel \
            zlib-devel \
            pandoc \
            geos-devel \
            make \
            gdal \
            libxml2-devel \
            cmake \
            proj-devel \
            sqlite-devel \
            gdal-devel \
            libicu-devel \
            udunits2-devel \
            coin-or-SYMPHONY-devel \
            git-all

      - name: Install dependencies
        run: |
          options(repos = "https://cloud.r-project.org/")
          install.packages("remotes")
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
        shell: Rscript {0}

      - name: Session information
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - name: Check
        run: |
          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-build-vignettes"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash