R-CMD-check.yaml

# NOTE: This script is a modification of the r-lib/actions standard cehcking script and the public-private sync script, on which it piggybacks to detect when it's in a private repo and can therefore skip some or even all tests. It also builds and uploads binaries for Windows and MacOS.

# 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

# Each entry in the config matrix must have the following keys:
#
# os: windows-latest, macOS-latest, ubuntu-20.04, etc. (as of this writing)
#
# r: devel or release
#
# rspm: Linux only, just leave it alone.
#
# timeout: in minutes
#
# flags: a comma (or some other aesthetically pleasing and
#   non-forbidden symbol) separated list of flags. Currently
#   supported:
#
#   binaries: build and upload as an artefact a binary version (particularly for MacOS and Windows).
#
#   full: run with ENABLE_statnet_TESTS.
#
#   vignettes: build vignettes and manuals; otherwise ignore.
#
#   ubsan: compile with -fsanitize=undefined and fail on any errors identified.
#
#   debug: compile package with -DDEBUG and -UNDEBUG
#
#   covr: run in covr mode may be used with 'full' but probably not with others.
#
#
# Typical public, private, and release configurations are provided in the variables below.

on: [push, pull_request]

name: R-CMD-check

# Set public and private repositories (i.e., USER/PKG). Leave blank to autodetect.
env:
  PUBLIC: ''
  PRIVATE: ''
  PUBLIC_CONFIG: '{"config":[
            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries"},
            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan"},
            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug"},
            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote"},
            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr"}]}'
  RELEASE_CONFIG: '{"config":[
            {"os":"windows-latest", "r":"release", "timeout":360, "flags":"binaries, vignettes, remote, strict"},
            {"os":"macOS-latest", "r":"release", "timeout":360, "flags":"binaries, ubsan, vignettes, remote, strict"},
            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, ubsan, debug, strict"},
            {"os":"ubuntu-latest", "r":"devel", "timeout":360, "flags":"vignettes, remote, strict"},
            {"os":"ubuntu-latest", "r":"release", "timeout":360, "flags":"full, covr, strict"}]}'
  PRIVATE_CONFIG: '{"config":[
            {"os":"ubuntu-latest", "r":"release", "timeout":10, "flags":"none"}
            ]}'

jobs:
  Set-Matrix-Private:
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.set-matrix.outputs.matrix }}
    steps:
      - name: check-config # Make sure either neither or both are set; abort if not.
        if: (env.PUBLIC == '') != (env.PRIVATE == '')
        run: |
          echo "Configuration problem: only one of the repositories is set."
          exit 1
      - name: detect-repos
        if: env.PUBLIC == '' && env.PRIVATE == '' # Autodetect always.
        run: |
          if [[ "${{ github.repository }}" == *-private ]]
          then # Current repo is private.
            IAM="private"
            PRIVATE="${{ github.repository }}"
            PUBLIC="${PRIVATE%-private}"
          else # Current repo is public.
            IAM="public"
            PUBLIC="${{ github.repository }}"
            PRIVATE="$PUBLIC-private"
          fi
          echo "IAM=$IAM" >> $GITHUB_ENV
          echo "PRIVATE=$PRIVATE" >> $GITHUB_ENV
          echo "PUBLIC=$PUBLIC" >> $GITHUB_ENV
      - name: public-check # Check if the branch/tag exists in the public repository.
        if: env.IAM == 'private' # Only check if from private repo.
        run: |
          set +e
          git ls-remote --exit-code https://github.com/${{ env.PUBLIC }} ${{ github.ref }}
          echo "FOUND_PUBLIC=$?" >> $GITHUB_ENV
      - name: set-matrix
        id: set-matrix
        run: |
          if [[ "${{ env.IAM }}" == 'public' ]] # Public: full set.
          then
            config='${{ env.RELEASE_CONFIG }}'
          elif [[ "${{ env.FOUND_PUBLIC }}" != '0' ]] # Private with no public analogue: reduced set.
          then
            config='${{ env.PRIVATE_CONFIG }}'
          else # Private with public analogue: no checking.
            config=''
          fi
          config="${config//$'\r'/' '}"
          config="${config//$'\n'/' '}"
          echo "matrix=$config" >> $GITHUB_OUTPUT

  R-CMD-check:
    needs: Set-Matrix-Private

    if: needs.Set-Matrix-Private.outputs.matrix != ''

    runs-on: ${{ matrix.config.os }}

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

    strategy:
      fail-fast: false
      matrix: ${{fromJson(needs.Set-Matrix-Private.outputs.matrix)}}

    env:
      HOMEBREW_NO_INSTALL_CLEANUP: 1
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

    steps:
      - name: If available, use the Janitor's key rather than the repository-specific key.
        id: set-pat
        run: |
          if [[ -n "${{ secrets.JANITORS_GITHUB_PAT }}" ]]
          then
            echo "GITHUB_PAT=${{ secrets.JANITORS_GITHUB_PAT }}" >> $GITHUB_ENV
          else
            echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV
          fi
        shell: bash

      - uses: actions/checkout@v4

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

      - name: Install tidy (on Linux if running vignettes)
        if: runner.os == 'Linux' && contains(matrix.config.flags, 'vignettes')
        run: |
          /usr/bin/sudo DEBIAN_FRONTEND=noninteractive apt-get install -y tidy
        shell: bash

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Install tinytex (system)
        if: contains(matrix.config.flags, 'vignettes')
        uses: r-lib/actions/setup-tinytex@v2

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::rcmdcheck
            any::covr
            any::V8
            any::xml2
          needs: |
            check
            coverage

      - name: Install tinytex (R)
        if: contains(matrix.config.flags, 'vignettes')
        run: |
          if(!requireNamespace("tinytex", quietly = TRUE)) pak::pkg_install("tinytex")
          tinytex:::install_yihui_pkgs()
          tinytex::tlmgr_install("makeindex")
        shell: Rscript {0}

      - name: Build
        if: contains(matrix.config.flags, 'binaries')
        run: |
          dir.create("binaries", FALSE)
          pkgbuild::build(binary=TRUE, vignettes=FALSE, dest_path = "binaries")
        shell: Rscript {0}

      - name: Upload build results
        if: contains(matrix.config.flags, 'binaries') && !failure()
        uses: actions/upload-artifact@v4
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-binaries
          path: binaries

      - name: Clean up build results
        if: contains(matrix.config.flags, 'binaries')
        run: rm -rf binaries
        shell: bash

      - name: Check
        if: contains(matrix.config.flags, 'covr') == false
        timeout-minutes: ${{ matrix.config.timeout }}
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: ${{ contains(matrix.config.flags, 'remote') }}
          _R_CHECK_FORCE_SUGGESTS_: false
          ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }}
          R_VIGNETTES: ${{ contains(matrix.config.flags, 'vignettes') }}
          FAIL_ON_WARN: ${{ contains(matrix.config.flags, 'strict') }}
          USE_UBSAN: ${{ contains(matrix.config.flags, 'ubsan') }}
          SET_DEBUG: ${{ contains(matrix.config.flags, 'debug') }}
        run: |
          if(Sys.getenv("R_VIGNETTES") == "true"){
            check_args <- c("--as-cran")
            build_args <- c("--compact-vignettes=gs+qpdf")
          }else{
            check_args <- c("--no-manual", "--as-cran", "--ignore-vignettes")
            build_args <- c("--no-manual", "--no-build-vignettes")
          }

          if(Sys.getenv("ENABLE_statnet_TESTS") == "true"){
            check_args <- c(check_args, "--run-donttest")
          }

          error_on <- if(Sys.getenv("FAIL_ON_WARN") == "true") "warning" else "error"

          extra_flags <- c()

          if(Sys.getenv("USE_UBSAN") == "true"){
            extra_flags <- c(extra_flags, "-fsanitize=undefined")
            Sys.setenv(UBSAN_OPTIONS=paste(Sys.getenv("UBSAN_OPTIONS"), "print_stacktrace=1"))
          }

          if(Sys.getenv("SET_DEBUG") == "true") extra_flags <- c(extra_flags, "-UNDEBUG", "-DDEBUG")

          # Before R 4.3.0, R itself was not compliant.
          if(getRversion() >= "4.3") extra_flags <- c(extra_flags, "-Wstrict-prototypes")

          Sys.setenv(PKG_LIBS=paste(c(Sys.getenv("PKG_LIBS"), extra_flags), collapse=" "),
                     PKG_CXXFLAGS=paste(c(Sys.getenv("PKG_CXXFLAGS"), extra_flags), collapse=" "),
                     PKG_CFLAGS=paste(c(Sys.getenv("PKG_CFLAGS"), extra_flags), collapse=" "))

          rcmdcheck::rcmdcheck(args = check_args, build_args = build_args, error_on = error_on, check_dir = "check")
        shell: Rscript {0}

      - name: Check UBSAN output
        if: contains(matrix.config.flags, 'ubsan')
        # NB: xargs -r only works in GNU, so not on MacOS.
        run: |
          find check/ -name '*.Rout' -print0 > check/Rout.list
          if [ -s check/Rout.list ]
          then
            cat check/Rout.list | xargs -0 grep -E '\.[hc]:[0-9]+:[0-9]+: +runtime error:' > check/ubsan.err || true
            if [ -s check/ubsan.err ]
            then
              echo "UBSAN errors:" >&2
              cat check/ubsan.err >&2
              exit 1
            fi
          fi
        shell: bash
        
      - name: Upload check results
        if: contains(matrix.config.flags, 'covr') == false && failure()
        uses: actions/upload-artifact@v4
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: |
            check
            !check/*/00_pkg_src

      - name: Test coverage
        if: contains(matrix.config.flags, 'covr')
        timeout-minutes: ${{ matrix.config.timeout }}
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          _R_CHECK_FORCE_SUGGESTS_: ${{ runner.os != 'macOS' }} # Rmpi is not available on macOS.
          ENABLE_statnet_TESTS: ${{ contains(matrix.config.flags, 'full') }}
        run: |
          cov <- covr::package_coverage(
            type=c("tests", "examples"),
            quiet = FALSE,
            clean = FALSE,
            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
          )
          covr::to_cobertura(cov)
        shell: Rscript {0}

      - name: Upload coverage results
        if: contains(matrix.config.flags, 'covr')
        uses: codecov/codecov-action@v4
        with:
          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
          file: ./cobertura.xml
          plugin: noop
          disable_search: true
          token: ${{ secrets.CODECOV_TOKEN }}