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:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  workflow_dispatch:
    inputs:
      ssh_debug:
        description: Launch shell for interactive debugging?
        type: boolean
        required: true
        default: false
name: R-CMD-check

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  R-CMD-check-base:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
      GIT_CRYPT_KEY64: ${{ secrets.GIT_CRYPT_KEY64 }}
    steps:
      - uses: actions/checkout@v3
      - name: Do a pre-emptive apt-update
        run: sudo apt-get update -qq
        if: ${{ !env.ACT }}
      - name: Decrypt repository using symmetric key
        if: ${{ env.GIT_CRYPT_KEY64 }}
        run: |
          sudo apt-get install -y --no-install-recommends git-crypt
          echo $GIT_CRYPT_KEY64 > git_crypt_key.key64 && base64 -di git_crypt_key.key64 > git_crypt_key.key && git-crypt unlock git_crypt_key.key
          rm git_crypt_key.key git_crypt_key.key64
          # Select all values in .env and print with "::add-mask::" to obfuscate
          grep -v '^#' .env | sed -E 's/(.*)=(.*)/\2/' | xargs -I '{}' echo "::add-mask::{}"
      - uses: r-lib/actions/setup-pandoc@v2
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: release
          use-public-rspm: true
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::sessioninfo, any::rcmdcheck, any::pkgdepends, any::covr, any::riskmetric, github::ropensci-review-tools/pkgcheck,
          needs: check
      - name: Run just package tests and record test coverage
        run: |
          cat("LOGNAME=", Sys.info()[["user"]], "\n", sep = "", file = Sys.getenv("GITHUB_ENV"), append = TRUE)
          cat("check-dir-path=", file.path(getwd(), ("check")), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
          coverage <- covr::package_coverage(code = "saveRDS(testthat::capture_output(testthat::test_package('relic', reporter = 'Progress')), file.path('check', 'test_results.rds'))", install_path = "check", clean=FALSE)
          saveRDS(coverage, file.path("check", "coverage.rds"))
          cat(readRDS(file.path('check', 'test_results.rds')))
        shell: Rscript {0}
      - name: Run R-CMD-check without tests
        run: |
          options(crayon.enabled = TRUE)
          cat("LOGNAME=", Sys.info()[["user"]], "\n", sep = "", file = Sys.getenv("GITHUB_ENV"), append = TRUE)
          if (Sys.getenv("_R_CHECK_FORCE_SUGGESTS_", "") == "") Sys.setenv("_R_CHECK_FORCE_SUGGESTS_" = "false")
          if (Sys.getenv("_R_CHECK_CRAN_INCOMING_", "") == "") Sys.setenv("_R_CHECK_CRAN_INCOMING_" = "false")
          cat("check-dir-path=", file.path(getwd(), ("check")), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
          rcmdcheck::rcmdcheck(args = c("--no-tests", "--no-manual"), error_on = "warning", check_dir = ("check"))
        shell: Rscript {0}
      - name: Print and upload coverage
        run: |
          library(covr)
          coverage <- readRDS(file.path("check", "coverage.rds"))
          coverage
          covr::codecov(coverage = coverage)
        shell: Rscript {0}
        continue-on-error: true
      - name: Additional diagnostics
        run: |
          pkc <- pkgcheck::pkgcheck(goodpractice = FALSE)
          gp <- goodpractice::goodpractice(checks = goodpractice::all_checks()[grep("(rcmdcheck|covr)", goodpractice::all_checks(), invert = TRUE)])
          pkc
          gp
        shell: Rscript {0}
        continue-on-error: true
      - name: Launch a temporary interactive debugging session
        uses: mxschmitt/action-tmate@v3.16
        if: always() && inputs.ssh_debug
        with:
          detached: true


     #  - uses: r-lib/actions/check-r-package@v2
     #   with:
     #     upload-snapshots: true

  R-CMD-check-grid:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
    needs: R-CMD-check-base
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macos-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
         #- {os: ubuntu-latest,   r: 'release'}
          - {os: ubuntu-latest,   r: 'oldrel-1'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v3
      - name: Install libgit2 on macOS
        run: |
          if [ "$RUNNER_OS" == "macOS" ]; then
            brew install libgit2
          fi
        shell: bash
      - uses: r-lib/actions/setup-pandoc@v2
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::sessioninfo, any::rcmdcheck, any::pkgdepends
          needs: check

      - uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true

      - name: Launch a temporary interactive debugging session
        uses: mxschmitt/action-tmate@v3.16
        if: always() && inputs.ssh_debug
        with:
          detached: true