r-cmd-check.yml

on:
  workflow_dispatch:
  workflow_call:
    inputs:
      error-on:
        description: Input for the 'error_on' parameter in rcmdcheck::rcmdcheck()
        required: false
        default: note
        type: string
  push:
    branches:
      - main
      - devel
  pull_request:
    branches:
      - main
      - devel

name: R CMD Check

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

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    container:
      image: "ghcr.io/pharmaverse/admiralci-${{ matrix.config.r }}:latest"
    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
    if: >
      !contains(github.event.commits[0].message, '[skip r-cmd-check]')
    strategy:
      fail-fast: false
      matrix:
        config:
          - {r: '4.1', repos: 'https://packagemanager.posit.co/cran/2021-05-03/'}
          - {r: '4.2', repos: 'https://packagemanager.posit.co/cran/2022-01-03/'}
          - {r: '4.3', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'}
          - {r: 'devel', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'} # not needed for devel ?

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      R_REPOS: ${{ matrix.config.repos }}

    steps:
      ##################### BEGIN boilerplate steps #####################
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v5.4

      - name: Checkout repo (PR) 🛎
        uses: actions/checkout@v3
        if: github.event_name == 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          repository: ${{ github.event.pull_request.head.repo.full_name }}

      - name: Checkout repository
        uses: actions/checkout@v3
        if: github.event_name != 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}

      - name: Restore cache
        uses: actions/cache@v3
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        with:
          run-system-dependencies: false
          renv-restore: false
          enable-check: false
          cran-repos: "CRAN=${{ matrix.config.repos }}"
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      #####################c#####################

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          _R_CHECK_FORCE_SUGGESTS_: false
        run: |
          description_old <- readLines("DESCRIPTION")
          description_dat <- description_old
          for (i in seq_along(description_dat)) {
            if (grepl("^Version:", description_dat[i])) {
              current_version <- sub("^Version: ", "", description_dat[i])
              version_parts <- strsplit(current_version, "\\.")[[1]]
              
              # check if maintenance version - if yes, temp update the DESCRIPTION for rcmdchecks
              if (length(version_parts) == 4) {
                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
                version_parts <- version_parts[1:3]
              }
              
              new_version <- paste(version_parts, collapse = ".")
              description_dat[i] <- paste("Version: ", new_version)
            }
          }
          
          # Write the updated DESCRIPTION file back
          #writeLines(description_dat, con = "DESCRIPTION")
        
          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
          options(crayon.enabled = TRUE)
          check_error_on <- "${{ inputs.error-on }}"
          if (check_error_on == "") {
            check_error_on <- "note"
          }
          rcmdcheck::rcmdcheck(
            args = c("--no-manual", "--as-cran"),
            error_on = check_error_on,
            check_dir = "check"
          )

          # Write back initial description file
          writeLines(description_dat, con = "DESCRIPTION")
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: r${{ matrix.config.r }}-results
          path: check