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-${{ matrix.r_version }}:latest"
    name: (${{ matrix.r_version }})
    if: >
      !contains(github.event.commits[0].message, '[skip r-cmd-check]')
    strategy:
      fail-fast: false
      matrix:
        r_version: ["release", "devel", "oldrel"]

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: true
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      R_REPOS: "https://cran.r-project.org"
      DEPS_IGNORE: >-
        pharmaversesdtm,
        pharmaverseadam,
        admiral,
        admiraldev,
        admiralophtha,
        admiralonco,
        admiralvaccine,
        staged.dependencies

      # DEPS_IGNORE: env variable to ignore package when building renv.lock (step Upload dependencies artifact)
      # (improvments ideas : get this list of deps to ignore from staged.dependencies yml file)

    steps:
      ##################### BEGIN boilerplate steps #####################
      - name: Get branch names
        id: branch-name
        uses: tj-actions/branch-names@v8

      - name: Checkout repo (PR) 🛎
        uses: actions/checkout@v4.2.2
        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@v4.2.2
        if: |
          github.event_name != 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          set-safe-directory: "."
          fetch-depth: 0

      - name: Restore cache
        uses: actions/cache@v4
        with:
          path: |
            ~/.staged.dependencies
          key: staged-deps

      - name: Run Staged dependencies
        uses: insightsengineering/staged-dependencies-action@v1
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        with:
          run-system-dependencies: false
          renv-restore: false
          enable-check: false
          cran-repos: "$R_REPOS"
          direction: upstream
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

      - name: Install dependencies from DESCRIPTION
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        run: |
          remotes::install_local(force = TRUE, dependencies = TRUE)
        shell: Rscript {0}

      ##################### END boilerplate steps #####################

      - name: Upload dependencies artifact
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        run: |
          dir.create("/workspace/tmp")
          library(dplyr)
          installed_packages <- as.data.frame(installed.packages())
          packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
          packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
          installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>%  # remove pre-built deps
          filter(!Package %in% packages_to_remove)
          # save deps as csv file
          write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
          # create also renv.lock file
          setwd("/workspace/tmp")

          renv_lock <- list(
            "R" = list(
              "Version" = paste(R.version$major, R.version$minor, sep=".")
            ),
            "Repositories" = list(
                list(Name = "CRAN", URL = Sys.getenv("R_REPOS"))
              ),
            "Packages" = list()
          )

          # Populate with information about each package
          for (package in installed_packages$Package) {
            dep_name <- package
            dep_version <- installed_packages[installed_packages$Package == package, "Version"]

            version_parts <- strsplit(dep_version, "\\.")[[1]]
            if (length(version_parts) == 4) {
              print(sprintf("skipping installation of dep %s", dep_name))
            } else {
              print(sprintf("append dependency %s - version %s", dep_name, dep_version))
              requirements <- tools::package_dependencies(dep_name, recursive = TRUE)
              have_requirements <- length(requirements[[1]]) > 0
              if (have_requirements) {
                  renv_lock[["Packages"]][[dep_name]] <- list(
                      "Package" = dep_name,
                      "Version" = dep_version,
                      "Source" = "Repository",
                      "Repository" = "CRAN",
                      "Requirements" = requirements[[dep_name]]
                  )
              } else {
                  renv_lock[["Packages"]][[dep_name]] <- list(
                      "Package" = dep_name,
                      "Version" = dep_version,
                      "Source" = "Repository",
                      "Repository" = "CRAN"
                  )
              }
            }
          }

          # Write the list to a JSON file (renv.lock)
          writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
          print("generated renv.lock content")
          system("cat renv-${{ matrix.r_version }}.lock")
        shell: Rscript {0}

      - name: Upload deps.csv and renv.lock artifacts
        uses: actions/upload-artifact@v4
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        with:
          name: deps-${{ matrix.r_version }}
          path: |
            /workspace/tmp/

      - name: Check Version
        id: check_version
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        run: |
          maintenance_version="F"
          description_dat <- readLines("DESCRIPTION")
          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 (length(version_parts) == 4) {
                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
                maintenance_version="T"
              }
            }
          }
          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
        shell: Rscript {0}

      - name: Check
        if: |
          (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
          matrix.r_version != 'devel'
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
          _R_CHECK_FORCE_SUGGESTS_: false
        run: |
          unlink("tmp",recursive=TRUE)
          if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
          }
          if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
          options(crayon.enabled = TRUE)
          check_error_on <- "${{ 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"
          )
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v4
        with:
          name: r${{ matrix.r_version }}-results
          path: check