R-CMD-check-bioc.yaml

# Based on workflows from https://github.com/Huber-group-EMBL/rhdf5
# Uses steps from https://github.com/grimbough/bioc-actions
on:
  push:
    branches:
      - devel
  pull_request:

name: R-CMD-check-bioc

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

env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
  R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

jobs:
  R-CMD-check-bioc:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }})

    strategy:
      fail-fast: false
      matrix:
        config:
        - { os: windows-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
        - { os: macOS-latest,   bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
        - { os: macOS-15-intel, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 2 }
        - { os: ubuntu-latest,  bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', cache: 1 }
        - { os: ubuntu-latest,  bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', cache: 1 }

    steps:

      ## R CMD check complains about Windows line endings without this
      - name: Configure git
        run: |
          git config --global core.autocrlf false

      - name: Checkout repository
        uses: actions/checkout@v6

      - name: Install Linux dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get -y install hdf5-tools libsz2 libaec-dev

      ## Workaround: data.table (indirect dep via Seurat) fails to compile
      ## on macOS ARM because libintl.h is missing.
      - name: Install macOS dependencies
        if: runner.os == 'macOS'
        run: |
          brew install gettext
          mkdir -p ~/.R
          echo "CPPFLAGS += -I$(brew --prefix gettext)/include" >> ~/.R/Makevars
          echo "LDFLAGS += -L$(brew --prefix gettext)/lib" >> ~/.R/Makevars

      - name: Setup R and Bioconductor
        # todo: remove this workaround line once it is working for windows and/or mac os x
        if: matrix.config.os != 'windows-latest' && matrix.config.os != 'macOS-latest'
        uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: ${{ matrix.config.bioc-version }}
          bioc-mirror: ${{ matrix.config.bioc-mirror }}

      ## windows-latest and macOS-latest (ARM) hit a bug in R-devel (commit
      ## dd03406, 2026-04-09) where BiocManager::install() crashes via
      ## old.packages(type="both") -> .available.both() -> subscript out of
      ## bounds. Work around by setting up R manually and calling
      ## BiocManager::install(update=FALSE) to skip the old.packages() call.
      - name: Setup R (Windows/macOS-ARM devel)
        if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest'
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: devel
          rtools-version: 45
          use-public-rspm: true

      - name: Setup Bioconductor (Windows/macOS-ARM devel)
        if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macOS-latest'
        shell: Rscript {0}
        run: |
          download.file(
            'https://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc',
            destfile = '~/.Renviron', mode = 'wb')
          write(
            'options(BioC_mirror = "${{ matrix.config.bioc-mirror }}")',
            file = '~/.Rprofile', append = TRUE)
          install.packages(c("BiocManager", "remotes"), quiet = TRUE)
          ## update=FALSE avoids calling old.packages(type="both") which
          ## triggers the R-devel bug in .available.both() (commit dd03406)
          BiocManager::install(version = "3.23", ask = FALSE, update = FALSE)
          cat("R_BIOC_VERSION=3.23\n", file = Sys.getenv("GITHUB_ENV"), append = TRUE)

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

      - name: Install R dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: ${{ matrix.config.cache }}
          extra-packages: any::rcmdcheck
          needs: check

      ## Workaround: llvmlite has no pre-built pip wheel on macOS x86_64,
      ## but conda-forge does have a build. Use reticulate + conda to install.
      ## See https://github.com/numba/numba/issues/10187#issuecomment-3800638403
      - name: Cache conda packages (macOS Intel)
        if: matrix.config.os == 'macOS-15-intel'
        uses: actions/cache@v5
        with:
          path: ~/.local/share/r-miniconda
          key: ${{ runner.os }}-conda-${{ hashFiles('DESCRIPTION') }}
          restore-keys: |
            ${{ runner.os }}-conda-

      - name: Install Python packages via conda (macOS Intel)
        id: install-conda
        if: matrix.config.os == 'macOS-15-intel'
        shell: Rscript {0}
        run: |
          reticulate::install_miniconda()
          reticulate::py_install(
            c("scanpy", "mudata"),
            method = "conda",
            channel = "conda-forge"
          )
          # need to store this in Renviron because there's no easy way of
          # passing env vars to bioc-actions/build-install-check
          writeLines(
            paste0("RETICULATE_PYTHON=", reticulate::conda_python("r-reticulate")),
            "~/.Renviron"
          )

      - name: Verify conda installation (macOS Intel)
        if: matrix.config.os == 'macOS-15-intel'
        shell: Rscript {0}
        run: |
          stopifnot(reticulate::py_module_available("scanpy"))
          stopifnot(reticulate::py_module_available("mudata"))
          cat("Python packages verified successfully\n")

      - name: Bioc - Build, Install, Check
        id: bioc-check
        uses: grimbough/bioc-actions/build-install-check@v1

      - name: Show testthat output
        if: always()
        run: find .. -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash
      
      - name: Upload check results
        if: failure() && steps.bioc-check.outputs.check-dir != ''
        uses: actions/upload-artifact@v7
        with:
          name: ${{ format('{0}-{1}-bioc-{2}-results', runner.os, runner.arch, env.R_BIOC_VERSION) }}
          path: ${{ steps.bioc-check.outputs.check-dir }}

      - name: Run BiocCheck
        if: matrix.config.os == 'ubuntu-latest' && matrix.config.bioc-version == 'devel'
        uses: grimbough/bioc-actions/run-BiocCheck@v1
        with:
          error-on: 'never'
          arguments: '--no-check-bioc-help'