diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml deleted file mode 100644 index 8ac46c6..0000000 --- a/.github/workflows/check.yml +++ /dev/null @@ -1,152 +0,0 @@ -on: - push: - pull_request: - -name: R-CMD-check - -jobs: - check: - runs-on: ${{ matrix.config.os }} - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - _R_CHECK_TESTS_NLINES_: 0 - NOT_CRAN: true - HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: true - _R_CHECK_FORCE_SUGGESTS_: false #TODO: drop this for now! - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - strategy: - fail-fast: false - matrix: - config: - - {os: macos-latest, r: 'devel'} - - {os: windows-latest, r: 'devel', rtools-version: '45'} - - {os: ubuntu-latest, r: 'devel'} - - {os: ubuntu-24.04, r: 'devel'} - - steps: - - ## Most of these steps are the same as the ones in - ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml - ## If they update their steps, we will also need to update ours. - - name: Checkout Repository - uses: actions/checkout@v3 - - ## pandoc - - name: Setup pandoc from r-lib - uses: r-lib/actions/setup-pandoc@v2 - - ## R is already included in the Bioconductor docker images - - name: Setup R from r-lib - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - rtools-version: ${{ matrix.config.rtools-version }} - - ## Windows dependencies - - name: Install Windows system dependencies - if: runner.os == 'Windows' - run: | - ## Edit below if you have any Windows system dependencies - shell: Rscript {0} - - ## linux dependencies - - name: Install linux system dependencies - if: runner.os == 'Linux' - run: | - sudo apt-get install -y libgdal-dev - sudo apt-get install -y libfftw3-dev - sudo apt-get install -y libmagick++-dev - sudo apt-get install -y cmake - sudo apt-get install -y libhdf5-dev - sudo apt-get install -y git - sudo apt-get install -y libssl-dev - sudo apt-get install -y libcurl4-openssl-dev - sudo apt-get install -y libgit2-dev - sudo apt-get install -y libxml2-dev - sudo apt-get install -y libfontconfig1-dev - sudo apt-get install -y libharfbuzz-dev - sudo apt-get install -y libfribidi-dev - sudo apt-get install -y libfreetype6-dev - sudo apt-get install -y libpng-dev - sudo apt-get install -y libtiff5-dev - sudo apt-get install -y libjpeg-dev - sudo apt-get install -y libz-dev - # install jdk - sudo apt-get install -y libz-dev - sudo apt upgrade -y - sudo apt-get install -y openjdk-21-jdk - export JAVA_HOME=/usr/lib/jvm/java-21-openjdk-arm64/ - R CMD javareconf -e - - ## macOS dependencies - - name: Install macOS system dependencies - if: runner.os == 'macOS' - run: | - ## Enable installing XML from source if needed - brew install libxml2 - echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV - - ## Required to install magick as noted at - ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 - brew install imagemagick@6 - - ## For textshaping, required by ragg, and required by pkgdown - brew install harfbuzz fribidi - - ## For installing usethis's dependency gert - brew install libgit2 - - ## hdf5 - brew install hdf5 - - ## Required for tcltk - brew install xquartz --cask - - ## remotes, devtools - - name: Query dependencies - run: | - install.packages('remotes') - install.packages('devtools') - shell: Rscript {0} - - ## BiocManager - - name: Install BiocManager - run: | - remotes::install_cran("BiocManager") - shell: Rscript {0} - - # All Other dependencies - - name: Install dependencies - run: | - ## Try installing the package dependencies in steps. First the local - ## dependencies, then any remaining dependencies to avoid the - ## issues described at - ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html - ## https://github.com/r-lib/remotes/issues/296 - ## Ideally, all dependencies should get installed in the first pass. - install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories()) - remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) - shell: Rscript {0} - - # All Other dependencies - - name: Install Suggested dependencies - run: | - BiocManager::install('RBioFormats') - shell: Rscript {0} - - ## R CMD Check - - name: Run CMD check - env: - _R_CHECK_CRAN_INCOMING_: false - DISPLAY: 99.0 - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck( - args = c("--no-manual", "--no-vignettes", "--timings"), - build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), - error_on = "error", - check_dir = "check" - ) - shell: Rscript {0} \ No newline at end of file diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml new file mode 100644 index 0000000..09cacec --- /dev/null +++ b/.github/workflows/r-universe.yml @@ -0,0 +1,14 @@ +name: Test R-universe + +on: + push: + branches: [devel] + pull_request: + +jobs: + build: + name: R-universe testing + uses: r-universe-org/workflows/.github/workflows/build.yml@v3 + with: + universe: bioc + organization: bioconductor \ No newline at end of file