implement GHA

Author: Artur-man

.github/workflows/check.yml

@@ -0,0 +1,92 @@
+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: 'release'}
+          - {os: windows-latest, r: 'release', rtools-version: '44'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-24.04,   r: 'release'}
+    
+    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 }}
+          
+      ## 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}