From 2c563a5526dd283def454837a02dc9e89223549c Mon Sep 17 00:00:00 2001
From: Victor Yuan <victor.2wy@gmail.com>
Date: Fri, 14 Jun 2024 16:27:15 -0700
Subject: [PATCH] Create R-CMD-bioccheck.yaml

---
 .github/workflows/R-CMD-bioccheck.yaml | 179 +++++++++++++++++++++++++
 1 file changed, 179 insertions(+)
 create mode 100644 .github/workflows/R-CMD-bioccheck.yaml

diff --git a/.github/workflows/R-CMD-bioccheck.yaml b/.github/workflows/R-CMD-bioccheck.yaml
new file mode 100644
index 0000000..fc1b104
--- /dev/null
+++ b/.github/workflows/R-CMD-bioccheck.yaml
@@ -0,0 +1,179 @@
+# from https://github.com/grimbough/biocActionsExamples/blob/main/.github/workflows/example-workflow.yml
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  
+name: Workflow that tests the actions 
+
+env:
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  pkg-at-root:
+    name: Root Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-22.04, windows-2019, windows-2022, macos-11, macos-12, macos-13, macos-14]
+        ## Test using both Bioconductor devel and release
+        bioc-version: [devel, release]
+
+    runs-on: ${{ matrix.os }}
+    
+    steps:
+    
+      - uses: actions/checkout@v4
+          
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: ${{ matrix.bioc-version }}
+          bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor
+          use-public-rspm: false
+          
+      - name: Install pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+          
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          
+      - name: Build, Install, Check
+        id: build-install-check
+        uses: grimbough/bioc-actions/build-install-check@v1
+        with:
+          package-directory: '.'
+      
+      ## Turn off the checks that we know will fail
+      ## Cause the workflow to error if any new errors appear
+      - name: Run BiocCheck with arguments
+        uses: grimbough/bioc-actions/run-BiocCheck@v1
+        with:
+          package-directory: '.'
+          arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help'
+          error-on: 'error'
+          
+      ## upload the Rcheck folder regardless of success of failure
+      - name: Upload output
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-Rcheck
+          path: |
+            ${{ steps.build-install-check.outputs.check-dir }}
+
+      ## upload source and binary packages
+      - name: Upload check output
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-pkgs
+          path: |
+            ${{ steps.build-install-check.outputs.source-tarball }}
+            ${{ steps.build-install-check.outputs.package-binary }}
+
+  pkg-in-subfolder:
+    name: Subfolder Pkg - Bioc ${{ matrix.bioc-version }} (${{ matrix.os }}) 
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04]
+        bioc-version: [release]
+        
+    runs-on: ${{ matrix.os }}
+    
+    steps:
+    
+      - uses: actions/checkout@v4
+      
+      ## We only using Ubuntu and BioC-release here, 
+      ## so lets use the Rstudio package manager
+      ## to install binary linux packages
+      - name: Setup R and Bioconductor
+        uses: grimbough/bioc-actions/setup-bioc@v1
+        with:
+          bioc-version: ${{ matrix.bioc-version }}
+          bioc-mirror: https://packagemanager.rstudio.com/bioconductor
+          
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+      
+      ## Run the complete build, install, check process like the Bioc Build System
+      - name: Build, Install, Check
+        id: build-install-check
+        uses: grimbough/bioc-actions/build-install-check@v1
+        with:
+          package-directory: 'inst/nestedPKG'
+      
+      ## Run all tests in BiocCheck, include those we know fail
+      ## Use the 'error-on' to prevent this failing the workflow
+      - name: Run BiocCheck without arguments
+        uses: grimbough/bioc-actions/run-BiocCheck@v1
+        with:
+          package-directory: 'inst/nestedPKG'
+          error-on: 'never'
+          
+      ## upload the Rcheck folder if the workflow fails
+      - name: Upload output
+        uses: actions/upload-artifact@v4
+        if: failure()
+        with:
+          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-sub_folder
+          path: |
+            ${{ steps.build-install-check.outputs.check-dir }}
+
+  using-bioc-docker:
+    name: Docker Devel
+    strategy:
+      fail-fast: false
+
+    runs-on: ubuntu-22.04
+    container: bioconductor/bioconductor_docker:devel
+    
+    steps:
+    
+      - uses: actions/checkout@v4
+      
+      ##################################################
+      ## no need to install R, BiocManager, or Pandoc ##
+      ##################################################
+      
+      ## cache installed packages
+      - name: Cache install R packages
+        uses: actions/cache@v4
+        with:
+          path: /usr/local/lib/R/site-library
+          key: docker-1
+          restore-keys: docker-
+      
+      ## we can use BiocManager will install binary packages in the Docker container
+      - name: Install dependencies
+        run: |
+            BiocManager::install(c('AnnotationHub', 'rtracklayer', 'knitr', 'rmarkdown', 'BiocStyle'))
+        shell: Rscript {0}
+          
+      - name: Build, Install, Check
+        id: build-install-check
+        uses: grimbough/bioc-actions/build-install-check@v1
+        with:
+          package-directory: '.'
+      
+      ## Turn off the checks that we know will fail
+      ## Cause the workflow to error if any new errors appear
+      - name: Run BiocCheck with arguments
+        uses: grimbough/bioc-actions/run-BiocCheck@v1
+        with:
+          package-directory: '.'
+          arguments: '--no-check-bioc-views --no-check-vignettes --no-check-bioc-help'
+          error-on: 'error'
+
+      - name: Upload built package binary
+        uses: actions/upload-artifact@v4
+        with:
+          name: docker-binary
+          path: |
+            ${{ steps.build-install-check.outputs.package-binary }}