Add R-CMD-check and BiocCheck GitHub Actions

Author: Zaoqu-Liu

.github/workflows/BiocCheck.yaml

@@ -0,0 +1,36 @@
+name: BiocCheck
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  BiocCheck:
+    runs-on: ubuntu-latest
+    
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'devel'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "BiocManager"))
+          BiocManager::install(c("BiocCheck"), ask = FALSE, update = TRUE)
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: BiocCheck
+        run: |
+          BiocCheck::BiocCheck(".", `quit-with-status` = TRUE, `no-check-bioc-help` = TRUE)
+        shell: Rscript {0}

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,46 @@
+name: R-CMD-check
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true