renovate GitHub Actions

- remove old CI files
- add R CMD check action
- add ProjectId in Rproj
- set CRAN env with CODENAME

Author: LiNk-NY

.github/.gitignore

@@ -0,0 +1,73 @@
+name: R CMD check
+
+on:
+  push:
+    branches:
+      - devel
+    paths:
+      - 'DESCRIPTION'
+      - '**basic_checks.yml'
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - devel
+
+env:
+  cache-version: v1
+
+jobs:
+  r-build-and-check:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Get Ubuntu Codename and Set CRAN URL
+        run: |
+          CODENAME=$(lsb_release -cs)
+          echo "CRAN=https://packagemanager.posit.co/cran/__linux__/${CODENAME}/latest" >> "$GITHUB_ENV"
+
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Query dependencies and update old packages
+        run: |
+          BiocManager::install(ask=FALSE)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v4
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories())
+          remotes::install_cran(c("rcmdcheck", "covr"))
+          BiocManager::install("BiocCheck")
+        shell: Rscript {0}
+
+      - name: Run rcmdcheck
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        env:
+          DISPLAY: ':99.0'
+        run: |
+          BiocCheck::BiocCheck(
+              dir('check', 'tar\\.gz$', full.names = TRUE),
+              `quit-with-status` = FALSE,
+              `no-check-R-ver` = TRUE,
+              `no-check-bioc-help` = TRUE
+          )
+        shell: Rscript {0}

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

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: c8e45341-d01a-414d-a98a-fb488c8baf55
 
 RestoreWorkspace: Default
 SaveWorkspace: Default