update yaml

mikejiang · mikejiang · commit 56bc6a814c6d · 2022-06-27T11:56:10.000-07:00
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -1,144 +1,45 @@
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-#
-
-name: build
-
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [ release, master ]
+    branches: [main, master]
   pull_request:
-    branches: [ release, master ]
-  workflow_dispatch:
+    branches: [main, master]
+
+name: R-CMD-check
 
 jobs:
-  build:
+  R-CMD-check:
     runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.r }})
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
       fail-fast: false
       matrix:
-        r: ['release', 'devel']
         config:
-#           - {os: windows-latest, suffix: 'zip'}
-          - {os: macOS-latest, suffix: 'tgz'}
-#           - {os: ubuntu-16.04, suffix: 'tar.gz', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-        isMaster:
-          - ${{ contains(github.ref, 'master') }}
-        exclude:
-          - isMaster: false
-            r: devel
-          - isMaster: true
-            r: release
+          - {os: macOS-latest,   r: 'release'}
+
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-    
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v2
-      - name: Set up R ${{ matrix.r }}
-        uses: r-lib/actions/setup-r@master
-        with:
-          r-version: ${{ matrix.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
-      
-      - uses: r-lib/actions/setup-tinytex@v1
-      - run: tlmgr --version
-      
-      - name: add more tex pkgs
-        run: |
-          install.packages('tinytex')
-          tinytex:::install_yihui_pkgs()
-        shell: Rscript {0}
-      
-#       - name: set token for cytoinstaller(and remotes) to increase github API rate limit
-#         env:
-#           SUPER_SECRET: ${{ secrets.CYTOINSTALLER_TOKEN }}
-#         run: echo "GITHUB_TOKEN=$SUPER_SECRET" >> $GITHUB_ENV
- 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
- 
-      - name: Install macOS system dependencies
-        if: runner.os == 'macOS'
-        run: brew install libgit2
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Get bioc ver
-        run: echo "bioc_ver=$(Rscript -e 'writeLines(as.character(remotes::bioc_version()))')" >> $GITHUB_ENV
-        shell: bash
-        
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: check bioc ver
-        run: echo $bioc_ver
-        shell: bash
-        
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
-          sudo apt-get install -y libcurl4-openssl-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_cran(c("rcmdcheck", "devtools"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_bioc("flowStats")
-          #remotes::install_github("RGLab/cytoinstaller")
-          #cytoinstaller::cyto_install_deps(dependencies = TRUE)
-        shell: Rscript {0}
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-#       - name: check rate limit
-#         run: |
-#           gh::gh("GET /rate_limit")$resources$core$remaining
-#         shell: Rscript {0}
-        
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
-          
-#       - name: build src pkg
-#         if: runner.os == 'Linux'
-#         run: devtools::build()
-#         shell: Rscript {0}
-        
-#       - name: build bin pkg
-#         if: runner.os != 'Linux'
-#         run: devtools::build(binary = TRUE)
-#         shell: Rscript {0}  
-        
-#       - name: Upload Release Asset
-#         uses: svenstaro/upload-release-action@v2
-#         with:
-#           repo_token: ${{ secrets.GITHUB_TOKEN }}
-#           file: '../*.${{ matrix.config.suffix }}'
-#           file_glob: true
-#           tag: bioc_${{ env.bioc_ver}}
-#           overwrite: true
-#           body: "This is my release text"
+          upload-snapshots: true
