Update the R-CMD-check workflow

lbbe-software · Jan 24, 2024 · 22e174b · 22e174b
1 parent 23b0e9a
commit 22e174b
Showing 1 changed file with 39 additions and 64 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,14 +1,11 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# 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:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,58 +19,37 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest,  r: 'release'}
+          - {os: macOS-latest,    r: 'devel',   http-user-agent: 'release'}
+          - {os: macOS-latest,    r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel',   http-user-agent: 'release'}
+          - {os: ubuntu-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
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-tinytex@master
-
       - name: Install libraries for Linux
         if: runner.os == 'Linux'
         run: |
           sudo apt-get install texlive-fonts-extra texlive-lang-european texlive-latex-recommended
           sudo apt-get install libcurl4-openssl-dev
        
-      - 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: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@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: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
       - name: Install dependencies
         run: |
+          install.packages("remotes")
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
           install.packages("BiocManager")
@@ -94,26 +70,25 @@ jobs:
           tinytex::tlmgr_install(c("bera", "titlesec", "fancyhdr", "enumitem", "parskip", "nowidow", "parnotes"))
         shell: Rscript {0}
 
-      - name: Install Windows dependencies
-        if: runner.os == 'Windows'
-        run: |
-          install.packages("BiocManager")
-          BiocManager::install("RCurl",type="binary",force=TRUE)
-          Sys.setenv(LOCAL_CPPFLAGS = "-I/mingw$(WIN)/include/libxml2")
-          install.packages("XML")
-        shell: Rscript {0}
+      # - name: Install Windows dependencies
+      #   if: runner.os == 'Windows'
+      #   run: |
+      #     install.packages("BiocManager")
+      #     BiocManager::install("RCurl",type="binary",force=TRUE)
+      #     Sys.setenv(LOCAL_CPPFLAGS = "-I/mingw$(WIN)/include/libxml2")
+      #     install.packages("XML")
+      #   shell: Rscript {0}
 
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          # pak-version: devel
+          # extra-packages: any::rcmdcheck, any::XML
+          extra-packages: any::rcmdcheck
+          needs: check
+          # See https://github.com/r-lib/actions/issues/559 for the XML issue
 
-      - 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
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"error"'
+          check-dir: '"check"'