workflow_fix

.github/workflows/r.yml

@@ -1,14 +1,19 @@
-# 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
+# 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
 on:
   push:
-    branches: [main, master, dev]
+    branches:
+      - main
+      - master
   pull_request:
-    branches: [main, master, dev]
+    branches:
+      - main
+      - master
   schedule:
     - cron:  '1 1 1 * *'
+  workflow_dispatch:
 
-name: R-CMD-check-hard
+name: R-CMD-check
 
 jobs:
   R-CMD-check:
@@ -20,45 +25,67 @@ jobs:
       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'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - name: Session info
-        run: Rscript -e 'sessionInfo()'
-
-      - name: Show MatrixExtra namespace
-        run: Rscript -e 'getNamespaceExports("MatrixExtra")'
-
-      - uses: actions/checkout@v4
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@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
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - 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:
-          dependencies: '"hard"'
-          cache: false
-          extra-packages: |
-            any::rcmdcheck
-            any::testthat
-            any::knitr
-            any::rmarkdown
-          needs: check
+          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: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+          remotes::install_cran("formatR")
+          remotes::install_cran("rmarkdown")
+          remotes::install_bioc("ggtree")
+        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 = "error", check_dir = "check")
+        shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
         with:
-          upload-snapshots: true
-          error-on: '"error"'
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check