upgrade github actions

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

@@ -16,66 +16,65 @@ jobs:
   R-CMD-check:
     runs-on: ubuntu-latest
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CHUNKEDGRAPH_SECRET: ${{ secrets.CHUNKEDGRAPH_SECRET }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      FLYTABLE_TOKEN: ${{ secrets.FLYTABLE_TOKEN }}
       RETICULATE_MINICONDA_PYTHON_VERSION: 3.8
-      RGL_USE_NULL: true
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RGL_USE_NULL: TRUE
       _R_CHECK_DONTTEST_EXAMPLES_: FALSE
-      _R_CHECK_CRAN_INCOMING_REMOTE_: false
       _R_CHECK_TESTS_NLINES_: 0
+      _R_CHECK_CRAN_INCOMING_REMOTE_: false
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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"))')
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-          remotes::install_cran("pkgdown")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::pkgdown, catmaid=natverse/rcatmaid
+          needs: check
 
       - name: Fix Conda permissions on macOS
         if: runner.os == 'macOS'
         run: sudo chown -R $UID $CONDA
 
       - name: Install fafbseg + python
         run: |
-          remotes::install_local()
+          pak::local_install()
           library(fafbseg)
-          simple_python(pkgs="caveclient")
+          simple_python()
           dr_fafbseg()
         shell: Rscript {0}
 
       - name: writetoken
         run: fafbseg::flywire_set_token(token=Sys.getenv("CHUNKEDGRAPH_SECRET"))
         shell: Rscript {0}
 
-      - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Upload check log results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ matrix.config.tag }}-results
+          path: ${{ github.event.repository.name }}.Rcheck/00check.log
+
+      - name: Test coverage
+        # if: runner.os == 'macOS'
+        if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}}
+        run: covr::codecov(errorsAreFatal=FALSE)
+        shell: Rscript {0}