From e710b97cfd1de2c3be621c217edc93adbb63fcc1 Mon Sep 17 00:00:00 2001
From: LiNk-NY <marcel.ramos@roswellpark.org>
Date: Wed, 14 Aug 2024 15:56:44 -0400
Subject: [PATCH] remove extra steps

---
 .github/workflows/test-coverage.yml | 47 +++++++----------------------
 1 file changed, 11 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/test-coverage.yml b/.github/workflows/test-coverage.yml
index cbcffd7..0a520f6 100644
--- a/.github/workflows/test-coverage.yml
+++ b/.github/workflows/test-coverage.yml
@@ -6,46 +6,28 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     container: bioconductor/bioconductor_docker:devel
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v4
-
-      - name: Query dependencies
-        run: |
-          BiocManager::install(c("remotes", "covr", "xml2"))
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
+      - uses: actions/checkout@v4
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: /usr/local/lib/R/site-library
-          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-1-
+          use-public-rspm: true
 
-      - name: Install Dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          BiocManager::install("rcmdcheck", ask = FALSE, update = TRUE)
-        shell: Rscript {0}
-
-      - name: Check Package
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
-      - name: Test coverage
+      - name: Run package coverage
         run: |
           cov <- covr::package_coverage(
             quiet = FALSE,
@@ -64,10 +46,3 @@ jobs:
           plugin: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Upload artifact on failure
-        if: failure()
-        uses: actions/upload-artifact@v4
-        with:
-          name: coverage-test-failures
-          path: ${{ runner.temp }}/package