unit test fix

.github/workflows/codecovr.yaml

@@ -33,54 +33,30 @@ name: code-coverage
 
 jobs:
   code-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
     steps:
       - uses: actions/checkout@v3
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: release
-      
-      - uses: r-lib/actions/setup-pandoc@v2
-        # with:
-        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
+          # use RStudio Package Manager to quickly install packages
+          use-public-rspm: true
 
-      - name: Query dependencies
-        # this will change once a week, so it will cache dependency updates
-        run: |
-          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
-        shell: Rscript {0}
-        
-      - name: Restore cached R packages
-        # this step will add the step 'Post Restore cached R packages' on a succesful run
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
-
-      - name: Unpack AMR and install R dependencies
-        run: |
-          tar -xf data-raw/AMR_latest.tar.gz
-          Rscript -e "source('data-raw/_install_deps.R')"
-        shell: bash
-        
-      - name: Show session info
-        run: |
-          options(width = 100)
-          utils::sessionInfo()
-          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
-        shell: Rscript {0}
+          extra-packages: any::covr
 
       - name: Test coverage
         env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
           R_RUN_TINYTEST: true
         run: |
-          install.packages("covr", repos = "https://cran.rstudio.com/")
-          library(AMR)
-          library(tinytest)
           x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
           print(x)
         shell: Rscript {0}