fix: Upgrade upload-artifact action to v4

.github/workflows/code-coverage.yml

@@ -166,7 +166,7 @@ jobs:
 
       - name: Upload report for review
         if: steps.check_coverage_reports.outputs.files_exists == 'true' && github.event_name == 'pull_request'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-report
           path: "coverage-report.html"

.github/workflows/push-docker-image.yml

@@ -56,7 +56,7 @@ jobs:
         run: |
           package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
           if [ "${{ matrix.tags }}" == "latest" ]; then image_name="$package_name-release"; else image_name="$package_name-${{ matrix.tags }}"; fi
-          if [ "${{ matrix.tags }}" == "devel" ]; then R_REPOS="https://packagemanager.posit.co/cran/__linux__/focal/latest"; fi 
+          if [ "${{ matrix.tags }}" == "devel" ]; then R_REPOS="https://packagemanager.posit.co/cran/__linux__/focal/latest"; fi
           echo "r_repos=$R_REPOS" >> $GITHUB_OUTPUT
           r_version="${{ matrix.tags }}"
           if [ "$r_version" == "${{ env.OLD_RELEASE }}" ]; then image_name="$package_name-oldrel"; fi # TODO: del temporary -test suffix for testing
@@ -71,7 +71,7 @@ jobs:
           sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq
           description-file: "https://raw.githubusercontent.com/pharmaverse/admiral/main/DESCRIPTION"
           repository-owner: ${{ github.repository_owner }}
-          repo-user: ${{ github.actor }} 
+          repo-user: ${{ github.actor }}
           repo-token: "${{ secrets.GITHUB_TOKEN }}"
           repos: ${{ steps.image_specs.outputs.r_repos }}
           packages: "DT,R.cache,R.methodsS3,R.oo,R.utils,backports,cellranger,collections,covr,crosstalk,cyclocomp,diffdf,git2r,hunspell,languageserver,lazyeval,lintr,progress,readxl,rematch,renv,rex,spelling,staged.dependencies,styler,xmlparsedata"
@@ -105,7 +105,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Upload deps.csv artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: deps
           path: "/workspace/deps-${{ steps.store_deps.outputs.r_version }}.csv"

.github/workflows/r-cmd-check.yml

@@ -170,12 +170,12 @@ jobs:
         shell: Rscript {0}
 
       - name: Upload deps.csv and renv.lock artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         if: |
           (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') ||
           matrix.r_version != 'devel'
         with:
-          name: deps
+          name: deps-${{ matrix.r_version }}
           path: |
             /workspace/tmp/
 
@@ -228,7 +228,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
           name: r${{ matrix.r_version }}-results
           path: check