Chore: customize github workflows to correctly install system dependencies #188
Workflow file for this run
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| # Source: https://github.com/pharmaverse/admiralci | ||
| # Stripped down version of admiralci checks. Good for | ||
| # the developement process. When package is ready to | ||
| # be published, revisit and add release-related | ||
| # workflows. | ||
| name: admiral CI/CD Workflows | ||
| on: | ||
| workflow_dispatch: | ||
| push: | ||
| branches: | ||
| - main | ||
| pull_request: | ||
| branches: | ||
| - main | ||
| concurrency: | ||
| group: admiral-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| env: | ||
| R_VERSION: "release" | ||
| jobs: | ||
| get_r_version: | ||
| name: Get R version | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| r-version: ${{ steps.get_r_version.outputs.R_VERSION }} | ||
| steps: | ||
| - name: Get R Version for Downstream Container Jobs | ||
| id: get_r_version | ||
| run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | ||
| shell: bash | ||
| spellcheck: | ||
| name: Spelling | ||
| uses: ./.github/workflows/spellcheck.yml | ||
| if: github.event_name == 'pull_request' | ||
| needs: get_r_version | ||
| with: | ||
| r-version: "${{ needs.get_r_version.outputs.r-version }}" | ||
| linter: | ||
| name: Lint | ||
| uses: ./.github/workflows/lintr.yml | ||
| needs: get_r_version | ||
| if: github.event_name == 'pull_request' | ||
| with: | ||
| r-version: "${{ needs.get_r_version.outputs.r-version }}" | ||
| man-pages: | ||
| name: Man Pages | ||
| uses: ./.github/workflows/man-pages.yml | ||
|
Check failure on line 51 in .github/workflows/main.yml
|
||
| needs: get_r_version | ||
| if: github.event_name == 'pull_request' | ||
| with: | ||
| r-version: "${{ needs.get_r_version.outputs.r-version }}" | ||
| tests: | ||
| name: Tests | ||
| runs-on: ubuntu-latest | ||
| needs: get_r_version | ||
| container: | ||
| image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest" | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v2 | ||
| - name: Install system dependencies | ||
| run: | | ||
| apt-get install -y --no-install-recommends \ | ||
| libudunits2-dev | ||
| - name: Install dependencies | ||
| run: | | ||
| Rscript -e 'remotes::install_deps(dependencies = TRUE)' | ||
| - name: Run tests | ||
| shell: Rscript {0} | ||
| run: | | ||
| devtools::load_all(".") | ||
| devtools::test() | ||
| check: | ||
| name: Check | ||
| uses: ./.github/workflows/r-cmd-check.yml | ||
| if: github.event_name == 'pull_request' | ||
| with: | ||
| error-on: error | ||
