remove BigKnn and fix mentions of ShinyAppBuilder #1145
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - '**' | |
| pull_request: | |
| branches: | |
| - '**' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release'} # Does not appear to have Java 32-bit, hence the --no-multiarch | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }} | |
| CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }} | |
| CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }} | |
| CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }} | |
| CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }} | |
| CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }} | |
| CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }} | |
| CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }} | |
| CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }} | |
| CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }} | |
| CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }} | |
| CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }} | |
| CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }} | |
| CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }} | |
| CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install system requirements | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install -y libssh-dev | |
| Rscript -e 'install.packages("remotes")' | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "22.04"))') | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran")' | |
| error-on: '"warning"' | |
| check-dir: '"check"' | |
| - name: Upload source package | |
| if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: package_tarball | |
| path: check/*.tar.gz | |
| - name: Install covr | |
| if: runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: runner.os == 'Linux' | |
| run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}") | |
| shell: Rscript {0} | |
| Release: | |
| needs: R-CMD-Check | |
| runs-on: macOS-latest | |
| env: | |
| GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
| if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check if version has increased | |
| run: | | |
| echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV | |
| - name: Display new version number | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| echo "${{ env.new_version }}" | |
| - name: Create release | |
| if: ${{ env.new_version != '' }} | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} | |
| with: | |
| tag_name: ${{ env.new_version }} | |
| release_name: Release ${{ env.new_version }} | |
| body: | | |
| See NEWS.md for release notes. | |
| draft: false | |
| prerelease: false | |
| - uses: r-lib/actions/setup-r@v2 | |
| if: ${{ env.new_version != '' }} | |
| - name: Install drat | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| install.packages('drat') | |
| shell: Rscript {0} | |
| - name: Remove any tarballs that already exists | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| rm -f *.tar.gz | |
| - name: Download package tarball | |
| if: ${{ env.new_version != '' }} | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: package_tarball | |
| - name: Push to drat | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| bash deploy.sh | |
| - name: Push to BroadSea | |
| if: ${{ env.new_version != '' }} | |
| run: | | |
| curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/ | |