Remove drug end date convention #314
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: | |
| - '**' | |
| schedule: | |
| - cron: '0 19 * * 0' # every Sunday at 7pm UTC | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| # Test create and drop tables in a database so they cannot be executed in parallel | |
| max-parallel: 1 | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: windows-latest, r: 'release'} # Does not appear to have Java 32-bit, hence the --no-multiarch | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| CDMDDLBASE_POSTGRESQL_USER: ${{ secrets.CDMDDLBASE_POSTGRESQL_USER }} | |
| CDMDDLBASE_POSTGRESQL_PASSWORD: ${{ secrets.CDMDDLBASE_POSTGRESQL_PASSWORD }} | |
| CDMDDLBASE_POSTGRESQL_SERVER: ${{ secrets.CDMDDLBASE_POSTGRESQL_SERVER }} | |
| CDMDDLBASE_POSTGRESQL_SCHEMA: ${{ secrets.CDMDDLBASE_POSTGRESQL_SCHEMA }} | |
| CDMDDLBASE_REDSHIFT_USER: ${{ secrets.CDMDDLBASE_REDSHIFT_USER }} | |
| CDMDDLBASE_REDSHIFT_PASSWORD: ${{ secrets.CDMDDLBASE_REDSHIFT_PASSWORD }} | |
| CDMDDLBASE_REDSHIFT_SERVER: ${{ secrets.CDMDDLBASE_REDSHIFT_SERVER }} | |
| CDMDDLBASE_REDSHIFT_SCHEMA: ${{ secrets.CDMDDLBASE_REDSHIFT_SCHEMA }} | |
| CDMDDLBASE_SQL_SERVER_USER: ${{ secrets.CDMDDLBASE_SQL_SERVER_USER }} | |
| CDMDDLBASE_SQL_SERVER_PASSWORD: ${{ secrets.CDMDDLBASE_SQL_SERVER_PASSWORD }} | |
| CDMDDLBASE_SQL_SERVER_SERVER: ${{ secrets.CDMDDLBASE_SQL_SERVER_SERVER }} | |
| CDMDDLBASE_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_SQL_SERVER_CDM_SCHEMA }} | |
| CDMDDLBASE_ORACLE_USER: ${{ secrets.CDMDDLBASE_ORACLE_USER }} | |
| CDMDDLBASE_ORACLE_PASSWORD: ${{ secrets.CDMDDLBASE_ORACLE_PASSWORD }} | |
| CDMDDLBASE_ORACLE_SERVER: ${{ secrets.CDMDDLBASE_ORACLE_SERVER }} | |
| CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/[email protected] | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install libssh | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install libssh-dev | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch")) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Install covr | |
| if: runner.os == 'macOS' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Remove check folder if exists | |
| if: runner.os == 'macOS' | |
| run: unlink("check", recursive = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Upload source package | |
| if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: package_tarball | |
| path: check/*.tar.gz | |
| - name: Test coverage | |
| if: runner.os == 'macOS' | |
| run: covr::codecov() | |
| shell: Rscript {0} | |