R check #73
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| on: | |
| schedule: | |
| - cron: '0 13 * * 6' # every Saturday at 13am UTC | |
| workflow_dispatch: | |
| name: 'R check' | |
| jobs: | |
| R-CMD-check-main: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macOS-latest, r: 'release'} | |
| 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 }} | |
| CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }} | |
| CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }} | |
| CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }} | |
| CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }} | |
| CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }} | |
| CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }} | |
| CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }} | |
| CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }} | |
| WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }} | |
| WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }} | |
| WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }} | |
| WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }} | |
| TORCH_INSTALL: '1' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: setup r-reticulate venv | |
| shell: Rscript {0} | |
| run: | | |
| python_packages <- | |
| c("polars", "tqdm", "connectorx", "pyarrow", "numpy==1.26.4") | |
| library(reticulate) | |
| virtualenv_create("r-reticulate", Sys.which("python"), packages=python_packages) | |
| virtualenv_install("r-reticulate", "torch", pip_options = c("--index-url https://download.pytorch.org/whl/cpu")) | |
| path_to_python <- virtualenv_python("r-reticulate") | |
| writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python), | |
| Sys.getenv("GITHUB_ENV")) | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran")' | |
| error-on: '"warning"' | |
| check-dir: '"check"' |