turn off hard dependencies r check on github actions for now. #98
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master, test] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| # if: github.repository == 'darwin-eu-dev/CDMConnector' || github.repository == 'darwin-eu/CDMConnector' | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} # takes a long time to compile duckdb. | |
| # - {os: ubuntu-latest, r: 'devel'} # takes a long time to compile duckdb. | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| CI_TEST_DB: duckdb | |
| TESTTHAT_CPUS : 1 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Install suggested packages | |
| run: | | |
| install.packages("knitr") | |
| install.packages("rmarkdown") | |
| install.packages("ggplot2") | |
| install.packages("odbc") | |
| install.packages("testthat") | |
| install.packages("DatabaseConnector") | |
| install.packages("lubridate") | |
| install.packages("duckdb") | |
| install.packages("covr") | |
| install.packages("RPostgres") | |
| install.packages("RSQLite") | |
| install.packages("bigrquery") | |
| install.packages("arrow") | |
| install.packages("tibble") | |
| install.packages("tictoc") | |
| install.packages("palmerpenguins") | |
| shell: Rscript {0} | |
| - name: Install CirceR | |
| run: | | |
| install.packages("rJava") | |
| install.packages("RJSONIO") | |
| install.packages("CirceR") | |
| # install.packages("CirceR", repos = "https://OHDSI.github.io/drat", type = "source") | |
| # install.packages("Capr", repos = "https://OHDSI.github.io/drat", type = "source") | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Install latest duckdb version on windows | |
| if: runner.os == 'Windows' | |
| run: | | |
| install.packages("duckdb", repos = "https://packagemanager.rstudio.com/all/latest", type = "win.binary") | |
| shell: Rscript {0} | |
| - name: List contents of home directory | |
| run: | | |
| print("Home directory content before R check") | |
| print(list.files(path.expand("~"))) | |
| shell: Rscript {0} | |
| - name: Add options to .Rprofile | |
| run: | | |
| echo "options(rmarkdown.html_vignette.check_title = FALSE)" >> ~/.Rprofile | |
| shell: bash | |
| # - uses: r-lib/actions/check-r-package@v2 | |
| # with: | |
| # upload-snapshots: true | |
| # args: 'c("--no-manual", "--as-cran", "--no-build-vignettes", "--ignore-vignettes")' | |
| # error-on: '"error"' | |
| - name: List contents of home directory after R check | |
| run: | | |
| print("Home directory content after R check. Should be the same as before R check.") | |
| print(list.files(path.expand("~"))) | |
| shell: Rscript {0} | |
| # - name: Upload coverage reports to Codecov | |
| # if: runner.os == 'macOS' | |
| # uses: codecov/[email protected] | |
| # with: | |
| # token: ${{ secrets.CODECOV_TOKEN }} | |
| # slug: ablack3/CDMConnector | |
| # - name: Test coverage | |
| # if: runner.os == 'macOS' | |
| # env: | |
| # CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| # run: | | |
| # install.packages("covr") | |
| # covr::codecov() | |
| # shell: Rscript {0} | |