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Update README.md #966
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| on: | |
| push: | |
| branches: main | |
| pull_request: | |
| branches: main | |
| schedule: | |
| - cron: "0 3 * * *" | |
| 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'} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v1 | |
| id: install-r | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| - uses: r-lib/actions/setup-pandoc@v1 | |
| - name: Install pak and query dependencies | |
| run: | | |
| install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/") | |
| saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds") | |
| shell: Rscript {0} | |
| - name: Restore R package cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| ${{ env.R_LIBS_USER }}/* | |
| !${{ env.R_LIBS_USER }}/pak | |
| key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }} | |
| restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| pak::local_system_requirements(execute = TRUE) | |
| pak::pkg_system_requirements("rcmdcheck", execute = TRUE) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| pak::local_install_dev_deps(upgrade = TRUE) | |
| pak::pkg_install("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Install Python | |
| run: | | |
| pak::pkg_install('rstudio/reticulate') | |
| reticulate::install_miniconda() | |
| install.packages('keras') | |
| keras::install_keras(extra_packages = c('IPython', 'requests', 'certifi', 'urllib3', 'tensorflow-hub', 'tabnet==0.1.4.1')) | |
| reticulate::py_install(c('torch', 'pycox', 'pandas==1.4.4'), pip = TRUE) | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Don't use tar from old Rtools to store the cache | |
| if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }} | |
| shell: bash | |
| run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH | |
| - name: Test coverage | |
| if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}} | |
| run: | | |
| install.packages('covr') | |
| covr::codecov() | |
| shell: Rscript {0} |