Test workaround #418
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| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| name: R-CMD-check.yaml | |
| permissions: read-all | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: macos-latest, r: "release", python: "3.x" } | |
| - { os: windows-latest, r: "release", python: "3.x" } | |
| - { os: ubuntu-latest, r: "devel", http-user-agent: "release", python: "3.x" } | |
| - { os: ubuntu-latest, r: "release", python: "3.x" } | |
| - { os: ubuntu-latest, r: "oldrel-1", python: "3.9" } | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| LAMIN_API_KEY: ${{ secrets.LAMIN_API_KEY_TESTUSER1 }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.config.python }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| # manually installing openblas as a workaround for issue | |
| # https://github.com/laminlabs/laminr/issues/57 | |
| - name: Install OpenBLAS on macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install openblas | |
| OPENBLAS=$(brew --prefix openblas) | |
| echo "LDFLAGS=-L$OPENBLAS/lib" >> $GITHUB_ENV | |
| echo "CPPFLAGS=-I$OPENBLAS/include" >> $GITHUB_ENV | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck, local::. | |
| needs: check | |
| - name: Install {tiledbsoma} | |
| if: runner.os == 'Linux' | |
| run: | | |
| options(repos = c("https://chanzuckerberg.r-universe.dev", getOption("repos"))) | |
| pak::pkg_install("tiledbsoma") | |
| shell: Rscript {0} | |
| - name: Install Python 3.12 on macOS | |
| # We use python 3.12 on mac os x so we can install scipy 1.13 from a wheel | |
| if: runner.os == 'macOS' | |
| run: | | |
| reticulate::install_python(version = "3.12") | |
| shell: Rscript {0} | |
| - name: Setup Python environment | |
| run: | | |
| laminr::install_lamindb(extra_packages = c("s3fs", "git+https://github.com/laminlabs/lamindb.git")) | |
| shell: Rscript {0} | |
| - name: Log in to Lamin | |
| run: | | |
| reticulate::use_virtualenv("r-lamindb") | |
| laminr::lamin_login() | |
| shell: Rscript {0} | |
| - name: Set lamindata as default instance | |
| run: | | |
| reticulate::use_virtualenv("r-lamindb") | |
| laminr::lamin_connect("laminlabs/lamindata") | |
| shell: Rscript {0} | |
| - name: Check whether we can import lamindb and connect to the default instance | |
| run: | | |
| reticulate::use_virtualenv("r-lamindb") | |
| reticulate::py_config() | |
| reticulate::import("lamindb") | |
| laminr::connect() | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |