➕ Install s3fs on CI #403
Workflow file for this run
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
| 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: | ||
| # note: we use python 3.12 on mac os x so we can install scipy 1.13 from a wheel | ||
| - { os: macos-latest, r: "release", python: "3.12" } | ||
| - { 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: ${{ matrix.config.http-user-agent }} | ||
| use-public-rspm: true | ||
| # manually installing openblas as a workaround for issue | ||
| # https://github.com/laminlabs/laminr/issues/57 | ||
| - name: Install OpenBLAS | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew install openblas | ||
| OPENBLAS=$(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 | ||
| needs: check | ||
| - name: Install {tiledbsoma} | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| options(repos = c("https://chanzuckerberg.r-universe.dev", getOption("repos"))) | ||
| install.packages("tiledbsoma") | ||
| shell: Rscript {0} | ||
| - name: Setup Python environment | ||
| run: | | ||
| laminr::install_lamindb(extra_packages = c("s3fs")) | ||
| 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 | ||
