chore: deps cleanup #51
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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: [dev] | |
| pull_request: | |
| branches: [dev] | |
| 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'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - 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 reticulate | |
| run: | | |
| Rscript -e "install.packages('reticulate')" | |
| - name: Create miniconda | |
| run: | | |
| Rscript -e "reticulate::install_miniconda()" | |
| Rscript -e "reticulate::conda_install(packages = 'scipy')" | |
| - name: Install pak | |
| run: | | |
| Rscript -e "install.packages('pak')" | |
| - name: Install remotes | |
| run: | | |
| Rscript -e "install.packages('remotes')" | |
| - name: Install GiottoUtils | |
| run: | | |
| Rscript -e "remotes::install_github('drieslab/GiottoUtils@dev')" | |
| - name: Install GiottoData | |
| run: | | |
| Rscript -e "remotes::install_github('drieslab/GiottoData')" | |
| - name: Install rcmdcheck | |
| run: | | |
| Rscript -e "install.packages('rcmdcheck')" | |
| - name: Install knitr | |
| run: | | |
| Rscript -e "install.packages('knitr')" | |
| - name: Install rmarkdown | |
| run: | | |
| Rscript -e "install.packages('rmarkdown')" | |
| - name: Install testthat | |
| run: | | |
| Rscript -e "install.packages('testthat')" | |
| - name: Install BiocCheck | |
| run: | | |
| Rscript -e "install.packages('BiocManager')" | |
| Rscript -e "BiocManager::install('BiocCheck')" | |
| - name: Install dbscan | |
| run: | | |
| Rscript -e "BiocManager::install('dbscan')" | |
| - name: Install deldir | |
| run: | | |
| Rscript -e "BiocManager::install('deldir')" | |
| - name: Install igraph | |
| run: | | |
| Rscript -e "BiocManager::install('igraph')" | |
| - name: Install magick | |
| run: | | |
| Rscript -e "BiocManager::install('magick')" | |
| - name: Install matrixStats | |
| run: | | |
| Rscript -e "BiocManager::install('matrixStats')" | |
| - name: Install sp | |
| run: | | |
| Rscript -e "BiocManager::install('sp')" | |
| - name: Install terra | |
| run: | | |
| Rscript -e "BiocManager::install('terra')" | |
| - name: Install scattermore | |
| run: | | |
| Rscript -e "install.packages('scattermore')" | |
| - name: Install exactextractr | |
| run: | | |
| Rscript -e "install.packages('exactextractr')" | |
| - name: Install future.apply | |
| run: | | |
| Rscript -e "BiocManager::install('future.apply')" | |
| - name: Install stars | |
| run: | | |
| Rscript -e "BiocManager::install('stars')" | |
| - name: Install qs | |
| run: | | |
| Rscript -e "BiocManager::install('qs')" | |
| - name: Install RTriangle | |
| run: | | |
| Rscript -e "BiocManager::install('RTriangle')" | |
| - name: Install geometry | |
| run: | | |
| Rscript -e "BiocManager::install('geometry')" | |
| - name: Install Seurat | |
| run: | | |
| Rscript -e "BiocManager::install('Seurat')" | |
| - name: Install chihaya | |
| run: | | |
| Rscript -e "BiocManager::install('chihaya')" | |
| - name: Install DelayedArray | |
| run: | | |
| Rscript -e "BiocManager::install('DelayedArray')" | |
| - name: Install DelayedMatrixStats | |
| run: | | |
| Rscript -e "BiocManager::install('DelayedMatrixStats')" | |
| - name: Install HDF5Array | |
| run: | | |
| Rscript -e "BiocManager::install('HDF5Array')" | |
| - name: Install rgl | |
| run: | | |
| Rscript -e "BiocManager::install('rgl')" | |
| - name: Install rhdf5 | |
| run: | | |
| Rscript -e "BiocManager::install('rhdf5')" | |
| - name: Install S4Vectors | |
| run: | | |
| Rscript -e "BiocManager::install('S4Vectors')" | |
| - name: Install ScaledMatrix | |
| run: | | |
| Rscript -e "BiocManager::install('ScaledMatrix')" | |
| - name: Install SingleCellExperiment | |
| run: | | |
| Rscript -e "BiocManager::install('SingleCellExperiment')" | |
| - name: Install SpatialExperiment | |
| run: | | |
| Rscript -e "BiocManager::install('SpatialExperiment')" | |
| - name: Install STexampleData | |
| run: | | |
| Rscript -e "BiocManager::install('STexampleData')" | |
| - name: Install SummarizedExperiment | |
| run: | | |
| Rscript -e "BiocManager::install('SummarizedExperiment')" | |
| - name: Run BiocCheck | |
| run: | | |
| Rscript -e "BiocCheck::BiocCheck()" | |
| - name: Run rcmdcheck | |
| run: | | |
| Rscript -e "rcmdcheck::rcmdcheck()" |