fix duplicate rownames introduced in CellPhoneDB v5 #64
Workflow file for this run
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| on: | |
| push: | |
| branches: | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "*" | |
| name: vignette | |
| jobs: | |
| vignette: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| config: | |
| - { os: macos-latest } | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| id: install-r | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - id: bioc | |
| name: Check bioc version | |
| run: | | |
| echo "##[set-output name=mainbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" | |
| echo "##[set-output name=subbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')" | |
| echo "##[set-output name=biocversion;]$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')" | |
| shell: bash -l {0} | |
| - 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: Cache R packages | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| ${{ env.R_LIBS_USER }} | |
| !${{ env.R_LIBS_USER }}/pak | |
| key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}- | |
| - name: Install dependencies | |
| run: | | |
| pak::local_install_dev_deps(upgrade = TRUE, dependencies = c("all", "Config/Needs/website")) | |
| pak::pkg_install("pkgdown") | |
| shell: Rscript {0} | |
| - name: Install package | |
| run: R CMD INSTALL . | |
| - name: Build and deploy pkgdown site | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' | |
| shell: bash -l {0} |