update tutorital #421
Workflow file for this run
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| name: R | |
| on: | |
| pull_request: | |
| branches: | |
| - "*" | |
| push: | |
| branches: | |
| - "master" | |
| - "*" | |
| env: | |
| cache-version: 'cache-v1' | |
| jobs: | |
| build: | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| config: | |
| - { r-version: release, os: ubuntu-latest} | |
| - { r-version: release, os: macos-latest} | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-node@v2 | |
| - name: Install ubuntu system dependencies | |
| if: matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get install git libcurl4-openssl-dev libssl-dev libicu-dev libxml2-dev make pandoc libgit2-dev libharfbuzz-dev libfribidi-dev | |
| - name: Install macOS system dependencies | |
| if: matrix.config.os == 'macos-latest' | |
| run: | | |
| brew install cairo pkg-config autoconf automake libtool | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r-version}} | |
| - name: Setup r-lib/remotes | |
| run: | | |
| install.packages(c("remotes", "devtools")) | |
| shell: Rscript {0} | |
| - id: bioc | |
| name: Check bioc version | |
| run: | | |
| echo "##[set-output name=mainbiocversion;]$(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: Cache ubuntu R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'" | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| 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: Cache macOS R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'" | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| 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-${{ matrix.config.r-version}}- | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("rcmdcheck", "covr")) | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| run: | | |
| Rscript -e 'rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")' | |
| shell: bash -l {0} | |
| - name: Test coverage | |
| run: | | |
| Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")' | |
| shell: bash -l {0} |