Revert "Update utils.R" #530
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
| 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 libglpk-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-${{ matrix.config.r-version}}- | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("rcmdcheck", "covr")) | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| run: | | |
| Rscript -e 'rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")' | |
| shell: bash -l {0} | |
| - name: Test coverage | |
| if: github.actor == 'zktuong' | |
| run: | | |
| Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")' | |
| shell: bash -l {0} |