ropensci / UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
https://docs.ropensci.org/UCSCXenaTools
GNU General Public License v3.0
106 stars 12 forks source link

引入 R actions #18

Closed ShixiangWang closed 5 years ago

ShixiangWang commented 5 years ago

From https://github.com/thomasp85/patchwork/blob/master/.github/workflows/R-CMD-check.yaml

on: [push, pull_request]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
        - { os: windows-latest, r: '3.6', args: "--no-manual"}
        - { os: macOS-latest, r: '3.6'}
        - { os: macOS-latest, r: 'devel', args: "--no-manual"}
        - { os: ubuntu-16.04, r: '3.2', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", args: "--no-manual" }
        - { os: ubuntu-16.04, r: '3.3', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", args: "--no-manual" }
        - { os: ubuntu-16.04, r: '3.4', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", args: "--no-manual" }
        - { os: ubuntu-16.04, r: '3.5', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", args: "--no-manual" }
        - { os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest", args: "--no-manual" }

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      CRAN: ${{ matrix.config.cran }}

    steps:
      - uses: actions/checkout@v1

      - uses: r-lib/actions/setup-r@master
        with:
          r-version: ${{ matrix.config.r }}

      - uses: r-lib/actions/setup-pandoc@master

      - uses: r-lib/actions/setup-tinytex@master
        if: contains(matrix.config.args, 'no-manual') == false

      - name: Cache R packages
        uses: actions/cache@v1
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('DESCRIPTION') }}

      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          Rscript -e "install.packages('remotes')" -e "remotes::install_github('r-hub/sysreqs')"
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
          sudo -s eval "$sysreqs"
      - name: Install dependencies
        run: Rscript -e "install.packages('remotes')" -e "remotes::install_deps(dependencies = TRUE)" -e "remotes::install_cran('rcmdcheck')"

      - name: Check
        run: Rscript -e "rcmdcheck::rcmdcheck(args = '${{ matrix.config.args }}', error_on = 'warning', check_dir = 'check')"

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: Test coverage
        if: matrix.config.os == 'macOS-latest' && matrix.config.r == '3.6'
        run: |
          Rscript -e 'remotes::install_github("r-lib/covr@gh-actions")'
          Rscript -e 'covr::codecov(token = "${{secrets.CODECOV_TOKEN}}")'