Merge pull request #8 from Sage-Bionetworks/add_required_columns #24
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| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| 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: macOS-latest, r: 'devel'} | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} | |
| - {os: ubuntu-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} | |
| - {os: ubuntu-latest, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} | |
| - {os: ubuntu-latest, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| RETICULATE_AUTOCONFIGURE: 'FALSE' | |
| CI: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_PAT }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}- | |
| - name: Install system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| export DEBIAN_FRONTEND=noninteractive | |
| sudo apt-get -y update | |
| sudo apt-get install -y make python-is-python3 pandoc pandoc-citeproc git-core libv8-dev libxml2-dev libcurl4-openssl-dev libssl-dev libssh2-1-dev zlib1g-dev libgit2-dev | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' && matrix.config.r == 'devel' | |
| run: | | |
| brew install libgit2 | |
| - name: Install dependencies | |
| run: | | |
| Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1) | |
| library(remotes) | |
| deps <- readRDS('depends.Rds') | |
| deps[['installed']] <- vapply(deps[['package']], remotes:::local_sha, character(1)) | |
| update(deps) | |
| remotes::install_cran('rcmdcheck') | |
| shell: Rscript {0} | |
| - name: Install Miniconda | |
| run: | | |
| Rscript -e "remotes::install_github('rstudio/reticulate')" | |
| Rscript -e "reticulate::install_miniconda()" | |
| - name: Add Miniconda to .Rprofile on macOS | |
| if: runner.os == 'macOS' | |
| run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile | |
| - name: Install Python deps | |
| run: | | |
| Rscript -e "reticulate::py_discover_config()" | |
| Rscript -e "reticulate::py_install(c('pandas', 'numpy', 'boto3', 'synapseclient'), pip = TRUE)" | |
| - name: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |