vignette updates #330
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
| ## This is a test | |
| ## Template from here: https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow | |
| ## ubuntu-latest | |
| on: | |
| push: | |
| branches: | |
| - devel | |
| pull_request: | |
| branches: | |
| - devel | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| if: "contains(toJSON(github.event.commits.*.message), 'build_check')" | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: ubuntu-20.04, r: '4.3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: macOS-latest, r: '4.3.3'} | |
| - {os: windows-latest, r: '4.3.3'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - 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), ".github/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('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| sudo apt-get install libv8-dev | |
| sudo apt install libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages(c("BiocManager", "knitcitations", "docopt")) | |
| remotes::install_github("HenrikBengtsson/matrixStats", ref="develop") ## temp fix - 03/15/22 | |
| BiocManager::install("tgirke/systemPipeR", dependencies=TRUE) | |
| BiocManager::install("tgirke/systemPipeRdata") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(build_args = c('--compact-vignettes=gs+qpdf'), args = c("--no-manual", "--no-build-vignettes", "--timings"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |