cheminfo wf #11
Workflow file for this run
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| ## Template from here: https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| 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: '4.1.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.SPR_DATA }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@master | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@master | |
| - 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 libcurl4-openssl-dev | |
| sudo apt-get install libv8-dev | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages(c("BiocManager", "knitcitations")) | |
| BiocManager::install("BiocStyle") | |
| BiocManager::install("lz100/systemPipeR") | |
| shell: Rscript {0} | |
| ## Update the workflows temapltes... | |
| - name: update version number | |
| run: | | |
| git pull | |
| awk -F. '{$3++;print > ".github/ref_vignette/vignette_version.txt"}' OFS=. .github/ref_vignette/vignette_version.txt | |
| - name: Update inst | |
| run: | | |
| bash .github/bash/update_inst.sh https://github.com/systemPipeR/systemPipeRdata.git inst/ | |
| - name: Update github | |
| run: | | |
| git config --local user.name "Github Action Bot" | |
| git config --local user.email "[email protected]" | |
| git add -A | |
| git commit -m "Bot update RMD/HTML files" -a | |
| - name: Push changes | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.SPR_DATA }} | |
| branch: ${{ github.ref }} | |
| ## Update the individuals single packages | |
| - name: Dispatch event systemPipeR/SPrnaseq | |
| uses: peter-evans/repository-dispatch@v2 | |
| with: | |
| token: ${{ secrets.SPR_DATA }} | |
| repository: 'systemPipeR/SPrnaseq' | |
| event-type: rmd-updated | |
| - name: Dispatch event systemPipeR/SPriboseq | |
| uses: peter-evans/repository-dispatch@v2 | |
| with: | |
| token: ${{ secrets.SPR_DATA }} | |
| repository: 'systemPipeR/SPriboseq' | |
| event-type: rmd-updated | |
| - name: Dispatch event systemPipeR/SPvarseq | |
| uses: peter-evans/repository-dispatch@v2 | |
| with: | |
| token: ${{ secrets.SPR_DATA }} | |
| repository: 'systemPipeR/SPvarseq' | |
| event-type: rmd-updated | |
| - name: Dispatch event systemPipeR/SPchipseq | |
| uses: peter-evans/repository-dispatch@v2 | |
| with: | |
| token: ${{ secrets.SPR_DATA }} | |
| repository: 'systemPipeR/SPchipseq' | |
| event-type: rmd-updated | |
| ## Build and check the package | |
| - 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@master | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |