PR in error #39
Workflow file for this run
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| name: build | |
| on: | |
| push: | |
| branches: [ release, master ] | |
| pull_request: | |
| branches: [ release, master ] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| r: ['release', 'devel'] | |
| config: | |
| # - {os: windows-latest, suffix: 'zip'} | |
| - {os: macOS-latest, suffix: 'tgz'} | |
| # - {os: ubuntu-16.04, suffix: 'tar.gz', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} | |
| isMaster: | |
| - ${{ contains(github.ref, 'master') }} | |
| exclude: | |
| - isMaster: false | |
| r: devel | |
| - isMaster: true | |
| r: release | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up R ${{ matrix.r }} | |
| uses: r-lib/actions/setup-r@master | |
| with: | |
| r-version: ${{ matrix.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| - uses: r-lib/actions/setup-pandoc@v1 | |
| # - name: set token for cytoinstaller(and remotes) to increase github API rate limit | |
| # env: | |
| # SUPER_SECRET: ${{ secrets.CYTOINSTALLER_TOKEN }} | |
| # run: echo "GITHUB_TOKEN=$SUPER_SECRET" >> $GITHUB_ENV | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Get bioc ver | |
| run: echo "bioc_ver=$(Rscript -e 'writeLines(as.character(remotes::bioc_version()))')" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: check bioc ver | |
| run: echo $bioc_ver | |
| shell: bash | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))') | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran(c("rcmdcheck", "devtools")) | |
| # remotes::install_github("RGLab/cytoinstaller") | |
| # cytoinstaller::cyto_install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| # - name: check rate limit | |
| # run: | | |
| # gh::gh("GET /rate_limit")$resources$core$remaining | |
| # shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), 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 | |
| # - name: build src pkg | |
| # if: runner.os == 'Linux' | |
| # run: devtools::build() | |
| # shell: Rscript {0} | |
| # - name: build bin pkg | |
| # if: runner.os != 'Linux' | |
| # run: devtools::build(binary = TRUE) | |
| # shell: Rscript {0} | |
| # - name: Upload Release Asset | |
| # uses: svenstaro/upload-release-action@v2 | |
| # with: | |
| # repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| # file: '../*.${{ matrix.config.suffix }}' | |
| # file_glob: true | |
| # tag: bioc_${{ env.bioc_ver}} | |
| # overwrite: true | |
| # body: "This is my release text" |