Fix_Bioc_3.19_release #117
Workflow file for this run
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| name: build-checks-release | |
| on: | |
| push: | |
| branches: [ devel ] | |
| pull_request: | |
| branches: [ devel ] | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| container: rocker/r-ver:4.2 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Install system requirements | |
| run: | | |
| apt-get update | |
| apt-get install -y --no-install-recommends apt-utils | |
| apt-get install -y --no-install-recommends zlib1g-dev libfftw3-dev libxml2-dev libxt-dev curl pandoc-citeproc libproj-dev libgdal-dev pandoc libmagick++-dev bzip2 | |
| apt-get clean | |
| rm -rf /var/lib/apt/ilists/* | |
| - name: Install dependencies | |
| run: | | |
| install.packages("BiocManager") | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), Ncpu = 2L) | |
| BiocManager::install("matrixStats", force = TRUE) | |
| shell: Rscript {0} | |
| - name: Find PhantomJS path | |
| id: phantomjs | |
| run: | | |
| echo "::set-output name=path::$(Rscript -e 'cat(shinytest:::phantom_paths()[[1]])')" | |
| - name: Cache PhantomJS | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ steps.phantomjs.outputs.path }} | |
| key: ${{ matrix.config.os }}-phantomjs | |
| restore-keys: ${{ matrix.config.os }}-phantomjs | |
| - name: Install PhantomJS | |
| run: > | |
| Rscript | |
| -e "if (!shinytest::dependenciesInstalled()) shinytest::installDependencies()" | |
| - name: Check | |
| run: | | |
| install.packages("rcmdcheck") | |
| rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| remotes::install_cran(c("covr")) | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} |