test-only #29
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| on: | |
| push: | |
| branches: | |
| - jameson_alpha | |
| pull_request: | |
| branches: | |
| - jameson_alpha | |
| workflow_dispatch: | |
| name: test-only | |
| jobs: | |
| test: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| R: | |
| - '4.0.2' | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R }} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: covr | |
| - name: Install system dependencies | |
| run: | | |
| brew install glpk | |
| brew install harfbuzz | |
| brew install fribidi | |
| - name: Install remote dependencies | |
| run: | | |
| Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')" | |
| Rscript -e "remotes::install_version('textshaping', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('ragg', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('pkgdown', upgrade = 'never')" | |
| Rscript -e "install.packages('devtools')" | |
| Rscript -e "remotes::install_version('Matrix', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('igraph', version = '1.3.0', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('magrittr', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('pbmcapply', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('zoo', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('R6', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('plyr', upgrade = 'never')" | |
| Rscript -e "remotes::install_version('arrow', upgrade = 'never')" | |
| - name: Install Bioconductor packages | |
| run: | | |
| Rscript -e "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager')" | |
| Rscript -e "BiocManager::install('BSgenome.Hsapiens.UCSC.hg38', version = '3.12', ask = FALSE)" | |
| Rscript -e "BiocManager::install('GenomicRanges', version = '3.12')" | |
| - name: Install dependencies from GitHub | |
| run: | | |
| Rscript -e "remotes::install_github('mskilab-org/gUtils', upgrade = 'never')" | |
| Rscript -e "remotes::install_github('mskilab-org/gChain', upgrade = 'never')" | |
| - name: Run tests | |
| run: | | |
| R CMD build . | |
| R CMD check *.tar.gz --no-manual | |
| shell: bash | |
| - name: Test coverage | |
| run: covr::codecov(token = Sys.getenv("CODECOV_TOKEN")) | |
| shell: Rscript {0} |