Merge branch 'main' of https://github.com/xihaoli/STAARpipeline #90
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| on: [push, pull_request] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: macOS-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.2.3 | |
| - name: Install BiocManager | |
| run: | | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| shell: Rscript {0} | |
| - name: Install GENESIS, GenomicFeatures | |
| run: | | |
| BiocManager::install(c("GENESIS", "GenomicFeatures")) | |
| shell: Rscript {0} | |
| - name: Install TxDb.Hsapiens.UCSC.hg38.knownGene | |
| run: | | |
| BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene") | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes", "rcmdcheck")) | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_github(c("xihaoli/STAAR", "xihaoli/MultiSTAAR", "zilinli1988/SCANG")) | |
| shell: Rscript {0} | |
| - name: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") | |
| shell: Rscript {0} |