Update layout_karyogram docs as keepSeqlevels was moved to GenomeInfoDb #29
Workflow file for this run
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| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| name: R-CMD-check-and-coverage | |
| jobs: | |
| R-CMD-check-and-coverage: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout Repository | |
| 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: Cache R packages | |
| uses: actions/cache@v2 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-1- | |
| - name: Install system dependencies | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| latexreq="texlive-latex-base texlive-fonts-recommended texlive-fonts-extra" | |
| sysreqs="$sysreqs $latexreq" | |
| echo $sysreqs | |
| sudo -s eval "$sysreqs" | |
| - name: Install dependencies | |
| run: | | |
| options(repos = c(CRAN = "https://cran.r-project.org")) | |
| BiocManager::repositories() | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | |
| build_args = c("--no-manual", "--no-resave-data"), | |
| error_on = "error", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Reveal testthat details | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Test coverage | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocversion-devel | |
| path: check |