R-CMD-check #117
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: "0 0 2 * *" | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install libgit2-dev | |
| run: sudo apt install -qq libgit2-dev | |
| - name: Install libcurl4-openssl-dev | |
| run: sudo apt install -qq libcurl4-openssl-dev | |
| - name: Install libharfbuzz-dev libfribidi-dev | |
| run: sudo apt install -qq libharfbuzz-dev libfribidi-dev | |
| - name: Fix rJava error # from https://travis-ci.community/t/cannot-connect-to-java-from-r/9754/8 | |
| run: sudo $(which R) CMD javareconf | |
| - name: Install bios2mds prerequisite 'libglu1-mesa-dev' | |
| run: sudo apt-get install libglu1-mesa-dev | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("remotes", "rcmdcheck")) | |
| remotes::install_github("richelbilderbeek/tmhmm") | |
| remotes::install_github("richelbilderbeek/pureseqtmr") | |
| remotes::install_github("richelbilderbeek/mhcnpreds") | |
| remotes::install_github("richelbilderbeek/nmhc2ppreds") | |
| remotes::install_github("jtextor/epitope-prediction") | |
| remotes::install_github("richelbilderbeek/epiprepreds") | |
| remotes::install_github("richelbilderbeek/cobaltr") | |
| remotes::install_github("richelbilderbeek/ormr") | |
| remotes::install_github("richelbilderbeek/mhcnuggetsr") | |
| remotes::install_github("richelbilderbeek/mhcnuggetsrinstall") | |
| remotes::install_bioc("msa") | |
| remotes::install_bioc("Biostrings") | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("tidyr") | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_cran("covr") | |
| remotes::install_cran("lintr") | |
| remotes::install_github("MangoTheCat/goodpractice") | |
| shell: Rscript {0} | |
| - name: Install MHCnuggetsr | |
| run: Rscript -e 'mhcnuggetsrinstall::install_mhcnuggets()' | |
| - name: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: Rscript -e 'covr::codecov()' | |
| - name: Lint | |
| run: Rscript -e 'lintr::lint_package()' | |