R-CMD-check #122
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| 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()' | |