v2.5.5 #177
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on: | |
push: | |
pull_request: | |
schedule: | |
- cron: "0 0 13 * *" | |
name: R-CMD-check | |
jobs: | |
R-CMD-check: | |
strategy: | |
fail-fast: false | |
matrix: | |
install_beast2: [true, false] | |
os: [ubuntu-latest] | |
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 libcurl4-openssl-dev | |
run: sudo apt install -qq libcurl4-openssl-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 libharfbuzz-dev libfribidi-dev | |
run: sudo apt install -qq libharfbuzz-dev libfribidi-dev | |
- name: Install libglpk-dev for igraph | |
run: sudo apt-get install libglpk-dev | |
- name: Install dependencies | |
run: | | |
install.packages(c("remotes", "rcmdcheck")) | |
remotes::install_github("ropensci/beautier", ref = "develop") | |
remotes::install_github("ropensci/beastier", ref = "develop") | |
remotes::install_deps(dependencies = TRUE) | |
remotes::install_cran("rcmdcheck") | |
remotes::install_cran("covr") | |
remotes::install_cran("lintr") | |
remotes::install_github("MangoTheCat/goodpractice") | |
remotes::install_github("richelbilderbeek/beastierinstall") | |
remotes::install_github("richelbilderbeek/mauricerinstall") | |
shell: Rscript {0} | |
- name: Install BEAST2 | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == true ]]; then Rscript -e "beastierinstall::install_beast2()"; fi | |
- name: Install BEAST2 NS package | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == true ]]; then ./scripts/install_beast2_ns_pkg.sh ; fi | |
- name: Check | |
run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") | |
shell: Rscript {0} | |
- name: Make sure that no files are created in the beautier .cache folder | |
run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "beautier")), 0) | |
shell: Rscript {0} | |
- name: Make sure that no files are created in the tracerer .cache folder | |
run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "tracerer")), 0) | |
shell: Rscript {0} | |
- name: Make sure that no files are created in the beastier .cache folder | |
run: testthat::expect_length(list.files(rappdirs::user_cache_dir(appname = "beastier")), 0) | |
shell: Rscript {0} | |
- name: Test coverage | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == true ]]; then Rscript -e 'covr::codecov()'; fi | |
- name: Lint | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == false ]]; then Rscript -e 'lintr::lint_package()'; fi | |
- name: Report | |
run: beastier::beastier_report() | |
shell: Rscript {0} | |
- name: Install mauricer | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == true ]]; then Rscript -e 'remotes::install_github("ropensci/mauricer")'; fi | |
- name: Show installed BEAST2 packages | |
env: | |
INSTALL_BEAST2: ${{ matrix.install_beast2 }} | |
run: if [[ "$INSTALL_BEAST2" == true ]]; then Rscript -e 'mauricer::get_beast2_pkg_names()'; fi | |