finish correcting unit test #345
Workflow file for this run
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| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - 'feature/**' | |
| - 'bug_fix/**' | |
| - 'bugfix/**' | |
| - 'maint/**' | |
| schedule: | |
| # run release on the 8th of every month to detect problems with new packages/R releases | |
| - cron: '19 3 8 * *' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| services: | |
| postgres: | |
| image: postgres | |
| env: | |
| POSTGRES_DB: RamsesDB | |
| POSTGRES_USER: user | |
| POSTGRES_PASSWORD: password | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # container action is not supported on windows or macOS | |
| # - {os: windows-latest, r: 'release'} | |
| # - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-20.04, r: '4.0.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOVETOKEN: ${{ secrets.CODECOVETOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| install.packages('devtools') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_github("msberends/AMR", build = TRUE) | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: | | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Code coverage | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: covr::codecov(type = "all", quiet = FALSE, token = Sys.getenv("CODECOVETOKEN")) | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: pkgdown::build_site(new_process = TRUE) | |
| shell: Rscript {0} | |
| - name: Deploy to Firebase | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| uses: w9jds/firebase-action@master | |
| with: | |
| args: deploy --only hosting | |
| env: | |
| PROJECT_ID: ramses-antibiotics | |
| FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }} | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| - name: Install TeX | |
| run: tlmgr --version | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| - name: Build source and PDF manual | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| run: | | |
| devtools::install() | |
| devtools::build(".", vignettes = TRUE, path = "~") | |
| devtools::build_manual(".", path = "~") | |
| shell: Rscript {0} | |
| - uses: actions/upload-artifact@v3 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| with: | |
| name: Ramses package source | |
| path: ~/Ramses_[0-9].[0-9].[0-9].tar.gz | |
| - uses: actions/upload-artifact@v3 | |
| if: (github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop') && github.event_name == 'push' && matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'release' | |
| with: | |
| name: Ramses package manual | |
| path: ~/Ramses_[0-9].[0-9].[0-9].pdf |