fix bug when using SVCs without Omega/Epsilon #247
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: [push, pull_request, workflow_dispatch] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release'} | |
| - {os: macOS-latest, r: 'release'} | |
| - {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 }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@master | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@master | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$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 for Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| # needed for package units? | |
| sudo apt install libudunits2-dev | |
| # needed for package rgdal? | |
| sudo apt-get install gdal-bin proj-bin libgdal-dev libproj-dev | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install system dependencies for Windows/OSX | |
| run: | | |
| remotes::install_deps(dependencies=TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check Ubuntu | |
| if: runner.os == 'Linux' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-install", "--no-manual", "--as-cran"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Check Windows or MacOS | |
| if: runner.os != 'Linux' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Run integrated tests via testthat on ubuntu | |
| if: runner.os == 'Linux' | |
| run: | | |
| devtools::install_local() | |
| out <- devtools::test(stop_on_failure=TRUE) | |
| print(getwd()) | |
| print(ls()) | |
| print(str(out)) | |
| file.copy('VAST.Rcheck/tests/testthat.Rout', to='check/testthat.Rout') | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check |