vignette polishing #42
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GJPAT2 }} | |
| # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RGL_USE_NULL: TRUE | |
| _R_CHECK_DONTTEST_EXAMPLES_: FALSE | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| NEUPRINT_TOKEN: ${{ secrets.NEUPRINT_TOKEN }} | |
| CLIO_TOKEN: ${{ secrets.CLIO_TOKEN }} | |
| FLYWIRE_PRINCIPLES: IAGREETOTHEFLYWIREPRINCIPLES | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| shell: Rscript {0} | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_cran("covr") | |
| remotes::install_cran("pkgdown") | |
| remotes::install_cran("devtools") | |
| shell: Rscript {0} | |
| - name: Add some R options for later steps | |
| run: | | |
| cat("\noptions(fafbseg.use_static_celltypes=TRUE)\n", file = "~/.Rprofile", append = TRUE) | |
| shell: Rscript {0} | |
| - name: Download flywire data | |
| run: | | |
| fafbseg::download_flywire_release_data() | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/check-r-package@v2 | |
| - name: Deploy package | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| Rscript -e 'devtools::install(); pkgdown::deploy_to_branch(new_process = FALSE)' |