Add warning for unset 'where' argument in toolGetMapping function #72
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| # Run CI for R using https://eddelbuettel.github.io/r-ci/ | |
| name: check | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| env: | |
| USE_BSPM: "true" | |
| _R_CHECK_FORCE_SUGGESTS_: "false" | |
| NO_BINARY_INSTALL_R_PACKAGES: 'c("madrat", "magclass", "citation", "gms", "goxygen", "GDPuc", "roxygen2")' | |
| jobs: | |
| check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Bootstrap | |
| run: | | |
| sudo chown runner -R . | |
| sudo locale-gen en_US.UTF-8 | |
| sudo add-apt-repository -y ppa:ubuntugis/ppa | |
| curl -OLs https://eddelbuettel.github.io/r-ci/run.sh | |
| chmod 0755 run.sh | |
| ./run.sh bootstrap | |
| rm -f bspm_*.tar.gz | |
| - name: Enable r-universe repo, modify bspm integration | |
| run: | | |
| # install packages from https://pik-piam.r-universe.dev and CRAN | |
| echo ' | |
| options(repos = c(universe = "https://pik-piam.r-universe.dev", | |
| CRAN = "https://cloud.r-project.org")) | |
| ' >> .Rprofile | |
| cat .Rprofile | |
| # modify bspm integration to never install binary builds of PIK CRAN packages | |
| sudo sed -i '/bspm::enable()/d' /etc/R/Rprofile.site | |
| # need double % because of printf, %s is replaced with "$NO_BINARY_INSTALL_R_PACKAGES" (see "env:" above) | |
| printf ' | |
| local({ | |
| expr <- quote({ | |
| if (!is.null(repos)) { | |
| noBinaryInstallRPackages <- %s | |
| pkgs <- c(bspm::install_sys(pkgs[!pkgs %%in%% noBinaryInstallRPackages]), | |
| pkgs[pkgs %%in%% noBinaryInstallRPackages]) | |
| } | |
| type <- "source" | |
| }) | |
| trace(utils::install.packages, expr, print = FALSE) | |
| }) | |
| ' "$NO_BINARY_INSTALL_R_PACKAGES" | sudo tee --append /etc/R/Rprofile.site >/dev/null | |
| cat /etc/R/Rprofile.site | |
| - name: Set up Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Cache R libraries | |
| if: ${{ !env.ACT }} # skip when running locally via nektos/act | |
| uses: pat-s/always-upload-cache@v3 | |
| with: | |
| path: /usr/local/lib/R/ | |
| key: 3-${{ runner.os }}-usr-local-lib-R-${{ hashFiles('DESCRIPTION') }} | |
| restore-keys: | | |
| 3-${{ runner.os }}-usr-local-lib-R- | |
| - name: Restore R library permissions | |
| run: | | |
| sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library | |
| - name: Install dependencies | |
| run: | | |
| ./run.sh install_aptget libhdf5-dev libharfbuzz-dev libfribidi-dev | |
| ./run.sh install_all | |
| ./run.sh install_r_binary covr rstudioapi | |
| ./run.sh install_r lucode2 | |
| - name: Install python dependencies if applicable | |
| run: | | |
| [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true | |
| [ -f requirements.txt ] && pip install -r requirements.txt || true | |
| - name: Remove bspm integration # to get rid of error when running install.packages | |
| run: | | |
| sudo sed -i '/ trace(utils::install.packages, expr, print = FALSE)/d' /etc/R/Rprofile.site | |
| cat /etc/R/Rprofile.site | |
| - name: Verify validation key | |
| shell: Rscript {0} | |
| run: lucode2:::validkey(stopIfInvalid = TRUE) | |
| - name: Checks | |
| shell: Rscript {0} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| lucode2::check(runLinter = FALSE) | |
| - name: Test coverage | |
| shell: Rscript {0} | |
| run: covr::codecov(quiet = FALSE) | |
| env: | |
| NOT_CRAN: "true" |