Fix R GitHub action #33
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| name: rworkflows | |
| 'on': | |
| push: | |
| branches: | |
| - master | |
| - main | |
| - devel | |
| - RELEASE_** | |
| pull_request: | |
| branches: | |
| - master | |
| - main | |
| - devel | |
| - RELEASE_** | |
| jobs: | |
| # From neurogenomics/rworkflows | |
| rworkflows: | |
| permissions: write-all | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| container: ${{ matrix.config.cont }} | |
| strategy: | |
| fail-fast: ${{ false }} | |
| matrix: | |
| config: | |
| - os: ubuntu-latest | |
| bioc: devel | |
| r: auto | |
| - os: macOS-latest | |
| bioc: release | |
| r: auto | |
| - os: windows-latest | |
| bioc: release | |
| r: auto | |
| steps: | |
| - name: 🔭 Collect Workflow Telemetry | |
| uses: runforesight/workflow-telemetry-action@v1 | |
| continue-on-error: true | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| comment_on_pr: false | |
| - name: 🌎 Set environment variables | |
| run: | | |
| echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV | |
| echo "R_REMOTES_NO_ERRORS_FROM_WARNINGS=${{ true }}" >> $GITHUB_ENV | |
| echo "TZ=UTC" >> $GITHUB_ENV | |
| shell: bash {0} | |
| ## Set the R library to the directory matching the | |
| ## R packages cache step further below when running on Docker (Linux). | |
| - name: 📚 Set R library home on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| mkdir -p /tmp/R/Library | |
| echo ".libPaths('/tmp/R/Library')" >> ~/.Rprofile | |
| git config --global --add safe.directory '*' | |
| shell: bash {0} | |
| ## Most of these steps are the same as the ones in | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## If they update their steps, we will also need to update ours. | |
| - name: ⏬ Checkout repository | |
| uses: actions/checkout@v4 | |
| ## R/Bioc are already installed on the Bioc Docker container, | |
| ## and reinstalling them causes errors. | |
| - name: 🛠 Setup R and Bioconductor | |
| if: runner.os != 'Linux' | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| ## pandoc is already included in the Bioconductor docker images | |
| - name: 🛠 Install Pandoc | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| with: | |
| pandoc-version: '2.19' | |
| - name: ❔ Query dependencies | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages('remotes') | |
| remotes::install_github("r-lib/remotes") | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: 🏦 Restore R package cache | |
| if: | | |
| !contains(github.event.head_commit.message, '[nocache]') && runner.os != 'Linux' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}- | |
| - name: 🏦 Cache R packages on Linux | |
| if: | | |
| !contains(github.event.head_commit.message, '[nocache]') && runner.os == 'Linux' | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/R/Library | |
| key: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}- | |
| - name: 🛠 Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') | |
| echo $sysreqs | |
| sudo -s eval "$sysreqs" | |
| sudo apt-get install -y qpdf rsync devscripts autoconf libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev | |
| shell: bash {0} | |
| - name: 🛠 Install macOS system dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| #### --- Justifications for each package --- #### | |
| ### libxml2 ### | |
| # Enable installing XML from source if needed | |
| ### imagemagick@6 ### | |
| # Required to install magick as noted at | |
| # https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| ### harfbuzz fribidi ### | |
| # For textshaping, required by ragg, and required by pkgdown | |
| ### libgit2 ### | |
| # For installing usethis's dependency gert | |
| ### xquartz --cask ### | |
| # Required for tcltk | |
| ### libxfont ### | |
| # Required for some ggplot2 functions | |
| ### texlive ### | |
| # Required for rendering Sweave files (even with r-lib/actions/setup-tinytex) | |
| #### --- Install packages --- #### | |
| ### Install normally ### | |
| brew install libxml2 imagemagick@6 harfbuzz fribidi libgit2 texlive autoconf | |
| ### Install via cask ### | |
| brew install xquartz --cask | |
| ### Set up xml2 ### | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| shell: bash {0} | |
| - name: 🛠 Configure | |
| if: runner.os == 'Linux' || runner.os == 'macOS' | |
| run: | | |
| autoconf | |
| ./configure | |
| - name: 🛠 Install dependencies pass 1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck ****')) | |
| install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE) | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****')) | |
| repos <- BiocManager::repositories() | |
| remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE) | |
| continue-on-error: true | |
| shell: Rscript {0} | |
| - name: 🛠 Install dependencies pass 2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout")) | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****')) | |
| repos <- BiocManager::repositories() | |
| remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE) | |
| shell: Rscript {0} | |
| - name: 🛠 Install covr | |
| if: runner.os == 'Linux' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages("covr") | |
| shell: Rscript {0} | |
| - name: 🛠 Install pkgdown | |
| if: runner.os == 'Linux' | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| install.packages("pkgdown") | |
| shell: Rscript {0} | |
| - name: ℹ️ Session info ️ | |
| run: | | |
| options(width = 100, crayon.enabled = TRUE) | |
| pkgs <- installed.packages()[,"Package"] | |
| if(!require("sessioninfo", quietly=TRUE)) install.packages("sessioninfo") | |
| tryCatch({ | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| }, error = function(x){utils::sessionInfo()}) | |
| shell: Rscript {0} | |
| - name: ✅ Run CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| RGL_USE_NULL: ${{ env.RGL_USE_NULL }} | |
| DISPLAY: 99.0 | |
| AS_CRAN: true | |
| run_vignettes: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| if(!require("rcmdcheck", quietly=TRUE)) install.packages("rcmdcheck") | |
| as_cran <- if(Sys.getenv("AS_CRAN")=='true') "--as-cran" else NULL | |
| run_build_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--no-build-vignettes" | |
| run_vignettes <- if(Sys.getenv("run_vignettes")=='true') NULL else "--ignore-vignettes" | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--timings", as_cran, run_vignettes), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data", run_build_vignettes), | |
| error_on = "warning", | |
| check_dir = "check") | |
| shell: Rscript {0} | |
| - name: 📋 Reveal testthat details | |
| run: | | |
| find . -name testthat.Rout -exec cat '{}' ';' | |
| shell: bash {0} | |
| - name: 📋 Test coverage | |
| if: runner.os == 'Linux' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: 🛠 Install package ️ | |
| if: runner.os == 'Linux' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: R CMD INSTALL . | |
| shell: bash {0} | |
| - name: 📦 Render README | |
| if: runner.os == 'Linux' | |
| env: | |
| DISPLAY: 99.0 | |
| run: | | |
| if(file.exists("README.Rmd")){ | |
| options(crayon.enabled = TRUE) | |
| if(!require("rmarkdown", quietly=TRUE)) install.packages("rmarkdown"); | |
| rmarkdown::render("README.Rmd", output_format = rmarkdown::github_document(html_preview = FALSE)); | |
| } | |
| shell: Rscript {0} | |
| - name: 📦 Build pkgdown site | |
| if: runner.os == 'Linux' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: 📦🚀 Deploy pkgdown site to GitHub pages | |
| if: runner.os == 'Linux' | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: ⏫ Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results | |
| path: check |