WIP: support for Sirius annotations #102
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| ## Acronyms: | |
| ## * GHA: GitHub Action | |
| ## * OS: operating system | |
| on: | |
| push: | |
| pull_request: | |
| # Define the GitHub Actions workflow for R CMD check of the MetFamily package | |
| name: R-CMD-check-MetFamily | |
| # Define environment variables for the workflow | |
| env: | |
| has_testthat: 'true' | |
| # run_covr: 'true' # Disabled until later | |
| run_covr: 'false' | |
| # run_pkgdown: 'true' # Disabled until later | |
| run_pkgdown: 'false' | |
| has_RUnit: 'false' | |
| has_BiocCheck: 'false' | |
| cache-version: 'cache-v1' | |
| # Define the jobs for different operating systems | |
| jobs: | |
| build-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| container: ${{ matrix.config.cont }} | |
| # Define the matrix for different configurations | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| # - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| # Disabling additional architectures until later | |
| # - { os: macOS-latest, r: 'next', bioc: '3.18'} | |
| # - { os: windows-latest, r: 'next', bioc: '3.18'} | |
| # Define environment variables for the job | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| NOT_CRAN: true | |
| TZ: UTC | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # Define the steps to be executed | |
| steps: | |
| # Step 1: Set R Library home on Linux | |
| - name: Set R Library home on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| mkdir /__w/_temp/Library | |
| echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | |
| # Step 2: Checkout the repository | |
| - name: Checkout Repository | |
| uses: actions/checkout@v2 | |
| # Step 3: Setup R from r-lib | |
| - name: Setup R from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| extra-repositories: https://janmarvin.r-universe.dev | |
| # Step 4: Setup pandoc from r-lib | |
| - name: Setup pandoc from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| # Step 5: Query dependencies and save RDS file | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| # Step 6: Cache R packages based on configuration | |
| - name: Cache R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | |
| # Step 7: Cache R packages on Linux | |
| - name: Cache R packages on Linux | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | |
| # Step 8: Install Linux system dependencies | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sysreqs=$(Rscript -e 'cat("apt-get update -y && ", paste(remotes::system_requirements("ubuntu", "20.04"), collapse = " && "))') | |
| echo $sysreqs | |
| sudo -s eval "$sysreqs" | |
| # Steps 9 and 10 (macOS and Windows dependencies) removed | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck, testthat, openxlsx2 | |
| needs: check | |
| dependencies: '"hard"' | |
| # Step 11: Install BiocManager | |
| - name: Install BiocManager | |
| run: | | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| # Step 12: Set BiocVersion | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | |
| shell: Rscript {0} | |
| # Step 13: Install dependencies pass 1 | |
| - name: Install dependencies pass 1 | |
| run: | | |
| ## Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| ## Pass #1 at installing dependencies | |
| BiocManager::install(c( | |
| "mzR", "htmltools", "shiny", "shinyBS", "shinyjs", "shinybusy", | |
| "DT", "colourpicker", "Matrix", "squash", "FactoMineR", "mixOmics", | |
| "pcaMethods", "cba", "tools", "stringr", "xcms", "matrixStats", | |
| "plotrix" | |
| )) | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
| BiocManager::install(c("rmarkdown", "BiocStyle")) | |
| continue-on-error: true | |
| shell: Rscript {0} | |
| # Step 14: Install dependencies pass 2 | |
| - name: Install dependencies pass 2 | |
| run: | | |
| ## Pass #2 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
| ## Manually install packages that seem to be skipped. | |
| message(paste('****', Sys.time(), 'force installation of selected packages ****')) | |
| BiocManager::install("mzR", type = "source", force = TRUE) | |
| BiocManager::install("Spectra") | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install(c("BiocCheck", "DBI")) | |
| shell: Rscript {0} | |
| # Step 15: Install BiocGenerics | |
| - name: Install BiocGenerics | |
| if: env.has_RUnit == 'true' | |
| run: | | |
| ## Install BiocGenerics | |
| BiocManager::install("BiocGenerics") | |
| shell: Rscript {0} | |
| # Skipping Step 16: Install covr | |
| # Step 17: Install pkgdown | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| remotes::install_github("r-lib/pkgdown") | |
| shell: Rscript {0} | |
| # Step 18: Session info | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| # Step 19: Run CMD check | |
| - name: Run CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | |
| build_args = c("--no-manual", "--no-resave-data"), | |
| error_on = "error", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| # Step 20: Reveal testthat details | |
| - name: Reveal testthat details | |
| if: env.has_testthat == 'true' && runner.os == 'Linux' | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| # Step 21: Run RUnit tests | |
| - name: Run RUnit tests | |
| if: env.has_RUnit == 'true' && runner.os == 'Linux' | |
| run: | | |
| BiocGenerics:::testPackage() | |
| shell: Rscript {0} | |
| # Step 22: Run BiocCheck | |
| - name: Run BiocCheck | |
| if: env.has_BiocCheck == 'true' && runner.os == 'Linux' | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| # Step 23: Test coverage | |
| - name: Test coverage | |
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| # Step 24: Install package | |
| - name: Install package | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: R CMD INSTALL . | |
| # Step 25: Test Shiny App in package | |
| - name: Test Shiny App | |
| uses: rstudio/shinytest2/actions/test-app@actions/v1 | |
| with: | |
| app-dir: "inst/MetFamily" | |
| # Step 26: Deploy package | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: | | |
| git config --global user.email "actions@github.com" | |
| git config --global user.name "GitHub Actions" | |
| git config --global --add safe.directory /__w/your-package-name | |
| Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | |
| shell: bash {0} | |
| ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | |
| ## at least one locally before this will work. This creates the gh-pages | |
| ## branch (erasing anything you haven't version controlled!) and | |
| ## makes the git history recognizable by pkgdown. | |
| # Step 27: Upload check results | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocversion-devel-r-devel-results | |
| path: check |