All features 202403 #26
Workflow file for this run
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/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: lint | |
| jobs: | |
| lint: | |
| 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, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18" } | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| ## 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 /__w/_temp/Library | |
| echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| # R is already included in the Bioconductor Docker image | |
| - name: "[Stage] Dependencies" | |
| run: | | |
| sudo apt install libopenmpi-dev | |
| - name: Query R dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages on Linux | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2- | |
| - 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" | |
| - name: Install BiocManager | |
| run: | | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install dependencies pass 1 | |
| run: | | |
| ## Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| ## Set the repos source depending on the OS | |
| ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/ | |
| ## though based on https://bit.ly/bioc2021-package-binaries | |
| ## the Azure link will be the main one going forward. | |
| gha_repos <- if( | |
| .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" | |
| ) c( | |
| "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc", | |
| BiocManager::repositories() | |
| ) else BiocManager::repositories() | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos) | |
| ## Pass #1 at installing dependencies | |
| ## This pass uses AnVIL-powered fast binaries | |
| ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries | |
| ## The speed gains only apply to the docker builds. | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE) | |
| continue-on-error: true | |
| shell: Rscript {0} | |
| - name: Install dependencies pass 2 | |
| run: | | |
| ## Pass #2 at installing dependencies | |
| ## This pass does not use AnVIL and will thus update any packages | |
| ## that have seen been updated in Bioconductor | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install lintr | |
| run: remotes::install_cran("lintr") | |
| shell: Rscript {0} | |
| - name: Lint | |
| run: lintr::lint_package() | |
| shell: Rscript {0} |