Fix a broken image. Closes #8 #77
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| ## Read more about GitHub actions the features of this GitHub Actions workflow | |
| ## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action | |
| ## | |
| ## For more details, check the biocthis developer notes vignette at | |
| ## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html | |
| ## | |
| ## You can add this workflow to other packages using: | |
| ## > biocthis::use_bioc_github_action() | |
| ## | |
| ## Using GitHub Actions exposes you to many details about how R packages are | |
| ## compiled and installed in several operating system.s | |
| ### If you need help, please follow the steps listed at | |
| ## https://github.com/r-lib/actions#where-to-find-help | |
| ## | |
| ## If you found an issue specific to biocthis's GHA workflow, please report it | |
| ## with the information that will make it easier for others to help you. | |
| ## Thank you! | |
| ## Acronyms: | |
| ## * GHA: GitHub Action | |
| ## * OS: operating system | |
| on: | |
| push: | |
| pull_request: | |
| name: R-CMD-bioc | |
| ## These environment variables control whether to run GHA code later on that is | |
| ## specific to testthat, covr, and pkgdown. | |
| ## | |
| ## If you need to clear the cache of packages, update the number inside | |
| ## cache-version as discussed at https://github.com/r-lib/actions/issues/86. | |
| ## Note that you can always run a GHA test without the cache by using the word | |
| ## "/nocache" in the commit message. | |
| env: | |
| cache-version: 'cache-v1' | |
| jobs: | |
| build-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| container: ${{ matrix.config.cont }} | |
| ## Environment variables unique to this job. | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: '4.0', bioc: '3.12', cont: "bioconductor/bioconductor_docker:RELEASE_3_12", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| #- { os: macOS-latest, r: '4.0', bioc: '3.12'} | |
| #- { os: windows-latest, r: '4.0', bioc: '3.12'} | |
| 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 }} | |
| 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 | |
| ## 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@v3 | |
| ## R is already included in the Bioconductor docker images | |
| - name: Setup R from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| ## pandoc is already included in the Bioconductor docker images | |
| - name: Setup pandoc from r-lib | |
| if: runner.os != 'Linux' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - 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-RELEASE_3_12-r-4.0-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0- | |
| - 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 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) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79 | |
| remotes::install_github("ropensci/bibtex") | |
| remotes::install_github("ropensci/RefManageR") | |
| remotes::install_github("cboettig/knitcitations") | |
| ## For building the website & getting the R session info | |
| ## Edit as necessary with other packages in the future | |
| BiocManager::install(c( | |
| "rmarkdown", | |
| "sessioninfo", | |
| "BiocStyle", | |
| "clusterProfiler", | |
| "edgeR", | |
| "getopt", | |
| "here", | |
| "LieberInstitute/jaffelab", | |
| "knitcitations", | |
| "limma", | |
| "org.Hs.eg.db", | |
| "pheatmap", | |
| "RColorBrewer", | |
| "recount", | |
| "SummarizedExperiment", | |
| "tidyr", | |
| "VariantAnnotation", | |
| "statmod", | |
| "usethis", | |
| "iSEE", | |
| "ggplot2", | |
| "plotly", | |
| "ExploreModelMatrix", | |
| "enrichplot", | |
| "ggnewscale" | |
| )) | |
| tinytex::install_tinytex() | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Build website | |
| run: | | |
| rmarkdown::render_site() | |
| system("touch docs/.nojekyll") | |
| shell: Rscript {0} | |
| - name: Install deploy dependencies | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: docs # The folder the action should deploy. | |