modify vignette to demonstrate use of 'geneSetSizes()' in limma example #61
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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() | |
| ## or | |
| ## > usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml") | |
| ## without having to install biocthis. | |
| ## | |
| ## Using GitHub Actions exposes you to many details about how R packages are | |
| ## compiled and installed in several operating systems. | |
| ## 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: | |
| branches: | |
| - devel | |
| - 'RELEASE_*' | |
| pull_request: | |
| branches: | |
| - devel | |
| - 'RELEASE_*' | |
| name: R-CMD-check-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: | |
| has_testthat: 'false' | |
| run_covr: 'true' | |
| run_pkgdown: 'false' | |
| has_RUnit: 'true' | |
| cache-version: 'cache-v1' | |
| jobs: | |
| ## This first job uses the GitHub repository branch name to infer what | |
| ## version of Bioconductor we will be working on. | |
| define-docker-info: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| imagename: ${{ steps.findinfo.outputs.imagename }} | |
| biocversion: ${{ steps.findinfo.outputs.biocversion }} | |
| steps: | |
| - id: findinfo | |
| run: | | |
| ## Find what Bioconductor RELEASE branch we are working on | |
| ## otherwise, assume we are working on bioc-devel. | |
| if echo "$GITHUB_REF" | grep -q "RELEASE_"; then | |
| biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')" | |
| else | |
| biocversion="devel" | |
| fi | |
| ## Define the image name and print the information | |
| imagename="bioconductor/bioconductor_docker:${biocversion}" | |
| echo $imagename | |
| echo $biocversion | |
| ## Save the information for the next job | |
| echo "::set-output name=imagename::${imagename}" | |
| echo "::set-output name=biocversion::${biocversion}" | |
| R-CMD-check-bioc: | |
| ## This job then checks the R package using the Bioconductor docker that | |
| ## was defined by the previous job. This job will determine what version of | |
| ## R to use for the macOS and Windows builds on the next job. | |
| runs-on: ubuntu-latest | |
| needs: define-docker-info | |
| ## Name shown on the GHA log | |
| name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }}) | |
| ## Information used by the next job that will run on macOS and Windows | |
| outputs: | |
| rversion: ${{ steps.findrversion.outputs.rversion }} | |
| biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }} | |
| ## Environment variables unique to this job. | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| TZ: UTC | |
| NOT_CRAN: true | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| ## The docker container to use. Note that we link a directory on the GHA | |
| ## runner to a docker directory, such that we can then cache the linked | |
| ## directory. This directory will contain the R packages used. | |
| container: | |
| image: ${{ needs.define-docker-info.outputs.imagename }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| steps: | |
| - name: Install latest git | |
| run: | | |
| ## git version provided | |
| git --version | |
| ## to be able to install software properties | |
| sudo apt-get update -y | |
| ## to be able to use add-apt-repository | |
| sudo apt-get install software-properties-common -y | |
| ## to use stable releases of git that are already in a PPA at | |
| ## https://launchpad.net/~git-core/+archive/ubuntu/candidate | |
| sudo add-apt-repository ppa:git-core/candidate -y | |
| ## Update | |
| sudo apt-get update -y | |
| ## Upgrade git and other tools | |
| sudo apt-get upgrade -y | |
| ## latest git version | |
| git --version | |
| shell: bash {0} | |
| ## Most of these steps are the same as the ones in | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## If they update their steps, we will also need to update ours. | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| ## Find the corresponding R version based on the Bioconductor version | |
| ## to use for the macOS and Windows checks by the next GHA job | |
| - id: findrversion | |
| name: Find Bioc and R versions | |
| run: | | |
| ## Find what branch we are working on | |
| if echo "$GITHUB_REF" | grep -q "devel"; then | |
| biocversion="devel" | |
| elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then | |
| biocversion="release" | |
| fi | |
| ## Define the R and Bioconductor version numbers | |
| biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))") | |
| rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))") | |
| ## Print the results | |
| echo $biocversion | |
| echo $biocversionnum | |
| echo $rversion | |
| ## Save the info for the next job | |
| echo "::set-output name=rversion::${rversion}" | |
| echo "::set-output name=biocversionnum::${biocversionnum}" | |
| shell: | |
| bash {0} | |
| - name: Cache R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache')" | |
| uses: actions/cache@v1 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}- | |
| - name: Install dependencies | |
| run: | | |
| ## Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| ## Pass #1 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]]) | |
| ## Pass #2 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(deps$package[deps$diff != 0]) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| 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: 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} | |
| - name: Reveal testthat details | |
| if: env.has_testthat == 'true' | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Run RUnit tests | |
| if: env.has_RUnit == 'true' | |
| run: | | |
| ## Install BiocGenerics | |
| BiocManager::install("BiocGenerics") | |
| ## Install the package itself, otherwise BiocGenerics:::testPackage() doesn't find it | |
| install.packages(".", repos=NULL) | |
| BiocGenerics:::testPackage() | |
| shell: Rscript {0} | |
| - name: Install covr | |
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' | |
| run: | | |
| remotes::install_github("r-lib/pkgdown") | |
| shell: Rscript {0} | |
| - name: Install package | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' | |
| run: R CMD INSTALL . | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "GitHub Action" | |
| 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. | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results | |
| path: check |