remove a name #41
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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 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 | |
| ## Specify which branches you want this GHA to run on. | |
| ## Bioconductor uses branches such as master (bioc-devel) and RELEASE_* like | |
| ## RELEASE_3_10. For more details check | |
| ## http://bioconductor.org/developers/how-to/git/ | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: "1 7 11 * *" | |
| name: compilation-check | |
| ## 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: 'true' | |
| run_covr: 'true' | |
| run_pkgdown: '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 }} | |
| steps: | |
| - id: findinfo | |
| run: | | |
| ## Define the image name and print the information | |
| imagename="bioconductor/bioconductor_docker" | |
| echo $imagename | |
| ## Save the information for the next job | |
| echo "::set-output name=imagename::${imagename}" | |
| compilation-check: | |
| ## 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 | |
| ## 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.GHTOKEN2 }} | |
| GITHUB_PAT: ${{ secrets.GHTOKEN2 }} | |
| ## 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: ${{ needs.define-docker-info.outputs.imagename }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| steps: | |
| - name: Install Git | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt install make libssl-dev libghc-zlib-dev libcurl4-gnutls-dev libexpat1-dev gettext unzip -y | |
| wget https://github.com/git/git/archive/v2.26.2.zip -O git.zip | |
| unzip git.zip | |
| cd git-* | |
| make prefix=/usr all | |
| sudo make prefix=/usr install | |
| cd - | |
| git --version | |
| shell: bash {0} | |
| ## Related to https://github.com/actions/checkout/issues/238 | |
| ## https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-18-04 | |
| ## Most of these steps are the same as the ones in | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## If they update their steps, we will also need to update ours. | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps("introToR/",dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| ## Find the corresponding R version based on the Bioconductor version | |
| ## to use for the macOS and Windows checks by the next GHA job | |
| - id: findrversion | |
| name: Find Bioc and R versions | |
| run: | | |
| ## Define the R and Bioconductor version numbers | |
| biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == 'release')[, 'Bioc']; cat(as.character(res))") | |
| rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == 'release')[, 'R']; cat(as.character(res))") | |
| ## Print the results | |
| 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-release-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-release-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("introToR/",dependencies = TRUE) | |
| deps <- remotes::dev_package_deps("introToR/",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("introToR/",dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(deps$package[deps$diff != 0]) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| BiocManager::install("rmarkdown") | |
| BiocManager::install("RockefellerUniversity/compileCourses",subdir="compileCourses") | |
| 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: Install package | |
| if: github.ref == 'refs/heads/master' | |
| run: R CMD INSTALL ./introToR/ | |
| - name: Session info | |
| run: | | |
| require(compileCourses) | |
| compileCourses::compileSingleCourseMaterial(repo="RockefellerUniversity",subdir="introToR",branch="master") | |
| shell: Rscript {0} | |
| - name: Move to docs | |
| run: | | |
| mkdir -p docs | |
| cp -r r_course/* docs/ | |
| echo "Copied to docs" | |
| shell: | |
| bash {0} | |
| - name: commit | |
| run: | | |
| git config --global user.email "tc.infomatics@gmail.com" | |
| git config --global http.postBuffer 263112000 | |
| git add docs/\* r_course/\* | |
| git commit -m 'Autobuild' | |
| git push origin HEAD:refs/heads/master | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocdocker-biocbranch-release-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results | |
| path: check |