speed up group_by operations with mutate #36
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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 | |
| 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: '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 }} | |
| 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: ${{ needs.define-docker-info.outputs.imagename }} | |
| volumes: | |
| - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library | |
| steps: | |
| - name: Install Git | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt install make libssl-dev libghc-zlib-dev libcurl4-gnutls-dev libexpat1-dev gettext unzip -y | |
| wget https://github.com/git/git/archive/v2.26.2.zip -O git.zip | |
| unzip git.zip | |
| cd git-* | |
| make prefix=/usr all | |
| sudo make prefix=/usr install | |
| cd - | |
| git --version | |
| shell: bash {0} | |
| ## Related to https://github.com/actions/checkout/issues/238 | |
| ## https://www.digitalocean.com/community/tutorials/how-to-install-git-on-ubuntu-18-04 | |
| ## Most of these steps are the same as the ones in | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## If they update their steps, we will also need to update ours. | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| ## Find the corresponding R version based on the Bioconductor version | |
| ## to use for the macOS and Windows checks by the next GHA job | |
| - id: findrversion | |
| name: Find Bioc and R versions | |
| run: | | |
| ## Find what branch we are working on | |
| if echo "$GITHUB_REF" | grep -q "master"; 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$diff != 0]) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | |
| build_args = c("--no-manual", "--no-resave-data"), | |
| error_on = "warning", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Reveal testthat details | |
| if: env.has_testthat == 'true' | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: BiocCheck | |
| run: | | |
| ## This syntax works on Windows as well as other OS | |
| ## plus it doesn't break the GHA workflow in case BiocCheck finds | |
| ## an error (for example, the package is bigger than the maximum | |
| ## allowed size). We want the rest of the GHA to proceed even if | |
| ## there is a BiocCheck error in order to see the full output and | |
| ## run the tests on all operating systems. | |
| BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE) | |
| ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html | |
| shell: Rscript {0} | |
| - name: Install covr | |
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' | |
| run: | | |
| remotes::install_cran("pkgdown") | |
| shell: Rscript {0} | |
| - name: Install package | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' | |
| run: R CMD INSTALL . | |
| - name: Deploy package | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' | |
| run: | | |
| git config --local user.email "action@github.com" | |
| 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 | |
| ## Run R CMD check on both macOS and Windows. You can also run the | |
| ## tests on Linux outside of the Bioconductor docker environment. If you | |
| ## do so, you might have to install system dependencies on Linux | |
| ## Bioconductor's docker includes all the system dependencies required by | |
| ## Bioconductor packages and their dependencies (which includes many CRAN | |
| ## dependencies as well, thus making this workflow useful beyond Bioconductor) | |
| R-CMD-check-r-lib: | |
| runs-on: ${{ matrix.config.os }} | |
| needs: [define-docker-info, R-CMD-check-bioc] | |
| name: ${{ matrix.config.os }} (r-${{ needs.R-CMD-check-bioc.outputs.rversion }} bioc-${{ needs.define-docker-info.outputs.biocversion }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| ## Comment/Un-comment in case you also want to run other versions | |
| - { os: ubuntu-latest, r: '4.1', bioc: '3.13', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| #- { os: macOS-latest, r: '4.1', bioc: '3.13'} | |
| #- { os: windows-latest, r: '4.1', bioc: '3.13'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| BIOCVERSIONNUM: ${{ needs.R-CMD-check-bioc.outputs.biocversionnum }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup R from r-lib | |
| uses: r-lib/actions/setup-r@master | |
| with: | |
| r-version: ${{ needs.R-CMD-check-bioc.outputs.rversion }} | |
| - name: Setup pandoc from r-lib | |
| uses: r-lib/actions/setup-pandoc@master | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: "!contains(github.event.head_commit.message, '/nocache')" | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}- | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| - name: Install macOS system dependencies | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| ## Enable installing XML from source if needed | |
| brew install libxml2 | |
| echo "::set-env name=XML_CONFIG::/usr/local/opt/libxml2/bin/xml2-config" | |
| ## Required to install magick as noted at | |
| ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| brew install imagemagick@6 | |
| - name: Install Windows system dependencies | |
| if: runner.os == 'Windows' | |
| run: | | |
| ## Edit below if you have any Windows system dependencies | |
| shell: Rscript {0} | |
| - name: Install BiocManager | |
| run: | | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = Sys.getenv('BIOCVERSIONNUM'), ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Install dependencies | |
| run: | | |
| ## Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| ## Pass #1 at installing dependencies | |
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$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$diff != 0]) | |
| ## For running the checks | |
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
| remotes::install_cran("rcmdcheck") | |
| BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | |
| build_args = c("--no-manual", "--no-resave-data"), | |
| error_on = "warning", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Reveal testthat details | |
| if: env.has_testthat == 'true' | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: BiocCheck | |
| run: | | |
| ## This syntax works on Windows as well as other OS | |
| ## plus it doesn't break the GHA workflow in case BiocCheck finds | |
| ## an error (for example, the package is bigger than the maximum | |
| ## allowed size). We want the rest of the GHA to proceed even if | |
| ## there is a BiocCheck error in order to see the full output and | |
| ## run the tests on all operating systems. | |
| BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE) | |
| ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-results | |
| path: check |