speeds up add_peptide_positions by dropping Biostrings::match (#53) #140
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| name: check-bioc | |
| jobs: | |
| build-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os}} (R ${{ matrix.config.r }}, Bioc ${{ matrix.config.bioc }}) | |
| container: | |
| image: ${{ matrix.config.cont }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16" } | |
| 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). | |
| ## (lcolladotor/biocthis) | |
| - name: Set R Library home on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| mkdir /__w/_temp/Library | |
| echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | |
| ## (r-lib/check-standard) | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| ## R and pandoc already installed in Bioconductor docker containers | |
| ## (lcolladotor/biocthis) | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| ## (lcolladotor/biocthis) | |
| - 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 }}-Bioc-RELEASE_3_16-R-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-Bioc-RELEASE_3_16-R-${{ matrix.config.r }}- | |
| ## Prevent an error due to 'libcurl4-openssl-dev is not available' | |
| ## (lcolladotor/biocthis) | |
| - name: Install Linux system dependencies | |
| run: | | |
| sysreqs=$(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 covr | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("pkgdown") | |
| 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: Run CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| DISPLAY: 99.0 | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--no-vignettes", "--timings"), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | |
| error_on = "warning", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Reveal testthat details | |
| run: find . -name testthat.Rout -exec cat '{}' ';' | |
| - name: Test coverage | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: Install package for pkgdown | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: R CMD INSTALL . | |
| - name: Build pkgdown site | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {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: Install deploy dependencies | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| run: | | |
| apt-get update && apt-get -y install rsync | |
| - name: Deploy pkgdown site to GitHub pages 🚀 | |
| if: github.ref == 'refs/heads/master' && runner.os == 'Linux' | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-Bioc-RELEASE_3_16-R-${{ matrix.config.bioc }}-results | |
| path: check |