fix error when intron not on same chr as any genes in the txdb (issue… #179
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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-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: 'false' | |
| has_RUnit: 'false' | |
| cache-version: 'cache-v1' | |
| run_docker: 'false' | |
| 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: | |
| # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. | |
| - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | |
| - { os: macOS-latest, r: '4.3', bioc: '3.18'} | |
| - { os: windows-latest, r: '4.3', bioc: '3.18'} | |
| ## Check https://github.com/r-lib/actions/tree/master/examples | |
| ## for examples using the http-user-agent | |
| 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: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Restore R package cache | |
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}- | |
| - 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-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}- | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| 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 macOS system dependencies | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| ## Enable installing XML from source if needed | |
| brew install libxml2 | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| ## Required to install magick as noted at | |
| ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| brew install imagemagick@6 | |
| ## For textshaping, required by ragg, and required by pkgdown | |
| brew install harfbuzz fribidi | |
| ## For installing usethis's dependency gert | |
| brew install libgit2 | |
| ## Required for tcltk | |
| brew install xquartz --cask | |
| - name: Install Windows system dependencies | |
| if: runner.os == 'Windows' | |
| run: | | |
| ## Edit below if you have any Windows system dependencies | |
| shell: Rscript {0} | |
| - name: Init tinytex | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| - name: Install tinytex packages | |
| run: | | |
| system("tlmgr --version") | |
| install.packages("tinytex") | |
| tinytex::tlmgr_install(pkgs = c("bera", "caption", "changepage", "enumitem", "everysel", "fancyhdr", "footmisc", "grfext", "index", "marginfix", "mathtools", | |
| "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring")) | |
| shell: Rscript {0} | |
| - name: Install BiocManager | |
| run: | | |
| message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| - name: Set BiocVersion | |
| run: | | |
| BiocManager::install(version = "${{ 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 dependencies pass 2 | |
| run: | | |
| ## Pass #2 at installing dependencies | |
| ## This pass does not use AnVIL and will thus update any packages | |
| ## that have seen been updated in Bioconductor | |
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | |
| shell: Rscript {0} | |
| - name: Install BiocGenerics | |
| if: env.has_RUnit == 'true' | |
| run: | | |
| ## Install BiocGenerics | |
| BiocManager::install("BiocGenerics") | |
| shell: Rscript {0} | |
| - name: Install covr | |
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | |
| run: | | |
| remotes::install_cran("covr") | |
| shell: Rscript {0} | |
| - name: Install pkgdown | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && 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} | |
| ## Might need an to add this to the if: && runner.os == 'Linux' | |
| - 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: | | |
| BiocGenerics:::testPackage() | |
| shell: Rscript {0} | |
| - name: Run BiocCheck | |
| env: | |
| DISPLAY: 99.0 | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `quit-with-status` = TRUE, | |
| `no-check-R-ver` = TRUE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | |
| run: | | |
| covr::codecov() | |
| shell: Rscript {0} | |
| - name: Install package | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
| run: R CMD INSTALL . | |
| - name: Build pkgdown site | |
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && 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' && env.run_pkgdown == 'true' && 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' && env.run_pkgdown == 'true' && 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: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results | |
| path: check | |
| ## Note that DOCKER_PASSWORD is really a token for your dockerhub | |
| ## account, not your actual dockerhub account password. | |
| ## This comes from | |
| ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo | |
| ## Check https://github.com/docker/build-push-action/tree/releases/v1 | |
| ## for more details. | |
| - uses: docker/build-push-action@v1 | |
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| repository: gagneurlab/fraser | |
| tag_with_ref: true | |
| tag_with_sha: true | |
| tags: latest |