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|---|---|---|
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@@ -34,12 +34,12 @@ name: R-CMD-check-bioc | |
| ## 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' | ||
| has_testthat: 'false' | ||
| run_covr: 'false' | ||
| run_pkgdown: 'false' | ||
| has_RUnit: 'false' | ||
| has_BiocCheck: 'false' | ||
| cache-version: 'cache-v1' | ||
| run_docker: 'false' | ||
|
|
||
| jobs: | ||
| build-check: | ||
|
|
@@ -52,15 +52,16 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
| - { os: macOS-latest, r: '4.4', bioc: '3.20'} ## was r: 'devel' | ||
| - { os: windows-latest, r: '4.4', bioc: '3.20'} ## was r: 'devel' | ||
| - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | ||
| - { os: macOS-latest, r: '4.4', bioc: '3.20'} | ||
| - { os: windows-latest, r: '4.4', bioc: '3.20'} | ||
| ## 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 | ||
| VDIFFR_RUN_TESTS: false | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
|
|
@@ -73,77 +74,75 @@ jobs: | |
| 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/v2-branch/examples/check-standard.yaml | ||
| ## 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@v2 | ||
| 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-branch | ||
| 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-branch | ||
| 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: Cache R packages | ||
| - name: Restore R package cache | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4- | ||
|
|
||
| - name: Cache R packages on Linux | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /home/runner/work/_temp/Library | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.4- | ||
|
|
||
| # - 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 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" >> $GITHUB_ENV | ||
| ## Required to install magick as noted at | ||
| ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | ||
| brew install imagemagick@6 | ||
| ## For textshaping, required by ragg, and required by pkgdown | ||
| brew install harfbuzz fribidi | ||
| ## For installing usethis's dependency gert | ||
| brew install libgit2 | ||
| ## Helps compile RCurl from source | ||
| ## brew uninstall curl | ||
| ## required for ncdf4 - can not use the homebrew one because that uses GCC | ||
| ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/ | ||
| curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz | ||
| tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C / | ||
| rm netcdf-4.7.4-darwin.17-x86_64.tar.gz | ||
| curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz | ||
| tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C / | ||
| rm hdf5-1.12.0-darwin.17-x86_64.tar.gz | ||
| curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz | ||
| tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C / | ||
| rm szip-2.1.1-darwin.17-x86_64.tar.gz | ||
| ## Required for tcltk | ||
| brew install xquartz --cask | ||
| - name: Install Windows system dependencies | ||
| if: runner.os == 'Windows' | ||
| run: | | ||
|
|
@@ -158,32 +157,40 @@ jobs: | |
|
|
||
| - name: Set BiocVersion | ||
| run: | | ||
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | ||
| BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install dependencies | ||
| - 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. | ||
| ## Manually install required packages | ||
| BiocManager::install("BiocStyle", ask = FALSE, update = TRUE, force = TRUE) | ||
| BiocManager::install("rmarkdown", ask = FALSE, update = TRUE, force = TRUE) | ||
| BiocManager::install("Spectra", ask = FALSE, update = FALSE, force = TRUE) | ||
| BiocManager::install("MsCoreUtils", ask = FALSE, update = FALSE, force = TRUE) | ||
| ## For running the checks | ||
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
| install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | ||
| ## Pass #1 at installing dependencies | ||
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | ||
| continue-on-error: true | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install dependencies pass 2 | ||
| run: | | ||
| ## Pass #2 at installing dependencies | ||
| 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) | ||
| ## For running the checks | ||
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
| remotes::install_cran("rcmdcheck") | ||
| BiocManager::install("BiocCheck") | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install BiocGenerics | ||
|
|
@@ -194,13 +201,13 @@ jobs: | |
| shell: Rscript {0} | ||
|
|
||
| - name: Install covr | ||
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && 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' | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| remotes::install_github("r-lib/pkgdown") | ||
| shell: Rscript {0} | ||
|
|
@@ -215,10 +222,12 @@ jobs: | |
| - name: Run CMD check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_: false | ||
| DISPLAY: 99.0 | ||
| run: | | ||
| options(crayon.enabled = TRUE) | ||
| rcmdcheck::rcmdcheck( | ||
| args = c("--no-build-vignettes", "--no-manual", "--timings"), | ||
| build_args = c("--no-manual", "--no-resave-data"), | ||
| args = c("--no-manual", "--no-vignettes", "--timings"), | ||
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | ||
| error_on = "warning", | ||
| check_dir = "check" | ||
| ) | ||
|
|
@@ -236,7 +245,8 @@ jobs: | |
| shell: Rscript {0} | ||
|
|
||
| - name: Run BiocCheck | ||
| if: env.has_BiocCheck == 'true' | ||
| env: | ||
| DISPLAY: 99.0 | ||
| run: | | ||
| BiocCheck::BiocCheck( | ||
| dir('check', 'tar.gz$', full.names = TRUE), | ||
|
|
@@ -247,31 +257,89 @@ jobs: | |
| shell: Rscript {0} | ||
|
|
||
| - name: Test coverage | ||
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| covr::codecov() | ||
| covr::codecov(coverage = covr::package_coverage(type = "all")) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install package | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: R CMD INSTALL . | ||
|
|
||
| - name: Deploy package | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| git config --global --add safe.directory /__w/MetCirc/MetCirc | ||
| git config --local user.email "[email protected]" | ||
| git config --local user.name "GitHub Actions" | ||
| Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
| shell: bash {0} | ||
| - name: Build pkgdown site | ||
| if: github.ref == 'refs/heads/devel' && 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/devel' && 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/devel' && 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-devel-r-devel-results | ||
| name: ${{ runner.os }}-biocversion-devel-r-4.4-results | ||
| path: check | ||
|
|
||
|
|
||
| ## Code adapted from | ||
| ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 | ||
| docker-build-and-push: | ||
| runs-on: ubuntu-latest | ||
| needs: build-check | ||
| steps: | ||
| - name: Checkout Repository | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Register repo name | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| id: reg_repo_name | ||
| run: | | ||
| echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | ||
| - name: Set up QEMU | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/setup-qemu-action@v2 | ||
|
|
||
| - name: Set up Docker Buildx | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/setup-buildx-action@v2 | ||
|
|
||
| - name: Login to Docker Hub | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
| ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub | ||
| ## account, not your actual dockerhub account password. You can get it | ||
| ## from https://hub.docker.com/settings/security. | ||
| ## Check https://github.com/docker/build-push-action/tree/v4.0.0 | ||
| ## for more details. | ||
| ## Alternatively, try checking | ||
| ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html. | ||
|
|
||
| - name: Build and Push Docker | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()" | ||
| uses: docker/build-push-action@v4 | ||
| with: | ||
| context: . | ||
| push: true | ||
| tags: > | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel | ||