Develop #680
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| on: | |
| push: | |
| branches: | |
| - master | |
| - testing | |
| - develop | |
| pull_request: | |
| branches: | |
| - master | |
| - testing | |
| - develop | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| # 0. Define the systems to run on: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # Latest macOS will use the big-sur-arm64 folder when deploying to the drat repo: | |
| - {os: macOS-latest, r: 'release', pkgext: '.tgz'} | |
| - {os: macOS-latest, r: '4.3', pkgext: '.tgz'} | |
| # macOS-13 will use the big-sur-x86_64 folder when deploying to the drat repo: | |
| - {os: macOS-13, r: 'release', pkgext: '.tgz'} | |
| - {os: macOS-13, r: '4.3', pkgext: '.tgz'} | |
| - {os: windows-latest, r: 'release', pkgext: '.zip'} | |
| - {os: windows-latest, r: '4.3', pkgext: '.zip'} | |
| - {os: ubuntu-latest, r: 'release', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} | |
| - {os: ubuntu-22.04, r: '4.3', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} | |
| - {os: ubuntu-22.04, r: '4.2', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| ################### | |
| #### 1. Setup: #### | |
| ################### | |
| - uses: actions/checkout@v3 | |
| - name: Prepare for deployment at push | |
| if: github.event_name == 'push' | |
| run: | | |
| curl "https://raw.githubusercontent.com/StoXProject/unstableRepo/main/scripts/checktag-actions.sh" --output unstableRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/unstableRepo/main/scripts/deploy-actions.sh" --output unstableRepo_deploy.sh | |
| chmod +x ./unstableRepo_checktag.sh ./unstableRepo_deploy.sh | |
| . unstableRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/checktag-actions.sh" --output testingRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/deploy-actions.sh" --output testingRepo_deploy.sh | |
| chmod +x ./testingRepo_checktag.sh ./testingRepo_deploy.sh | |
| . testingRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/repo/master/scripts/checktag-actions.sh" --output repo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/repo/master/scripts/deploy-actions.sh" --output repo_deploy.sh | |
| chmod +x ./repo_checktag.sh ./repo_deploy.sh | |
| . repo_checktag.sh | |
| echo "PRERELEASE=${PRERELEASE}" >> $GITHUB_ENV | |
| echo "FINAL_TAG=${FINAL_TAG}" >> $GITHUB_ENV | |
| echo "PKG_FILE_PREFIX=${PKG_FILE_PREFIX}" >> $GITHUB_ENV | |
| echo "PKG_FILE=${PKG_FILE_PREFIX}${{ matrix.config.pkgext }}" >> $GITHUB_ENV | |
| echo "PKG_FREL=${PKG_FILE_PREFIX}-R.${{ matrix.config.r }}-${{ runner.os }}${{ matrix.config.pkgext }}" >> $GITHUB_ENV | |
| echo "PKG_REPO=${GITHUB_WORKSPACE}" >> $GITHUB_ENV | |
| shell: bash | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| ############################################################################# | |
| #### 2. R package installation (with system and R package dependencies): #### | |
| ############################################################################# | |
| ## 2a. Cache R packages: | |
| #- name: Query R package dependencies | |
| # run: | | |
| # install.packages('remotes') | |
| # saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) | |
| # writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | |
| # shell: Rscript {0} | |
| #- name: Cache R packages | |
| # if: runner.os != 'Windows' | |
| # uses: actions/cache@v3 | |
| # with: | |
| # path: ${{ env.R_LIBS_USER }} | |
| # key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }} | |
| # restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r-${{ matrix.config.r }}- | |
| ## 2b. System dependencies: | |
| - name: Install system dependencies on macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| # gfortran may not exist in a period after a new R minor release: | |
| gfortranFile='/usr/local/bin/gfortran' | |
| if [ -f "$gfortranFile" ] ; then | |
| rm "$gfortranFile" | |
| fi | |
| rm '/usr/local/bin/2to3' | |
| rm '/usr/local/bin/2to3-3.11' | |
| rm '/usr/local/bin/idle3.11' | |
| rm '/usr/local/bin/idle3' | |
| rm '/usr/local/bin/pydoc3' | |
| rm '/usr/local/bin/python3' | |
| rm '/usr/local/bin/python3-config' | |
| rm '/usr/local/bin/pydoc3.11' | |
| rm '/usr/local/bin/python3.11' | |
| rm '/usr/local/bin/python3.11-config' | |
| export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source". | |
| brew install gdal udunits | |
| shell: bash | |
| - name: Install system dependencies on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Prepare for CRANdependencies on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| sudo apt-get install -y libudunits2-dev | |
| shell: bash | |
| ## 2c. R packages needed for this yaml script (not related to the Rstox package itself): | |
| - name: Install CRANdependencies | |
| run: | | |
| install.packages(c("rcmdcheck", "git2r", "sessioninfo", "knitr", "remotes")) | |
| # Using the latest drat that supports big sur (after inputs from us). | |
| # When the next drat appears on CRAN this can be changed to install from CRAN: | |
| remotes::install_github(repo = 'eddelbuettel/drat', dependencies = FALSE) | |
| shell: Rscript {0} | |
| ## 2d. Install dependencies: | |
| - name: Install R package dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE, repos = "https://cloud.r-project.org/") | |
| shell: Rscript {0} | |
| ## 2e. Session info: | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| ## 2f. Additional installs to secure specific versions to patch incompatibilities with older R versions: | |
| - name: Additional installs to secure specific versions | |
| run: | | |
| pkgs <- installed.packages()[, "Package"] | |
| s <- sessioninfo::session_info(pkgs, include_base = TRUE) | |
| onlyStringi <- subset(s$packages, package == "stringi") | |
| if("stringi" %in% as.data.frame(s$packages)$package && is.na(subset(s$packages, package == "stringi")$ondiskversion)) { | |
| remotes::install_github("gagolews/stringi") | |
| } | |
| shell: Rscript {0} | |
| ##################################### | |
| #### 3. Check the Rstox package: #### | |
| ##################################### | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| ####################################################### | |
| #### 4. Build the package source and binary files: #### | |
| ####################################################### | |
| - name: Build package source archive from branches develop, testing and master (on Linux for some reason) | |
| if: runner.os == 'Linux' && matrix.config.r == 'release' && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop') | |
| run: | | |
| pkgbuild::build(".", dest_path = ".", binary = FALSE) | |
| system(paste0("PKG_FREL=", Sys.getenv("PKG_FILE"), " >> ", Sys.getenv("GITHUB_ENV"))) | |
| shell: Rscript {0} | |
| - name: Build package binary archive from branches develop, testing and master for Windows and macOS (this builds also on matrix.config.r = release, which can or can not be a duplicate) | |
| if: (runner.os == 'Windows' || runner.os == 'macOS') && github.event_name == 'push' && (github.ref_name == 'master' || github.ref_name == 'testing' || github.ref_name == 'develop') | |
| run: | | |
| pkgbuild::build(".", dest_path = ".", binary = TRUE) | |
| print("PKG_FILE") | |
| print(Sys.getenv("PKG_FILE")) | |
| print("PKG_FREL") | |
| print(Sys.getenv("PKG_FREL")) | |
| file.copy(Sys.getenv("PKG_FILE"), Sys.getenv("PKG_FREL")) | |
| shell: Rscript {0} | |
| ###################################### | |
| #### 5. Deploy to the drat repos: #### | |
| ###################################### | |
| ## 5a. Upload to the official (DRAT) repo, but only from the master branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config: | |
| - name: Upload to the official (DRAT) repo | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'release') || (runner.os == 'macOS' && matrix.config.r != 'release') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'master' | |
| env: | |
| BUILD_NUMBER: ${{ github.sha }} | |
| DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }} | |
| run: . repo_deploy.sh | |
| shell: bash | |
| ## 5b. Upload to the (DRAT) testingRepo, but only from the testing branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config: | |
| - name: Upload to the testing (DRAT) repo | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'release') || (runner.os == 'macOS' && matrix.config.r != 'release') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'testing' | |
| env: | |
| BUILD_NUMBER: ${{ github.sha }} | |
| DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }} | |
| run: . testingRepo_deploy.sh | |
| shell: bash | |
| ## 5c. Upload to the (DRAT) unstableRepo, but only from the develop branch. Here we skip the matrix.config.r = release, as a new StoX release should be ready shortly after each R minor release and listed specifically in the matrix.config: | |
| - name: Upload to the unstable (DRAT) repo | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'release') || (runner.os == 'macOS' && matrix.config.r != 'release') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'develop' | |
| env: | |
| BUILD_NUMBER: ${{ github.sha }} | |
| DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }} | |
| run: . unstableRepo_deploy.sh | |
| shell: bash | |
| ############################### | |
| #### 6. Release on GitHub: #### | |
| ############################### | |
| - name: Create release on GitHub and upload files for testing branch | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'release') || (runner.os == 'macOS' && matrix.config.r != 'release') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'testing' | |
| uses: ncipollo/release-action@v1 | |
| with: | |
| allowUpdates: true | |
| commit: testing | |
| tag: ${{ env.FINAL_TAG }} | |
| name: ${{ env.FINAL_TAG }} | |
| artifacts: ${{ env.PKG_REPO }}/${{ env.PKG_FREL }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Create release on GitHub and upload files for master branch | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'release') || (runner.os == 'macOS' && matrix.config.r != 'release') || (runner.os == 'Linux' && matrix.config.r == 'release') ) && github.event_name == 'push' && github.ref_name == 'master' | |
| uses: ncipollo/release-action@v1 | |
| with: | |
| allowUpdates: true | |
| commit: master | |
| tag: ${{ env.FINAL_TAG }} | |
| name: ${{ env.FINAL_TAG }} | |
| artifacts: ${{ env.PKG_REPO }}/${{ env.PKG_FREL }} | |
| token: ${{ secrets.GITHUB_TOKEN }} |