analytical estimation functions #271
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| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| # We include 'next' in order to always test the latest patched release, but mac and Windows binaries are not deployed to the drat repo: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # for windows and mac all builds are pushed to drat repo on merge to master (except pre-release builds), except 'next' | |
| # 2023-08-23 fails, not getting Reca. Because it is not built yet for macos and next or 4.3. | |
| #- {os: macOS-latest, r: 'next', pkgext: '.tgz'} | |
| #- {os: macOS-latest, r: '4.3', pkgext: '.tgz'} | |
| - {os: macOS-latest, r: '4.2', pkgext: '.tgz'} | |
| - {os: macOS-latest, r: '4.1', pkgext: '.tgz'} | |
| - {os: macOS-latest, r: '4.0', pkgext: '.tgz'} | |
| # 2023-08-23 fails, not getting Reca. Because it is not built yet for windows and next or 4.3. | |
| - {os: windows-latest, r: 'next', pkgext: '.zip'} | |
| - {os: windows-latest, r: '4.3', pkgext: '.zip'} | |
| - {os: windows-latest, r: '4.2', pkgext: '.zip'} | |
| - {os: windows-latest, r: '4.1', pkgext: '.zip'} | |
| - {os: windows-latest, r: '4.0', pkgext: '.zip', rspm: "https://cloud.r-project.org"} | |
| - {os: ubuntu-latest, r: 'next', 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"} | |
| # 4.1 is pushed to drat repo on merge to master for ubunutu (except pre-release builds), update script if 4.1 is taken out | |
| - {os: ubuntu-20.04, r: '4.1', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} | |
| - {os: ubuntu-20.04, r: '4.0', pkgext: '.tar.gz', rspm: "https://cloud.r-project.org"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Do autorelease increment, tagging, and environment setup | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| run: | | |
| curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/checktag-actions.sh" --output testingRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/testingRepo/main/scripts/deploy-actions.sh" --output testingRepo_deploy.sh | |
| chmod +x ./testingRepo_checktag.sh ./testingRepo_deploy.sh | |
| . testingRepo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/repo/master/scripts/checktag-actions.sh" --output repo_checktag.sh | |
| curl "https://raw.githubusercontent.com/StoXProject/repo/master/scripts/deploy-actions.sh" --output repo_deploy.sh | |
| chmod +x ./repo_checktag.sh ./repo_deploy.sh | |
| . repo_checktag.sh | |
| echo "PRERELEASE=${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 }} | |
| rtools-version: ${{ matrix.config.rtools }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| - name: Anticipate Bintray shutdown | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew update | |
| shell: bash | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| writeLines(sprintf("R-%i.%i", getRversion()$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: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| while read -r cmd | |
| do | |
| eval sudo $cmd | |
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | |
| - name: Install MacOS dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| rm -f '/usr/local/bin/gfortran' | |
| rm -f '/usr/local/bin/2to3' | |
| rm -f '/usr/local/bin/2to3-3.11' | |
| rm -f '/usr/local/bin/idle3' | |
| rm -f '/usr/local/bin/idle3.11' | |
| rm -f '/usr/local/bin/pydoc3' | |
| rm -f '/usr/local/bin/pydoc3.11' | |
| rm -f '/usr/local/bin/python3' | |
| rm -f '/usr/local/bin/python3.11' | |
| rm -f '/usr/local/bin/python3-config' | |
| rm -f '/usr/local/bin/python3.11-config' | |
| export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=false # This prevents Homebrew from re-installing R, which will lead to .Platform$pkgType = "source". | |
| brew install gdal | |
| shell: bash | |
| - name: Prepare for dependencies on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install libgdal-dev libproj-dev libgeos-dev libudunits2-dev | |
| shell: bash | |
| - name: Install dependencies on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| - name: Install dependencies on Windows and macOS | |
| if: runner.os != 'Linux' | |
| run: | | |
| # First try binary and then possibly source: | |
| options(install.packages.check.source = "no") | |
| remotes::install_deps(dependencies = TRUE, type = "binary") | |
| installed <- utils::installed.packages()[, "Package"] | |
| needed <- remotes::dev_package_deps() | |
| missing <- setdiff(needed$package, installed) | |
| if(length(missing)) { | |
| message("Installing the following packages using default type:\n", paste0(missing, collapse = ", ")) | |
| utils::install.packages(missing, dependencies = TRUE) | |
| } | |
| shell: Rscript {0} | |
| - name: Install CRANdependencies | |
| run: | | |
| remotes::install_cran("rcmdcheck") | |
| #remotes::install_cran("git2r") | |
| remotes::install_cran("drat") | |
| remotes::install_cran("sessioninfo") | |
| 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-manual", "--as-cran"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: check | |
| - name: Build package source archive | |
| if: runner.os == 'Linux' && matrix.config.r == '4.1' && github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| 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 | |
| if: (runner.os == 'Windows' || runner.os == 'macOS') && github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| run: | | |
| pkgbuild::build(".", dest_path = ".", binary = TRUE) | |
| file.copy(Sys.getenv("PKG_FILE"), Sys.getenv("PKG_FREL")) | |
| shell: Rscript {0} | |
| # Upload to drat repo only for one version (4.1) on Linux, and only for all the specifically given R versions for macOS and Windows (not next). Next is included to detect errors immediatelly when the new R is patched: | |
| - name: Upload to DRAT repo | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| env: | |
| BUILD_NUMBER: ${{ github.sha }} | |
| DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }} | |
| run: . repo_deploy.sh | |
| shell: bash | |
| - name: Upload to DRAT testingRepo | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| env: | |
| BUILD_NUMBER: ${{ github.sha }} | |
| DRAT_DEPLOY_TOKEN: ${{ secrets.DRAT_DEPLOY_TOKEN }} | |
| run: . testingRepo_deploy.sh | |
| shell: bash | |
| - name: Create release and upload files | |
| if: ( (runner.os == 'Windows' && matrix.config.r != 'next') || (runner.os == 'macOS' && matrix.config.r != 'next') || (runner.os == 'Linux' && matrix.config.r == '4.1') ) && github.event_name == 'push' && github.ref == 'refs/heads/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 }} |