R-CMD-check #682
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| pull_request: | |
| schedule: | |
| - cron: '0 3 * * 4' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}${{ matrix.config.dep }}, ${{ matrix.config.qgis }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macOS-latest, qgis: 'none', r: 'oldrel', dep: '', r-pkg-cache: 'v0'} | |
| - {os: macOS-latest, qgis: 'none', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'none', r: 'oldrel', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'none', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'none', r: 'devel', dep: '', r-pkg-cache: 'v0'} | |
| - {os: ubuntu-22.04, qgis: 'none', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: macOS-latest, qgis: 'macos-brew', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'chocolatey', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'chocolatey-ltr', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: windows-latest, qgis: 'chocolatey', r: 'devel', dep: '', r-pkg-cache: 'v0'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntu-nightly', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntu-nightly', r: 'devel', dep: '', r-pkg-cache: 'v0'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntugis', r: 'release', dep: '', r-pkg-cache: 'v1'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntu', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntu', r: 'release', dep: ' [hard-deps]', r-pkg-cache: 'v3'} | |
| - {os: ubuntu-22.04, qgis: 'ubuntu-ltr', r: 'release', dep: '', r-pkg-cache: 'v0'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| SAGANGV: 0.0.7 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| use-public-rspm: true | |
| extra-repositories: https://geocompr.r-universe.dev | |
| - name: Prepare Ubuntu for installing QGIS (common code) | |
| if: runner.os == 'Linux' && matrix.config.qgis != 'none' | |
| run: | | |
| # Prepare Ubuntu for installing QGIS (common code) | |
| echo "::group::Dynamically set QGIS_PLUGINPATH environment var (available to next steps)" | |
| mkdir ../extra_plugins | |
| echo "QGIS_PLUGINPATH=$(pwd)/../extra_plugins" >> $GITHUB_ENV | |
| echo "::endgroup::" | |
| echo "::group::Install the QGIS Signing Key" | |
| sudo wget -qO /etc/apt/keyrings/qgis-archive-keyring.gpg https://download.qgis.org/downloads/qgis-archive-keyring.gpg | |
| echo "::endgroup::" | |
| - name: Add repo to install QGIS development version for Ubuntu | |
| if: matrix.config.qgis == 'ubuntu-nightly' | |
| run: | | |
| # Add repo to install QGIS development version for Ubuntu (using an often outdated GRASS release from Ubuntu repo) | |
| sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/qgis-archive-keyring.gpg] https://qgis.org/ubuntu-nightly `lsb_release -c -s` main" > /etc/apt/sources.list.d/qgis.list' | |
| - name: Add repos to install upcoming QGIS point release for Ubuntugis (becoming latest release in < 1 month) | |
| if: matrix.config.qgis == 'ubuntugis' | |
| run: | | |
| # Add repos to install upcoming QGIS point release (becoming latest release in < 1 month) for Ubuntugis (ubuntugis-unstable PPA, with current GRASS release) | |
| sudo mkdir -p /root/.gnupg | |
| sudo chmod 700 /root/.gnupg | |
| sudo gpg --no-default-keyring --keyring /etc/apt/keyrings/ubuntugis-unstable-archive-keyring.gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 6B827C12C2D425E227EDCA75089EBE08314DF160 | |
| sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/ubuntugis-unstable-archive-keyring.gpg] http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu `lsb_release -c -s` main" > /etc/apt/sources.list.d/ubuntugis-unstable.list' | |
| sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/qgis-archive-keyring.gpg] https://qgis.org/ubuntugis-nightly-release `lsb_release -c -s` main" > /etc/apt/sources.list.d/qgis.list' | |
| - name: Add repo to install latest QGIS release for Ubuntu | |
| if: matrix.config.qgis == 'ubuntu' | |
| run: | | |
| # Add repo to install latest QGIS release for Ubuntu (using an often outdated GRASS release from Ubuntu repo) | |
| sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/qgis-archive-keyring.gpg] https://qgis.org/ubuntu `lsb_release -c -s` main" > /etc/apt/sources.list.d/qgis.list' | |
| - name: Add repo to install QGIS LTR (long-term release) for Ubuntu | |
| if: matrix.config.qgis == 'ubuntu-ltr' | |
| run: | | |
| # Add repo to install QGIS LTR (long-term release) for Ubuntu (using an often outdated GRASS release from Ubuntu repo) | |
| sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/qgis-archive-keyring.gpg] https://qgis.org/ubuntu-ltr `lsb_release -c -s` main" > /etc/apt/sources.list.d/qgis.list' | |
| - name: Install QGIS, GRASS, SAGA and the SAGA NextGen plugin (Ubuntu) from preset repos | |
| if: runner.os == 'Linux' && matrix.config.qgis != 'none' | |
| run: | | |
| # Install QGIS, GRASS, SAGA and the SAGA NextGen plugin (Ubuntu) from preset repos | |
| sudo apt-get update | |
| sudo apt-get install -y qgis qgis-plugin-grass saga | |
| wget -qO ../sagang_plugin.zip https://plugins.qgis.org/plugins/processing_saga_nextgen/version/$SAGANGV/download/ | |
| unzip -q ../sagang_plugin.zip -d ../extra_plugins | |
| - name: Install QGIS (MacOS homebrew) | |
| if: matrix.config.qgis == 'macos-brew' | |
| run: | | |
| brew install --cask qgis | |
| # installs last nightly build of QGIS | |
| # works locally, hangs on GHA after download | |
| # leaving this out until can figure out how to run reliably | |
| - name: Install QGIS (MacOS nightly) | |
| if: matrix.config.qgis == 'macos-nightly' | |
| run: | | |
| # Setup QGIS from MacOS nightly | |
| curl https://qgis.org/downloads/macos/qgis-macos-nightly.dmg --output qgis-macos-nightly.dmg | |
| yes | hdiutil attach -nobrowse -noverify -mountpoint qgis qgis-macos-nightly.dmg > /dev/null | |
| sudo cp -R qgis/QGIS.app /Applications | |
| - name: Install QGIS (Windows chocolatey) | |
| if: matrix.config.qgis == 'chocolatey' | |
| uses: crazy-max/ghaction-chocolatey@v3 | |
| with: | |
| args: install qgis | |
| - name: Install QGIS LTR (Windows chocolatey) | |
| if: matrix.config.qgis == 'chocolatey-ltr' | |
| uses: crazy-max/ghaction-chocolatey@v3 | |
| with: | |
| args: install qgis-ltr | |
| - name: Query R dependencies and report available versions | |
| id: query | |
| if: matrix.config.dep == '' | |
| run: | | |
| # Query R dependencies and report available versions | |
| cat("::group::Install pak\n") | |
| install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/") | |
| cat("::endgroup::\n") | |
| cat("::group::Create minimal data frame with pkg deps and store them\n") | |
| depends <- rbind( | |
| pak::pkg_deps("deps::.", dependencies = c("Config/Needs/check", "all")), | |
| pak::pkg_deps("any::sessioninfo", dependencies = c("Config/Needs/check", "all")), | |
| pak::pkg_deps("any::rcmdcheck", dependencies = c("Config/Needs/check", "all")), | |
| pak::pkg_deps("any::covr", dependencies = c("Config/Needs/check", "all")), | |
| pak::pkg_deps("any::commonmark", dependencies = c("Config/Needs/check", "all")), | |
| pak::pkg_deps("any::xml2", dependencies = c("Config/Needs/check", "all")) | |
| )[, c("ref", "version")] | |
| depends <- depends[!duplicated(depends), ] | |
| depends <- depends[depends$ref != "deps::.", ] | |
| saveRDS(depends, ".github/depends.Rds") | |
| cat("::endgroup::\n") | |
| cat("::group::Store R-version\n") | |
| cat("r-version=", sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | |
| cat("::endgroup::\n") | |
| cat("::group::Print results\n") | |
| cat("R version:", sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), "\n") | |
| print(as.data.frame(depends), row.names = FALSE) | |
| cat("::endgroup::\n") | |
| shell: Rscript {0} | |
| - name: Restore (or define new) R package cache | |
| if: matrix.config.dep == '' | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.R_LIBS_USER }}/* | |
| !${{ env.R_LIBS_USER }}/pak | |
| key: ${{ matrix.config.os }}-${{ steps.query.outputs.r-version }}-${{ matrix.config.r-pkg-cache }}-${{ hashFiles('.github/depends.Rds') }} | |
| - name: Install missing package dependencies | |
| if: matrix.config.dep == '' | |
| run: | | |
| # Install missing package dependencies | |
| cat("::group::Install\n") | |
| pak::pkg_install(c("deps::.", "any::sessioninfo", "any::rcmdcheck", "any::covr", "any::commonmark", "any::xml2"), upgrade = FALSE, dependencies = c("Config/Needs/check", "all")) | |
| # This is based on the minimum needed version, not the hash of what is available at RSPM | |
| cat("::endgroup::\n") | |
| cat("::group::Session info\n") | |
| sessioninfo::session_info(pkgs = "installed", include_base = TRUE) | |
| cat("::endgroup::\n") | |
| shell: Rscript {0} | |
| # raster, sf, terra and lwgeom from RSPM use older sysdeps than ubuntugis | |
| - name: In the ubuntugis job, reinstall some pkgs from source if needed | |
| if: matrix.config.qgis == 'ubuntugis' | |
| run: | | |
| # Rebuild and install sf, terra etc. if the RSPM binaries (or cached pkgs) don't load | |
| cat("::group::sf\n") | |
| if (!requireNamespace("sf", quietly = TRUE)) { | |
| install.packages("sf", repos = "https://cloud.r-project.org") | |
| } | |
| cat("::endgroup::\n") | |
| cat("::group::terra\n") | |
| if (!requireNamespace("terra", quietly = TRUE)) { | |
| install.packages("terra", repos = "https://cloud.r-project.org") | |
| } | |
| cat("::endgroup::\n") | |
| cat("::group::raster\n") | |
| if (!requireNamespace("raster", quietly = TRUE)) { | |
| install.packages("raster", repos = "https://cloud.r-project.org") | |
| } | |
| cat("::endgroup::\n") | |
| cat("::group::lwgeom (needed by stars)\n") | |
| if (!requireNamespace("lwgeom", quietly = TRUE)) { # needed for stars | |
| install.packages("lwgeom", repos = "https://cloud.r-project.org") | |
| } | |
| cat("::endgroup::\n") | |
| cat("::group::Session info\n") | |
| sessioninfo::session_info(pkgs = "installed", include_base = TRUE) | |
| cat("::endgroup::\n") | |
| shell: Rscript {0} | |
| - name: Install hard R pkg dependencies only | |
| if: matrix.config.dep == ' [hard-deps]' | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' | |
| cache: false | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::testthat | |
| any::knitr | |
| any::rmarkdown | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| # run with CMD check because installing QGIS is expensive | |
| - name: Test Coverage | |
| if: matrix.config.qgis == 'ubuntu' && matrix.config.dep == '' | |
| run: | | |
| # Setup code coverage with Codecov | |
| covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Show platform-info output | |
| if: always() | |
| run: find check -name 'platform-info.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.config.os }}_r-${{ matrix.config.r }}_qgis-${{ matrix.config.qgis }}_results | |
| path: check |