R-CMD-check #687
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |