Feature/#37 doc review #643
Workflow file for this run
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| # See https://github.com/r-lib/actions/tree/v2/examples#readme for | |
| # additional example workflows available for the R community. | |
| name: ci-tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| schedule: | |
| - cron: '12 23 13,28 * *' | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.config.os-name }}-${{ matrix.config.os-version }} | |
| name: >- | |
| ${{ matrix.config.os-name }}-${{ matrix.config.os-version }} | |
| R ${{ matrix.config.r-version}} - java ${{ matrix.config.java}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - os-name: ubuntu # windows-2019, macos-10.15] | |
| os-version: latest | |
| r-version: oldrel | |
| java: 17 #8 | |
| vignettes: true | |
| timezone-name: Europe/Zurich | |
| - os-name: ubuntu # windows-2019, macos-10.15] | |
| os-version: latest | |
| r-version: release | |
| java: 21 | |
| vignettes: true | |
| timezone-name: Asia/Kathmandu | |
| - os-name: ubuntu # windows-2019, macos-10.15] | |
| os-version: "20.04" | |
| r-version: devel | |
| java: 17 | |
| vignettes: true | |
| timezone-name: Pacific/Marquesas | |
| - os-name: macos # TODO fix java / R interaction | |
| os-version: latest | |
| r-version: release | |
| # java: 13 | |
| vignettes: false | |
| - os-name: windows # windows-2019, macos-10.15] | |
| os-version: "2019" | |
| r-version: release | |
| java: 8 | |
| vignettes: false | |
| timezone-name: "W. Europe Standard Time" | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| XLCONNECT_JAVA_REPO_URL: ${{ matrix.config.xlc-repo }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup java (x64) | |
| uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'zulu' | |
| java-version: ${{ matrix.config.java }} | |
| java-package: jdk | |
| architecture: x64 | |
| if: matrix.config.os-name != 'macos' && matrix.config.java != 11 | |
| - name: Set up R ${{ matrix.config.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r-version }} | |
| use-public-rspm: true | |
| - name: print effective R version | |
| run: version | |
| shell: Rscript {0} | |
| - name: test additional java env var | |
| if: ${{!matrix.config.vignettes}} # covering with / without the var being present | |
| run: echo 'JAVA_TOOL_OPTIONS="-Dlog4j.formatMsgNoLookups=true"' >> $GITHUB_ENV | |
| # todo not sure if this is run again during "Install and cache dependencies" before rJava install | |
| - name: run javareconf # Yes it actually needs JAVA_HOME=$JAVA_HOME, doesn't use actual env vars (!) | |
| if: runner.os != 'Windows' && matrix.config.java != 11 | |
| run: | | |
| java -version | |
| echo java_home:$JAVA_HOME | |
| echo library paths: $LD_LIBRARY_PATH | |
| sudo R CMD javareconf JAVA_HOME=$JAVA_HOME | |
| - name: effective java version # Yes it actually needs JAVA_HOME=$JAVA_HOME, doesn't use actual env vars (!) | |
| if: runner.os == 'Windows' | |
| run: java -version | |
| - name: Install and cache dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: ${{ matrix.config.java }} | |
| extra-packages: | | |
| any::covr | |
| any::rcmdcheck | |
| any::remotes | |
| - name: Install tinytex | |
| if: matrix.config.vignettes | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| - name: Install extra Tex packages | |
| if: matrix.config.vignettes | |
| run: | | |
| pak::pkg_install('tinytex') | |
| library(tinytex) | |
| tlmgr_update(self=TRUE, all=FALSE) | |
| tlmgr_install('datetime') | |
| tlmgr_install('hyperref') | |
| tlmgr_install('url') | |
| tlmgr_install('fmtcount') | |
| tinytex:::install_yihui_pkgs() | |
| shell: Rscript {0} | |
| - name: Install PDF system dependencies | |
| if: runner.os == 'Linux' && matrix.config.vignettes | |
| run: | | |
| sudo apt-get install -y qpdf ghostscript tidy | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessionInfo() | |
| shell: Rscript {0} | |
| - name: set TZ for tests / check | |
| run: echo 'TZ=${{ matrix.config.timezone-name }}' >> $GITHUB_ENV | |
| - uses: 'szenius/set-timezone@v2.0' | |
| if: matrix.config.os-name == 'ubuntu' | |
| with: | |
| timezoneLinux: ${{ matrix.config.timezone-name }} | |
| - uses: 'szenius/set-timezone@v2.0' | |
| if: matrix.config.os-name == 'macos' | |
| with: | |
| timezoneMacos: ${{ matrix.config.timezone-name }} | |
| - uses: 'szenius/set-timezone@v2.0' | |
| if: matrix.config.os-name == 'windows' | |
| with: | |
| timezoneWindows: ${{ matrix.config.timezone-name }} | |
| - name: Check without doc | |
| if: ${{!matrix.config.vignettes}} | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--no-vignettes", "--no-build-vignettes", "--check-subdirs=no", | |
| "--no-multiarch"["${{matrix.config.os-name}}" == "windows"])' | |
| build_args: 'c("--no-build-vignettes")' | |
| error-on: '"error"' | |
| env: | |
| FULL_TEST_SUITE: 1 | |
| - name: Check with doc | |
| if: matrix.config.vignettes | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--as-cran")' | |
| build_args: 'c("--compact-vignettes=gs+qpdf")' | |
| env: | |
| FULL_TEST_SUITE: 0 | |
| - name: run complete test suite # some tests are not run in r check, as test xls(x) files are Rbuild-ignored | |
| if: always() | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| FULL_TEST_SUITE: 1 | |
| RCMDCHECK: "FALSE" | |
| run: | | |
| install_opts = if("${{matrix.config.os-name}}" == "windows") { | |
| c("--no-multiarch") | |
| } else { | |
| c() | |
| } | |
| install.packages(list.files("./check", pattern = "XLConnect_.*.tar.gz", full.names = TRUE), repos=NULL, type="source", INSTALL_opts=install_opts) | |
| setwd("tests") | |
| source("run_tests.R") | |
| shell: Rscript {0} | |
| - name: Show test output | |
| if: always() | |
| run: | | |
| echo $(date) | |
| cat inst/unitTests/resources/XLConnect_Unit_Tests.txt || true | |
| git clean -fd "*xls*" | |
| grep -i "0 errors, 0 failures" inst/unitTests/resources/XLConnect_Unit_Tests.txt | |
| shell: bash | |
| continue-on-error: true | |
| - name: coverage report | |
| if: success() && matrix.config.r-version == 'release' && matrix.config.os-name == 'ubuntu' | |
| run: | | |
| library(covr) | |
| covr::codecov(function_exclusions=c("onLoad", "onAttach", "xlcEnsureDependencies", "checkSystemPackage")) | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ matrix.config.os-name }}${{matrix.config.os-version}}-java${{ matrix.config.java }}-R${{ matrix.config.r-version }}-results | |
| path: | | |
| inst/unitTests/resources/XLConnect_Unit_Tests.* | |
| check/XLConnect.Rcheck/ | |
| !check/XLConnect.Rcheck/**/*.jar | |
| !check/XLConnect.Rcheck/00_pkg_src/ | |
| - name: Upload successfully built package | |
| if: success() && matrix.config.vignettes | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ matrix.config.os-name }}${{matrix.config.os-version}}-java${{ matrix.config.java }}-R${{ matrix.config.r-version }}-results | |
| path: | | |
| check/XLConnect_*.tar.gz | |
| - name: checkout XLConnect java | |
| if: success() && matrix.config.r-version == 'release' && matrix.config.os-name == 'ubuntu' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: miraisolutions/xlconnect-java | |
| # specify the below if you are working on a parallel xlconnect-java branch | |
| # ref: dependabot/maven/poi-707d71ec25 | |
| - name: retrieve POM dependencies using maven | |
| if: success() && matrix.config.r-version == 'release' && matrix.config.os-name == 'ubuntu' | |
| run: | | |
| ls -la | |
| mvn dependency:copy-dependencies | |
| - name: compare JAR hashes | |
| if: success() && matrix.config.r-version == 'release' && matrix.config.os-name == 'ubuntu' | |
| run: | | |
| set -eux -o pipefail | |
| XLC_JAR_PATH=$(Rscript -e "cat(.libPaths()[1])")/XLConnect/java | |
| rm -f "$XLC_JAR_PATH"/XLConnect* | |
| find "$XLC_JAR_PATH" -maxdepth 1 -type f -name "*.jar" -exec sha512sum {} + |\ | |
| sort | awk '{print $1}' > effective_hashes | |
| find "$GITHUB_WORKSPACE"/target/dependency/ -maxdepth 1 -type f -name "*.jar" -exec sha512sum {} + |\ | |
| grep -v -E "poi-ooxml-lite|junit|hamcrest" |\ | |
| sort | awk '{print $1}' > expected_hashes | |
| cmp expected_hashes effective_hashes ||\ | |
| (echo "JARs are different!" && ls -la "$GITHUB_WORKSPACE"/target/dependency/ &&\ | |
| ls -la "$XLC_JAR_PATH" &&\ | |
| exit 1) |