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ci-tests.yml
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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 * *'
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: 11
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: ${{ matrix.config.java }}
extra-packages: |
any::covr
any::rcmdcheck
any::remotes
- name: Install tinytex
if: matrix.config.vignettes
uses: r-lib/actions/setup-tinytex@v2
- name: Install extra Tex packages
if: matrix.config.vignettes
run: |
pak::pkg_install('tinytex')
library(tinytex)
tlmgr_install('datetime')
tlmgr_install('inputenc')
tlmgr_install('hyperref')
tlmgr_install('url')
tlmgr_install('fmtcount')
tinytex:::install_yihui_pkgs()
shell: Rscript {0}
- name: Install PDF system dependencies
if: runner.os == 'Linux' && matrix.config.vignettes
run: |
sudo apt-get install -y qpdf ghostscript tidy
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessionInfo()
shell: Rscript {0}
- name: set TZ for tests / check
run: echo 'TZ=${{ matrix.config.timezone-name }}' >> $GITHUB_ENV
- uses: 'szenius/[email protected]'
if: matrix.config.os-name == 'ubuntu'
with:
timezoneLinux: ${{ matrix.config.timezone-name }}
- uses: 'szenius/[email protected]'
if: matrix.config.os-name == 'macos'
with:
timezoneMacos: ${{ matrix.config.timezone-name }}
- uses: 'szenius/[email protected]'
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: 1
- 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 tests/XLConnect_Unit_Tests.txt || true
git clean -fd "*xls*"
grep -i "0 errors, 0 failures" tests/XLConnect_Unit_Tests.txt
shell: bash
- 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: |
tests/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: feature/...
- 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"|\
xargs -l sha512sum | sort | awk '{print $1}' > effective_hashes
find /home/runner/work/xlconnect/xlconnect/target/dependency/ -maxdepth 1 -type f -name "*.jar"|\
grep -v -E "poi-ooxml-lite|junit|hamcrest" |\
xargs -l sha512sum | sort | awk '{print $1}' > expected_hashes
cmp expected_hashes effective_hashes ||\
(echo "JARs are different!" && ls -la /home/runner/work/xlconnect/xlconnect/target/dependency/ &&\
ls -la "$XLC_JAR_PATH" &&\
exit 1)