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appveyor.yml
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appveyor.yml
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# DO NOT CHANGE the "init" and "install" sections below
# Download script file from GitHub
init:
- ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest https://raw.githubusercontent.com/rickhelmus/r-appveyor/rtools43/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
Import-Module '..\appveyor-tool.ps1'
install:
- ps: Bootstrap
#- ps: $blockRdp = $true; iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/appveyor/ci/master/scripts/enable-rdp.ps1'))
# - ps: mkdir -Force c:\deps
# - ps: >-
# if (-Not (Test-Path C:\deps\biotransformer)) {
# git clone --depth 1 -q https://bitbucket.org/djoumbou/biotransformer.git C:/deps/biotransformer
# pushd C:\deps\biotransformer
# Invoke-WebRequest https://github.com/rickhelmus/patRoonDeps/raw/master/ext/biotransformer-3.0.0.jar -OutFile "biotransformer-3.0.0.jar"
# popd
# }
# - ps: >-
# if (-Not (Test-Path C:\deps\openms27.exe)) {
# Invoke-WebRequest https://github.com/OpenMS/OpenMS/releases/download/Release2.7.0/OpenMS-2.7.0-Win64.exe -OutFile "C:\deps\openms27.exe"
# }
# C:\deps\openms27.exe /S
# - ps: >-
# if (-Not (Test-Path C:\deps\MetFragCommandLine-2.5.0.jar)) {
# Invoke-WebRequest https://github.com/ipb-halle/MetFragRelaunched/releases/download/v.2.5.0/MetFragCommandLine-2.5.0.jar -OutFile "C:\deps\MetFragCommandLine-2.5.0.jar"
# }
# - ps: >-
# if (-Not (Test-Path C:\deps\sirius-5.6.3.zip)) {
# Invoke-WebRequest https://github.com/boecker-lab/sirius/releases/download/v5.6.3/sirius-5.6.3-win64-headless.zip -OutFile "C:\deps\sirius-5.6.3.zip"
# if (Test-Path c:\deps\sirius)
# {
# rm -r -fo c:\deps\sirius
# }
# 7z x -aoa -oC:\deps\ C:\deps\sirius-5.6.3.zip
# }
# - ps: >-
# if (-Not (Test-Path C:\deps\openbabel311.exe)) {
# Invoke-WebRequest https://github.com/openbabel/openbabel/releases/download/openbabel-3-1-1/OpenBabel-3.1.1-x64.exe -OutFile "C:\deps\openbabel311.exe"
# }
# C:\deps\openbabel311.exe /S
cache:
#- C:\RLibrary
#- C:\Program Files\Pandoc\
#- C:\deps
# Adapt as necessary starting from here
# Install Pandoc: https://github.com/krlmlr/r-appveyor/issues/82#issuecomment-261695154
before_test:
- ps: >-
if (-Not (Test-Path "C:\Program Files\Pandoc\")) {
cinst pandoc
}
- ps: $env:Path += ";C:\Program Files\Pandoc\"
- pandoc -v
platform: x64
environment:
R_ARCH: x64
R_VERSION: stable
BIOC_USE_DEVEL: FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
R_CHECK_ARGS: --no-build-vignettes --no-manual --no-multiarch
av_token:
secure: JJT6ZdxNWo6wf+xPRwfOXAXW1M65jtdzRXCKFGarzzQ=
GITHUB_PAT:
secure: VNNpZ/vmYAXvbXKtPfD/JNj4PPJOgbyUGMowVtH0Q//HULJrlOo62MWSuhksQ2MR
build_script:
- travis-tool.sh install_r tibble # workaround for MSnbase
- travis-tool.sh install_bioc mzR xcms CAMERA Rdisop ropls BiocStyle Rgraphviz
- travis-tool.sh install_github blosloos/enviPick
- travis-tool.sh install_github rickhelmus/patRoonExt
- travis-tool.sh install_github rickhelmus/patRoonData
- travis-tool.sh install_github blosloos/nontargetData
- travis-tool.sh install_github blosloos/nontarget
- travis-tool.sh install_github cran/InterpretMSSpectrum@1.3.3 # workaround for https://github.com/cbroeckl/RAMClustR/issues/48
- travis-tool.sh install_r RAMClustR
#- travis-tool.sh install_github cbroeckl/RAMClustR
- travis-tool.sh install_github rickhelmus/KPIC2
- travis-tool.sh install_github rickhelmus/cliqueMS
- travis-tool.sh install_github souravc83/fastAdaboost # For Metaclean, removed from CRAN (9/22)
# - Rscript -e "install.packages('fastAdaboost', repos = 'https://mran.revolutionanalytics.com/snapshot/2022-07-01')"
- travis-tool.sh install_github KelseyChetnik/MetaClean
- travis-tool.sh install_github KelseyChetnik/MetaCleanData
- travis-tool.sh install_github berlinguyinca/spectra-hash/splashR
- travis-tool.sh install_github kruvelab/MS2Tox
- travis-tool.sh install_github kruvelab/MS2Quant
- travis-tool.sh install_r vdiffr
- travis-tool.sh install_r covr
- travis-tool.sh install_deps
test_script:
- set JAVA_HOME=C:\PROGRA~1\Java\jdk11
- set PATH=%JAVA_HOME%\bin;C:\Program Files\OpenMS-2.7.0\bin;C:\Program Files\OpenBabel-3.1.1;%PATH%
# - set OPENMS_DATA_PATH=C:\Program Files\OpenMS-2.7.0\share\OpenMS
# - set PATROON_METFRAG=C:\deps\MetFragCommandLine-2.5.0.jar
# - set PATROON_SIRIUS=C:\deps\sirius
- set PATROON_JUNIT=%APPVEYOR_BUILD_FOLDER%\junit.xml
# - set PATROON_BIOTRANSFORMER=C:\deps\biotransformer\biotransformer-3.0.0.jar
# HACK for SIRIUS
- del C:\tools\Coverity\bin\jnidispatch.dll
- travis-tool.sh run_tests
on_failure:
- if exist %APPVEYOR_BUILD_FOLDER%\junit.xml ( type %APPVEYOR_BUILD_FOLDER%\junit.xml && appveyor PushArtifact %APPVEYOR_BUILD_FOLDER%\junit.xml )
- 7z a failure.zip *.Rcheck\* "-xr!*.sqlite"
- appveyor PushArtifact failure.zip
on_success:
# NOTE: disable coverage compiler flags as they don't work with GenForm
# --> Leave coverage calculation to CircleCI for now as it is difficult to parallelize with AppVeyor.
# - Rscript -e "options(covr.flags = list(CXXFLAGS = '', LDFLAGS = '')); covr::codecov()"
- ps: if ($env:APPVEYOR_REPO_BRANCH -eq "master") { .\av_trigger_deps.ps1 }
on_finish:
- ps: (New-Object 'System.Net.WebClient').UploadFile("https://ci.appveyor.com/api/testresults/junit/$($env:APPVEYOR_JOB_ID)", "$($env:PATROON_JUNIT)")
artifacts:
- path: '*.Rcheck\**\*.log'
name: Logs
- path: '*.Rcheck\**\*.out'
name: Logs
- path: '*.Rcheck\**\*.fail'
name: Logs
- path: '*.Rcheck\**\*.Rout'
name: Logs
- path: '\*_*.tar.gz'
name: Bits
- path: '\*_*.zip'
name: Bits