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ANTsX / ANTsR

R interface to the ANTs biomedical image processing library
https://antsx.github.io/ANTsR
Apache License 2.0
127 stars 35 forks source link

I got the installation error as follows on windows 10. #275

Closed tuxxon closed 4 years ago

tuxxon commented 5 years ago

Hello.

ITKR has installed on windows 10 successfully with R CMD INSTALL ITKR. I couldn't find out where the ITKInternalEigen3 modules are.

Anybody knows how to fix this problem?

C:\radiomics>R CMD INSTALL ANTsRCore
* installing to library 'C:/Users/tuxxon/Documents/R/win-library/3.6'
* installing *source* package 'ANTsRCore' ...
** using staged installation
msys 0
SHLIB_CXXLD=
Running libitk
Running -LC:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/ -lITKBiasCorrection-5.0 -lITKCommon-5.0 -lITKEXPAT-5.0 -lITKIOBMP-5.0 -lITKIOBioRad-5.0 -lITKIOBruker-5.0 -lITKIOCSV-5.0 -lITKIOGDCM-5.0 -lITKIOGE-5.0 -lITKIOGIPL-5.0 -lITKIOHDF5-5.0 -lITKIOIPL-5.0 -lITKIOImageBase-5.0 -lITKIOJPEG-5.0 -lITKIOJPEG2000-5.0 -lITKIOLSM-5.0 -lITKIOMINC-5.0 -lITKIOMRC-5.0 -lITKIOMeshBYU-5.0 -lITKIOMeshBase-5.0 -lITKIOMeshFreeSurfer-5.0 -lITKIOMeshGifti-5.0 -lITKIOMeshOBJ-5.0 -lITKIOMeshOFF-5.0 -lITKIOMeshVTK-5.0 -lITKIOMeta-5.0 -lITKIONIFTI-5.0 -lITKIONRRD-5.0 -lITKIOPNG-5.0 -lITKIOSiemens-5.0 -lITKIOSpatialObjects-5.0 -lITKIOStimulate-5.0 -lITKIOTIFF-5.0 -lITKIOTransformBase-5.0 -lITKIOTransformHDF5-5.0 -lITKIOTransformInsightLegacy-5.0 -lITKIOTransformMatlab-5.0 -lITKIOVTK-5.0 -lITKIOXML-5.0 -lITKKLMRegionGrowing-5.0 -lITKLabelMap-5.0 -lITKMesh-5.0 -lITKMetaIO-5.0 -lITKNrrdIO-5.0 -lITKOptimizers-5.0 -lITKOptimizersv4-5.0 -lITKPath-5.0 -lITKPolynomials-5.0 -lITKQuadEdgeMesh-5.0 -lITKReview-5.0 -lITKSpatialObjects-5.0 -lITKStatistics-5.0 -lITKTestKernel-5.0 -lITKTransform-5.0 -lITKTransformFactory-5.0 -lITKVNLInstantiation-5.0 -lITKVTK-5.0 -lITKWatersheds-5.0 -lITKgiftiio-5.0 -lITKniftiio-5.0 -lITKznz-5.0 -litkMGHIO-5.0 -litkNetlibSlatec-5.0 -litkdouble-conversion-5.0 -litkgdcmCommon-5.0 -litkgdcmDICT-5.0 -litkgdcmDSED-5.0 -litkgdcmIOD-5.0 -litkgdcmMEXD-5.0 -litkgdcmMSFF-5.0 -litkgdcmcharls-5.0 -litkgdcmjpeg12-5.0 -litkgdcmjpeg16-5.0 -litkgdcmjpeg8-5.0 -litkgdcmopenjp2-5.0 -litkgdcmsocketxx-5.0 -litkjpeg-5.0 -litklbfgs-5.0 -litkminc2-5.0 -litknetlib-5.0 -litkopenjpeg-5.0 -litkpng-5.0 -litksys-5.0 -litktestlib-5.0 -litktiff-5.0 -litkv3p_netlib-5.0 -litkvcl-5.0 -litkvnl-5.0 -litkvnl_algo-5.0 -litkzlib-5.0 -llibitkhdf5 -llibitkhdf5_cpp
fatal: destination path 'ants' already exists and is not an empty directory.
Already on 'master'
M       data/antsVersions.csv
Your branch is up to date with 'origin/master'.
Already up to date.
fatal: reference is not a tree: 2d026609093af654e2b72736c216c0211977060f
cmake.exe
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Failed
-- SuperBuild - ANTS => Requires ITKv5,
-- SuperBuild -   ITKv5[OK]
-- SuperBuild - ANTS[OK]
-- Configuring done
-- Generating done
-- Build files have been written to: C:/radiomics/ANTsRCore/src/antb
** libs
: this package has a non-empty 'configure.win' file,
so building only the main architecture

mkdir -p libs; cd antb && mingw32-make -j 4 && cd ANTS-build && mingw32-make all install && rm -rf C:/Users/tuxxon/Documents/R/win-library/3.6/00LOCK-ANTsRCore/00new/ANTsRCore/libs/bin && cd /radiomics/ANTsRCore/src
mingw32-make[1]: Entering directory 'C:/radiomics/ANTsRCore/src/antb'
mingw32-make[2]: Entering directory 'C:/radiomics/ANTsRCore/src/antb'
mingw32-make[3]: Entering directory 'C:/radiomics/ANTsRCore/src/antb'
mingw32-make[3]: Leaving directory 'C:/radiomics/ANTsRCore/src/antb'
[ 47%] Built target ITKv5
mingw32-make[3]: Entering directory 'C:/radiomics/ANTsRCore/src/antb'
mingw32-make[3]: Leaving directory 'C:/radiomics/ANTsRCore/src/antb'
mingw32-make[3]: Entering directory 'C:/radiomics/ANTsRCore/src/antb'
[ 52%] Performing configure step for 'ANTS'
Not searching for unused variables given on the command line.
-- Performing Test C_HAS_WARNING-Wformat=2
-- Performing Test C_HAS_WARNING-Wformat=2 - Success
-- Performing Test CXX_HAS_WARNING-Wformat=2
-- Performing Test CXX_HAS_WARNING-Wformat=2 - Failed
-- Building ANTS version "3.0.0.0.dev1-g8f99c"
CMake Error at C:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/cmake/ITK-5.0/Modules/ITKEigen3.cmake:15 (find_package):
  Could not find a package configuration file provided by "ITKInternalEigen3"
  (requested version 3.3) with any of the following names:

    ITKInternalEigen3Config.cmake
    itkinternaleigen3-config.cmake

  Add the installation prefix of "ITKInternalEigen3" to CMAKE_PREFIX_PATH or
  set "ITKInternalEigen3_DIR" to a directory containing one of the above
  files.  If "ITKInternalEigen3" provides a separate development package or
  SDK, be sure it has been installed.
Call Stack (most recent call first):
  C:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/cmake/ITK-5.0/ITKModuleAPI.cmake:76 (include)
  C:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/cmake/ITK-5.0/ITKModuleAPI.cmake:31 (itk_module_load)
  C:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/cmake/ITK-5.0/ITKModuleAPI.cmake:129 (_itk_module_config_recurse)
  C:/Users/tuxxon/Documents/R/win-library/3.6/ITKR/libs/lib/cmake/ITK-5.0/ITKConfig.cmake:82 (itk_module_config)
  ANTS.cmake:61 (find_package)
  CMakeLists.txt:86 (include)

-- Configuring incomplete, errors occurred!
See also "C:/radiomics/ANTsRCore/src/antb/ANTS-build/CMakeFiles/CMakeOutput.log".
See also "C:/radiomics/ANTsRCore/src/antb/ANTS-build/CMakeFiles/CMakeError.log".
CMakeFiles\ANTS.dir\build.make:107: recipe for target 'ANTS-prefix/src/ANTS-stamp/ANTS-configure' failed
mingw32-make[3]: *** [ANTS-prefix/src/ANTS-stamp/ANTS-configure] Error 1
mingw32-make[3]: Leaving directory 'C:/radiomics/ANTsRCore/src/antb'
CMakeFiles\Makefile2:108: recipe for target 'CMakeFiles/ANTS.dir/all' failed
mingw32-make[2]: *** [CMakeFiles/ANTS.dir/all] Error 2
mingw32-make[2]: Leaving directory 'C:/radiomics/ANTsRCore/src/antb'
makefile:115: recipe for target 'all' failed
mingw32-make[1]: *** [all] Error 2
mingw32-make[1]: Leaving directory 'C:/radiomics/ANTsRCore/src/antb'
make: *** [Makevars.win:11: libs] Error 2
ERROR: compilation failed for package 'ANTsRCore'
* removing 'C:/Users/tuxxon/Documents/R/win-library/3.6/ANTsRCore'
kaspermarstal commented 4 years ago

Did you ever find the cause and solution to this problem?

stnava commented 4 years ago

No real support for windows .... but see various other issues that discuss windows installs.