# Compiling TubeTK v1.1 or v1.0.0 with ITK 5.3rc03

**URL:** https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853
**Category:** Community
**Tags:** remotemodule, itkv5, build, cmake
**Created:** [March 7, 2022, 11:36pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853 "2022-03-07T23:36:04Z")
**Posts on this page:** 14
**Page:** 1

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 7, 2022, 11:36pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/1 "2022-03-07T23:36:04Z")

</div>

Continuing the discussion from [Compiling ~MinimalPathExtraction~ with ITK 5.2.1](https://discourse.itk.org/t/compiling-minimalpathextraction-with-itk-5-2-1/4784):

> [@Compiling ~MinimalPathExtraction~ with ITK 5.2.1](https://discourse.itk.org/t/compiling-minimalpathextraction-with-itk-5-2-1/4784/4):
>
> I just posted a new version of TubeTK (1.1rc01) last night (hence the -pre argument). TubeTKv1.1rc01 works with ITKv5.3rc03. It will automatically bring in MinimalPathExtraction wheels

Hello! (This is not a request for help) I’m getting this error with v1.1 (8cb12a20) and v1.0.0 of TubeTK.

```auto
  samu: file is missing and not created by any action: '/usr/lib/libdl.so'

```

When using GNU Make, this is the result:

```auto
  [46%] Built target ITKImageLabelSwig
  make[2]: *** No rule to make target '/usr/lib/libdl.so', needed by 'Wrapping/Generators/Python/itk/libitkTubeTK-5.3.so.1'. Stop.
  make[1]: *** [CMakeFiles/Makefile2:14113: Modules/Remote/TubeTK/src/CMakeFiles/TubeTK.dir/all] Error 2

```

I (regex-)replaced ‘libdl._.so’ and 'libdl._.a’ with ‘libdl.so.2’ (which exists in my system) in the source directories before running /CMake/ like this:

```bash
  find . -type f -exec grep -l libdl \{\} + |
      parallel 'sed -i "s%libdl.*\.\(so\|a\)[[:digit:].]*%libdl.so.2%g" {}'

```

After this change, the compilation seems to be working with Samurai (Ninja equivalent; did not try with GNU Make, because it takes longer to show the error).

I have checked, and `gnu/lib-names-64.h` does include `"libdl.so.2"`

These are my compilation options (I use the same to build ITK with other modules):

```auto
    -S "${srcdir}"/"${_pkgbase}"
    -B "${_build_dir}"

    -DCMAKE_INSTALL_PREFIX:FILEPATH=/usr
    -DCMAKE_BUILD_TYPE:STRING=Release
    -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
    --log-level="NOTICE"

    -DCMAKE_CXX_FLAGS:STRING="-std=c++11 -pipe -fno-plt -fPIC -fopenmp -march=native -mtune=native -Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS -fcf-protection -fno-plt -fstack-clash-protection -Wformat -Werror=format-security -O2 -L/usr/lib -ldl"
    -DCMAKE_C_FLAGS:STRING="-pipe -fno-plt -fPIC -fopenmp -march=native -mtune=native -Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS -fcf-protection -fno-plt -fstack-clash-protection -Wformat -Werror=format-security -O2"
    -DITK_CXX_OPTIMIZATION_FLAGS:STRING="-pipe -fno-plt -fPIC -fopenmp -march=native -mtune=native -Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS -fcf-protection -fno-plt -fstack-clash-protection -Wformat -Werror=format-security -O3"
    -DITK_C_OPTIMIZATION_FLAGS:STRING="-pipe -fno-plt -fPIC -fopenmp -march=native -mtune=native -Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS -fcf-protection -fno-plt -fstack-clash-protection -Wformat -Werror=format-security -O3"
    -DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON
    -G Ninja

    -DBUILD_TESTING:BOOL=OFF
    -DBUILD_EXAMPLES:BOOL=OFF
    -DITK_BUILD_DOCUMENTATION:BOOL=OFF
    -DITK_BUILD_DEFAULT_MODULES:BOOL=ON

    -DITK_WRAP_PYTHON:BOOL=ON
    -DITK_USE_SYSTEM_SWIG:BOOL=ON
    -DITK_USE_SYSTEM_CASTXML:BOOL=ON

    -DITK_LEGACY_SILENT:BOOL=ON
    -DBUILD_SHARED_LIBS:BOOL=ON
    -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON
    -DITK_USE_SYSTEM_JPEG:BOOL=ON
    -DITK_USE_SYSTEM_PNG:BOOL=ON
    -DITK_USE_SYSTEM_ZLIB:BOOL=ON
    -DITK_USE_SYSTEM_TIFF:BOOL=ON
    -DITK_USE_SYSTEM_GDCM:BOOL=ON
    -DITK_USE_SYSTEM_EXPAT:BOOL=ON
    -DITK_USE_SYSTEM_FFTW:BOOL=ON
    -DITK_USE_SYSTEM_HDF5:BOOL=ON
    -DITK_USE_64BITS_IDS:BOOL=ON

    -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4"
    -DITK_WRAP_VECTOR_COMPONENTS:STRING="2;3;4"
    -DITK_WRAP_float:BOOL=ON
    -DITK_WRAP_vector_float:BOOL=ON

    -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON

    -DModule_Montage:BOOL=ON
    -DModule_MorphologicalContourInterpolation:BOOL=ON
    -DModule_MultipleImageIterator:BOOL=ON
    -DModule_PhaseSymmetry:BOOL=ON
    -DModule_IsotropicWavelets:BOOL=OFF # Not working
    -DModule_LabelErodeDilate:BOOL=ON
    -DModule_Strain:BOOL=ON
    -DModule_TwoProjectionRegistration:BOOL=ON
    -DModule_TubeTK:BOOL=ON
    -DModule_MinimalPathExtraction:BOOL=ON

```

I hope that this is useful 🙂 . Thanks.

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 9, 2022, 1:32am UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/2 "2022-03-09T01:32:32Z")

</div>

(I can’t edit my first post, possibly because I had deleted it.)

The situation is not solved. The compilation does fail despite my efforts. I get the same errors.

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 10, 2022, 12:23am UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/3 "2022-03-10T00:23:49Z")

</div>

As I am writing this post, the progress is [1423/3386] with Samurai. I am attaching a patch which **may** be useful  
[libdl\_fix.diff.gz](https://discourse.itk.org/uploads/short-url/7t79YQxZjBKaQnbHSOYWdMDNMIL.gz) (629 Bytes). I will come back to report if the compilation was successful.

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 10, 2022, 1:50pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/4 "2022-03-10T13:50:45Z")

</div>

I was getting the following error (replaced some spaces with “newlines”), and I made some changes:

```
[2928/4286] Building CXX object Wrapping/Modules/TubeTK/CMakeFiles/TubeTKPython.dir/tubeEnhanceContrastUsingPriorPython.cpp.o
samu: job failed: /usr/bin/c++
-DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB
-DDIY_NO_THREADS
-DFMT_LOCALE
-DFMT_SHARED
-DH5_BUILT_AS_DYNAMIC_LIB
-DHDF_NO_NAMESPACE
-DITK_FFT_FACTORY_REGISTER_MANAGER
-DITK_IMAGEIO_FACTORY_REGISTER_MANAGER
-DITK_MESHIO_FACTORY_REGISTER_MANAGER
-DITK_TRANSFORMIO_FACTORY_REGISTER_MANAGER
-DMPICH_SKIP_MPICXX
-DMPI_NO_CPPBIND
-DNO_STATIC_CAST
-DOLD_HEADER_FILENAME
-DOMPI_SKIP_MPICXX
-DQT_CORE_LIB
-DQT_GUI_LIB
-DQT_NETWORK_LIB
-DQT_NO_DEBUG
-DQT_OPENGL_LIB
-DQT_QMLMODELS_LIB
-DQT_QML_LIB
-DQT_QUICK_LIB
-DQT_SQL_LIB
-DQT_WIDGETS_LIB
-DRKCOMMON_TASKING_TBB
-DTubeTKPython_EXPORTS
-DVTKMDIY_MPI_AS_LIB
-DVTKMDIY_NO_THREADS
-DVTK_HAS_OGGTHEORA_SUPPORT
-D_FORTIFY_SOURCE=2
-D_MPICC_H
-Dkiss_fft_scalar=double
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/wrapping
-I"${srcdir}"/insight-toolkit/build/Wrapping/ITKFactoryRegistration
-I"${srcdir}"/insight-toolkit/Modules/Remote/TwoProjectionRegistration/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Segmentation
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Registration
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/ObjectDocuments
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Numerics
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/MetaIO
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/IO
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Common
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src
-I"${srcdir}"/insight-toolkit/build/Modules/Remote/TubeTK/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/Strain/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/PhaseSymmetry/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/MultipleImageIterator/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/MorphologicalContourInterpolation/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/Montage/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/MinimalPathExtraction/include
-I"${srcdir}"/insight-toolkit/Modules/Remote/LabelErodeDilate/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/Watersheds/include
-I"${srcdir}"/insight-toolkit/Modules/Video/IO/include
-I"${srcdir}"/insight-toolkit/Modules/Video/Filtering/include
-I"${srcdir}"/insight-toolkit/Modules/Video/Core/include
-I"${srcdir}"/insight-toolkit/Modules/Bridge/VTK/include
-I"${srcdir}"/insight-toolkit/Modules/Core/TestKernel/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/SuperPixel/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/SpatialFunction/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/RegistrationMethodsv4/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/RegionGrowing/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/QuadEdgeMeshFiltering/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/Metricsv4/include
-I"${srcdir}"/insight-toolkit/Modules/Numerics/Optimizersv4/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/MarkovRandomFieldsClassifiers/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/LevelSetsv4/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/LabelVoting/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/libLBFGS/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/KLMRegionGrowing/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageNoise/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageFusion/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageFrequency/include
-I"${srcdir}"/insight-toolkit/Modules/IO/VTK/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TransformMatlab/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TransformInsightLegacy/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TransformHDF5/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TransformBase/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TransformFactory/include
-I"${srcdir}"/insight-toolkit/Modules/IO/Stimulate/include
-I"${srcdir}"/insight-toolkit/Modules/IO/SpatialObjects/include
-I"${srcdir}"/insight-toolkit/Modules/IO/XML/include
-I"${srcdir}"/insight-toolkit/Modules/IO/Siemens/include
-I"${srcdir}"/insight-toolkit/Modules/IO/RAW/include
-I"${srcdir}"/insight-toolkit/Modules/IO/PNG/include
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/PNG/src
-I"${srcdir}"/insight-toolkit/Modules/IO/NRRD/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/NrrdIO/src/NrrdIO
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/NrrdIO/src/NrrdIO
-I"${srcdir}"/insight-toolkit/Modules/IO/NIFTI/include
-I"${srcdir}"/insight-toolkit/Modules/IO/Meta/include
-I"${srcdir}"/insight-toolkit/Modules/IO/Mesh/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshVTK/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshOFF/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshOBJ/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshGifti/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshFreeSurfer/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshBYU/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MeshBase/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/Voronoi/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MRC/include
-I"${srcdir}"/insight-toolkit/Modules/IO/MINC/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MINC/src/libminc/volume_io/Include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MINC/src/libminc/libsrc2
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MINC/src/libminc/libcommon
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MINC/src/libminc
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MINC
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/MINC
-I"${srcdir}"/insight-toolkit/Modules/IO/LSM/include
-I"${srcdir}"/insight-toolkit/Modules/IO/TIFF/include
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/TIFF/src
-I"${srcdir}"/insight-toolkit/Modules/IO/JPEG2000/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/OpenJPEG/src/openjpeg
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/OpenJPEG/src/openjpeg
-I"${srcdir}"/insight-toolkit/Modules/IO/JPEG/include
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/JPEG/src
-I"${srcdir}"/insight-toolkit/Modules/IO/HDF5/include
-I"${srcdir}"/insight-toolkit/Modules/IO/GIPL/include
-I"${srcdir}"/insight-toolkit/Modules/IO/GE/include
-I"${srcdir}"/insight-toolkit/Modules/IO/IPL/include
-I"${srcdir}"/insight-toolkit/Modules/IO/GDCM/include
-I"${srcdir}"/insight-toolkit/Modules/IO/CSV/include
-I"${srcdir}"/insight-toolkit/Modules/IO/Bruker/include
-I"${srcdir}"/insight-toolkit/Modules/IO/BioRad/include
-I"${srcdir}"/insight-toolkit/Modules/IO/BMP/include
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/HDF5/src
-I"${srcdir}"/insight-toolkit/Modules/Filtering/GPUThresholding/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/GPUSmoothing/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/GPUPDEDeformable/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/PDEDeformable/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/Common/include
-I"${srcdir}"/insight-toolkit/Modules/Registration/GPUCommon/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/GPUImageFilterBase/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/GPUAnisotropicSmoothing/include
-I"${srcdir}"/insight-toolkit/Modules/Core/GPUFiniteDifference/include
-I"${srcdir}"/insight-toolkit/Modules/Core/GPUCommon/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/GIFTI/src/gifticlib
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/NIFTI/src/nifti/znzlib
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/NIFTI/src/nifti/niftilib
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/Expat/src
-I"${srcdir}"/insight-toolkit/Modules/Numerics/Eigen/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/DisplacementField/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/DiffusionTensorImage/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Denoising/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/DeformableMesh/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Deconvolution/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/DICOMParser/src/DICOMParser
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/DICOMParser/src/DICOMParser
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Convolution/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/FFT/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Colormap/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/Classifiers/include
-I"${srcdir}"/insight-toolkit/Modules/Bridge/NumPy/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/BiasCorrection/include
-I"${srcdir}"/insight-toolkit/Modules/Numerics/Polynomials/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/AntiAlias/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/LevelSets/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/SignedDistanceFunction/include
-I"${srcdir}"/insight-toolkit/Modules/Numerics/Optimizers/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageFeature/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageSources/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageGradient/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Smoothing/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageCompare/include
-I"${srcdir}"/insight-toolkit/Modules/IO/ImageBase/include
-I"${srcdir}"/insight-toolkit/build/Modules/IO/ImageBase
-I"${srcdir}"/insight-toolkit/Modules/Filtering/FastMarching/include
-I"${srcdir}"/insight-toolkit/Modules/Core/QuadEdgeMesh/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/DistanceMap/include
-I"${srcdir}"/insight-toolkit/Modules/Numerics/NarrowBand/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/BinaryMathematicalMorphology/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/MathematicalMorphology/include
-I"${srcdir}"/insight-toolkit/Modules/Segmentation/ConnectedComponents/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Thresholding/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/LabelMap/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageLabel/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageIntensity/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/Path/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageStatistics/include
-I"${srcdir}"/insight-toolkit/Modules/Core/SpatialObjects/include
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/MetaIO/src/MetaIO/src
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/MetaIO/src/MetaIO/src
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/ZLIB/src
-I"${srcdir}"/insight-toolkit/Modules/Core/Mesh/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageCompose/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/AnisotropicSmoothing/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageGrid/include
-I"${srcdir}"/insight-toolkit/Modules/Core/ImageFunction/include
-I"${srcdir}"/insight-toolkit/Modules/Core/Transform/include
-I"${srcdir}"/insight-toolkit/Modules/Numerics/Statistics/include
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/Netlib
-I"${srcdir}"/insight-toolkit/Modules/Core/ImageAdaptors/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/CurvatureFlow/include
-I"${srcdir}"/insight-toolkit/Modules/Filtering/ImageFilterBase/include
-I"${srcdir}"/insight-toolkit/Modules/Core/FiniteDifference/include
-I"${srcdir}"/insight-toolkit/Modules/Core/Common/include
-I"${srcdir}"/insight-toolkit/build/Modules/Core/Common
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/VNL/src/vxl/core
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/VNL/src/vxl/vcl
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/VNL/src/vxl/v3p/netlib
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/VNL/src/vxl/core
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/VNL/src/vxl/vcl
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/VNL/src/vxl/v3p/netlib
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/KWSys/src
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/Eigen3/src
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/DoubleConversion/src/double-conversion
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/DoubleConversion/src
-I"${srcdir}"/insight-toolkit/build/Wrapping/Typedefs
-I"${srcdir}"/insight-toolkit/Wrapping/Generators/Python
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo
-I"${srcdir}"/insight-toolkit/Modules/ThirdParty/VNL/src/vxl/core/vnl
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/VNL/src/vxl/core/vnl
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/NIFTI/src/nifti/znzlib
-I"${srcdir}"/insight-toolkit/build/Modules/ThirdParty/NIFTI/src/nifti/niftilib
-isystem /usr/include/gdcm-3.0
-isystem /usr/include/python3.10
-isystem /usr/include/eigen3
-isystem /usr/include/vtk
-isystem /usr/include/freetype2
-isystem /usr/include/qt
-isystem /usr/include/qt/QtOpenGL
-isystem /usr/include/qt/QtWidgets
-isystem /usr/include/qt/QtGui
-isystem /usr/include/qt/QtCore
-isystem /usr/lib/qt/mkspecs/linux-g++
-isystem /usr/lib/jvm/default/include
-isystem /usr/lib/jvm/default/include/linux
-isystem /usr/include/openvr
-isystem /usr/lib/python3.10/site-packages/mpi4py/include
-isystem /usr/include/libxml2
-isystem /usr/include/vtk/vtkxdmf3/core
-isystem /usr/include/vtk/vtkfides/fides
-isystem /usr/include/vtk/vtkvtkm/vtk-m
-isystem /usr/include/vtk/vtkvtkm/vtk-m/vtkm/thirdparty/optionparser
-isystem /usr/include/vtk/vtkvtkm/vtk-m/vtkm/thirdparty/diy
-isystem /usr/include/vtk/vtkvtkm/vtk-m/vtkm/thirdparty/diy/vtkmdiy/include
-isystem /usr/include/vtk/vtkvtkm/vtk-m/vtkm/thirdparty/diy/vtkmdiy/include/vtkmdiy/mpi
-isystem /usr/include/vtk/vtkvtkm/vtk-m/vtkm/thirdparty/lcl/vtkmlcl
-isystem /usr/include/qt/QtSql
-isystem /usr/include/qt/QtQuick
-isystem /usr/include/qt/QtQmlModels
-isystem /usr/include/qt/QtQml
-isystem /usr/include/qt/QtNetwork
-isystem /usr/include/double-conversion
-isystem /usr/include/utf8cpp -std=c++14 -pipe -fno-plt -fPIC -fopenmp -march=native -mtune=native -Wp,-D_FORTIFY_SOURCE=2,-D_GLIBCXX_ASSERTIONS -fcf-protection -fstack-clash-protection -Wformat -Werror=format-security -O2 -O3 -Wall -Wcast-align -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel -msse2 -msse2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fPIC -fno-strict-aliasing -w -fopenmp -fPIC -pthread -ffunction-sections -std=c++14 -MD -MT Wrapping/Modules/TubeTK/CMakeFiles/TubeTKPython.dir/tubeEnhanceEdgesUsingDiffusionPython.cpp.o -MF Wrapping/Modules/TubeTK/CMakeFiles/TubeTKPython.dir/tubeEnhanceEdgesUsingDiffusionPython.cpp.o.d -o Wrapping/Modules/TubeTK/CMakeFiles/TubeTKPython.dir/tubeEnhanceEdgesUsingDiffusionPython.cpp.o -c "${srcdir}"/insight-toolkit/build/Wrapping/Modules/TubeTK/tubeEnhanceEdgesUsingDiffusionPython.cpp
In file included from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicDiffusionTensorImageFilter.h:228,
                 from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicEdgeEnhancementDiffusionImageFilter.h:27,
                 from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/include/tubeEnhanceEdgesUsingDiffusion.h:32,
                 from "${srcdir}"/insight-toolkit/build/Wrapping/Typedefs/tubeEnhanceEdgesUsingDiffusionSwigInterface.h:18,
                 from "${srcdir}"/insight-toolkit/build/Wrapping/Modules/TubeTK/tubeEnhanceEdgesUsingDiffusionPython.cpp:3201:
"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicDiffusionTensorImageFilter.hxx: In instantiation of 'itk::tube::AnisotropicDiffusionTensorImageFilter<TInputImage, TOutputImage>::TimeStepType itk::tube::AnisotropicDiffusionTensorImageFilter<TInputImage, TOutputImage>::CalculateChange() [with TInputImage = itk::Image<float, 3>; TOutputImage = itk::Image<float, 3>; itk::tube::AnisotropicDiffusionTensorImageFilter<TInputImage, TOutputImage>::TimeStepType = double]':
"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicDiffusionTensorImageFilter.hxx:254:1: required from here
"${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicDiffusionTensorImageFilter.hxx:285:9: error: cannot convert 'std::vector<bool>' to 'const std::vector<unsigned char>&'
  285 | str.ValidTimeStepList );
      | ~~~~^~~~~~~~~~~~~~~~~
      | |
      | std::vector<bool>
In file included from "${srcdir}"/insight-toolkit/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.h:380,
                 from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicDiffusionTensorImageFilter.h:28,
                 from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/src/Filtering/itktubeAnisotropicEdgeEnhancementDiffusionImageFilter.h:27,
                 from "${srcdir}"/insight-toolkit/Modules/Remote/TubeTK/include/tubeEnhanceEdgesUsingDiffusion.h:32,
                 from "${srcdir}"/insight-toolkit/build/Wrapping/Typedefs/tubeEnhanceEdgesUsingDiffusionSwigInterface.h:18,
                 from "${srcdir}"/insight-toolkit/build/Wrapping/Modules/TubeTK/tubeEnhanceEdgesUsingDiffusionPython.cpp:3201:
"${srcdir}"/insight-toolkit/Modules/Core/FiniteDifference/include/itkFiniteDifferenceImageFilter.hxx:170:107: note: initializing argument 2 of 'itk::FiniteDifferenceImageFilter<TInputImage, TOutputImage>::TimeStepType itk::FiniteDifferenceImageFilter<TInputImage, TOutputImage>::ResolveTimeStep(const std::vector<typename itk::FiniteDifferenceFunction<TOutputImage>::TimeStepType>&, const std::vector<unsigned char>&) const [with TInputImage = itk::Image<float, 3>; TOutputImage = itk::Image<float, 3>; itk::FiniteDifferenceImageFilter<TInputImage, TOutputImage>::TimeStepType = double; typename itk::FiniteDifferenceFunction<TOutputImage>::TimeStepType = double]'
  170 | const std::vector<uint8_t> & valid) const
      | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
samu: subcommand failed

```

In `itktubeAnisotropicDiffusionTensorImageFilter.h` (in line 202) shows

```
std::vector< bool > ValidTimeStepList;

```

This is called in the definition of `CalculateChange` (_template_ in `itktubeAnisotropicDiffusionTensorImageFilter.hxx`). Then, `itkFiniteDifferenceImageFilter.h` states: _“Although they are uint8\_t, they should be treated like bools.”_, and it shows

```
virtual TimeStepType
  ResolveTimeStep(const std::vector<TimeStepType> & timeStepList, const std::vector<uint8_t> & valid) const;

```

So, I changed line 202 of `itktubeAnisotropicDiffusionTensorImageFilter.h` to

```
std::vector< uint8_t > ValidTimeStepList;

```

I also slightly modified the diff file which I had previously uploaded: [libdl\_fix.diff.gz](https://discourse.itk.org/uploads/short-url/jrLJbsUxxI2KoNfiV54EO9As7hg.gz) (622 Bytes). In the meantime, I should note that using Samurai’s `-f` directive is needed, and that doing the regex may also be necessary after running CMake.

---

<div class="post-metadata">

### Author: ![dzenanz](https://discourse.itk.org/user_avatar/discourse.itk.org/dzenanz/32/1093_2.png) [@dzenanz](https://discourse.itk.org/u/dzenanz)
#### Post date: [March 10, 2022, 2:50pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/5 "2022-03-10T14:50:49Z")

</div>

@Niels_Dekker @seanm @Lee_Newberg @Stephen_Aylward anyone wants to turn @edgar’s diff into a PR?

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 10, 2022, 3:47pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/6 "2022-03-10T15:47:00Z")

</div>

The build is faulty. I am getting errors even with this:

```auto
>>> import itk; itk.auto_progress(2); itk.Version.GetITKVersion()
Loading ITKPyBase... done
Loading ITKCommon... Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.10/site-packages/itk/support/lazy.py", line 137, in __getattribute__
    base.itk_load_swig_module(module, namespace)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 110, in itk_load_swig_module
    l_module = loader.load(swig_module_name)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 259, in load
    l_spec.loader.exec_module(l_module) # pytype: disable=attribute-error
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/lib/python3.10/site-packages/itk/support/../ITKCommonPython.py", line 13, in <module>
    from . import _ITKCommonPython
ImportError: libjawt.so: cannot open shared object file: No such file or directory

```

I will try to rebuild. In any case, any help is welcome 🙂 .

---

<div class="post-metadata">

### Author: ![Stephen\_Aylward](https://discourse.itk.org/user_avatar/discourse.itk.org/stephen_aylward/32/654_2.png) [@Stephen\_Aylward](https://discourse.itk.org/u/Stephen_Aylward)
#### Post date: [March 10, 2022, 4:05pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/7 "2022-03-10T16:05:38Z")

</div>

**Regarding the DL issue:**

Thanks for the details. I see that you have defined  
-ldl  
In the build cmake variable  
CMAKE\_CXX\_FLAGS

The DL library isn’t specified for inclusion by TubeTk, but perhaps itk uses it. Regardless, if it is needed, it’s inclusion should be automatically managed by cmake. You should never have to specify it as a compiler option. Have you tried removing it from your specification?

**Regarding the ValidTimeStepList bug**

That API has been changed multiple times during the ITKv5.3rc series. The v1.1 tag of TubeTK works with ITKv5.3rc03. The master of TubeTK works with the master of ITK. The two cannot be mixed.

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 11, 2022, 3:10am UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/9 "2022-03-11T03:10:56Z")

</div>

Thank you, very much to both of you.

> [@Stephen\\\_Aylward](#):
>
> The DL library isn’t specified for inclusion by TubeTk, but perhaps itk uses it

Yes, I saw that. It’s puzzling, because that error message only happens when TubeTK is enabled in the compilation options of CMake.

> [@Stephen\\\_Aylward](#):
>
> Have you tried removing it from your specification?

Indeed, the `-ldl` has no effect. Frankly, I had removed it already, and failed to tell you about it, sorry [(repo)](https://www.notabug.org/broncodev/itk-pkgbuild/src/extra-modules).

I could try to check which of the replacements of `libdl.so` and `libdl-2.9.so` (in `TubeTK/CMake/TubeTKValgrind.supp` or `testDynamicLoader.cxx`) is helping me. As it is, I still had to replace them in `build.ninja` after running CMake.

```
sed -i "s%libdl[^[:space:];]*\.so[[:digit:].]*%libdl.so.2%g" "${_build_dir}"/build.ninja

```

At the end, I was getting some errors about Java libraries for whatever reason. If I add some paths to my `LD_LIBRARY_PATH`, I can get ITK’s version in Python. I have not tested TubeTK’s functionalities, but this thread is about compilation.

```
 $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib:/usr/lib/jvm/java-8-openjdk/lib/amd64"
 $ python
Python 3.10.2 (main, Jan 15 2022, 19:56:27) [GCC 11.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk; itk.auto_progress(2); itk.Version.GetITKVersion()
Loading ITKPyBase... done
Loading ITKCommon... Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.10/site-packages/itk/support/lazy.py", line 137, in __getattribute__
    base.itk_load_swig_module(module, namespace)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 110, in itk_load_swig_module
    l_module = loader.load(swig_module_name)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 259, in load
    l_spec.loader.exec_module(l_module) # pytype: disable=attribute-error
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/lib/python3.10/site-packages/itk/support/../ITKCommonPython.py", line 13, in <module>
    from . import _ITKCommonPython
ImportError: libjvm.so: cannot open shared object file: No such file or directory
>>>
 $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib:/usr/lib/jvm/java-8-openjdk/lib/amd64:/usr/lib/jvm/java-17-openjdk/lib/server"
 $ python
Python 3.10.2 (main, Jan 15 2022, 19:56:27) [GCC 11.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk; itk.auto_progress(2); itk.Version.GetITKVersion()
Loading ITKPyBase... done
Loading ITKCommon... Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.10/site-packages/itk/support/lazy.py", line 137, in __getattribute__
    base.itk_load_swig_module(module, namespace)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 110, in itk_load_swig_module
    l_module = loader.load(swig_module_name)
  File "/usr/lib/python3.10/site-packages/itk/support/base.py", line 259, in load
    l_spec.loader.exec_module(l_module) # pytype: disable=attribute-error
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/lib/python3.10/site-packages/itk/support/../ITKCommonPython.py", line 13, in <module>
    from . import _ITKCommonPython
ImportError: libawt_xawt.so: cannot open shared object file: No such file or directory
>>>
 $ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib:/usr/lib/jvm/java-8-openjdk/lib/amd64:/usr/lib/jvm/java-17-openjdk/lib/server:/usr/lib/jvm/java-17-openjdk/lib"
 $ python
Python 3.10.2 (main, Jan 15 2022, 19:56:27) [GCC 11.1.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import itk; itk.auto_progress(2); itk.Version.GetITKVersion()
Loading ITKPyBase... done
Loading ITKCommon... done
'5.3.0'

```

> [@Stephen\\\_Aylward](#):
>
> That API has been changed multiple times during the ITKv5.3rc series. The v1.1 tag of TubeTK works with ITKv5.3rc03. The master of TubeTK works with the master of ITK. The two cannot be mixed.

Yes, thank you. As I was following our previous conversation [(#4784)](https://discourse.itk.org/t/compiling-minimalpathextraction-with-itk-5-2-1/4784), I did try to match them, and tried an earlier version, just in case. Anyway, what I do think that needs to be changed is this:

[uint8.diff.gz](https://discourse.itk.org/uploads/short-url/qugZRqJmyPwVPQwjmNzlSp5vvtN.gz) (267 Bytes)

I’m sure that this leaves more questions than answers 😛 ! If you want me to test something, let me know. I will later formulate a question regarding the Java libraries.

Thank you again.

---

<div class="post-metadata">

### Author: ![Stephen\_Aylward](https://discourse.itk.org/user_avatar/discourse.itk.org/stephen_aylward/32/654_2.png) [@Stephen\_Aylward](https://discourse.itk.org/u/Stephen_Aylward)
#### Post date: [March 11, 2022, 5:33pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/10 "2022-03-11T17:33:30Z")

</div>

Hi,

I think it might be a good idea to start from an empty build directory. Sometimes stuff from prior configurations linger in build, cmakecache, and intermediate config files, or object files don’t get rebuilt. That might be causing your continued problems with dl.

For configuration, you should only need to do

> cmake …/ITK -G Ninja -DITK\_WRAP\_PYTHON=ON -DModule\_TubeTK=ON

- any deviations from that are at your own risk 🙂 (Ok, not really, but you’re definitely moving into uncharted territory that could have funky consequences).

Looks like the API for the ResolveTimeStep function has changed, again. I’ll commit a fix…again…

s

---

<div class="post-metadata">

### Author: ![Stephen\_Aylward](https://discourse.itk.org/user_avatar/discourse.itk.org/stephen_aylward/32/654_2.png) [@Stephen\_Aylward](https://discourse.itk.org/u/Stephen_Aylward)
#### Post date: [March 11, 2022, 5:54pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/11 "2022-03-11T17:54:14Z")

</div>

Hi @edgar

What is your github login? I’d like to acknowledge you in the commit:

> <https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/107>
>
> Keeping up with API changes in ITK.
> 
> PDE-\>ResolveTimeStep now expects a itk::S…tdBooleanVector for the ValidTimeStep argument.
> 
> Thanks to Edgar for his contributions!

Thanks,  
s

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 12, 2022, 6:11pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/12 "2022-03-12T18:11:02Z")

</div>

Oh, don’t worry about that. I mean, I appreciate all the help and that you took the diff already. (Besides, I don’t have an account with them).

Cheers!

---

<div class="post-metadata">

### Author: ![Stephen\_Aylward](https://discourse.itk.org/user_avatar/discourse.itk.org/stephen_aylward/32/654_2.png) [@Stephen\_Aylward](https://discourse.itk.org/u/Stephen_Aylward)
#### Post date: [March 12, 2022, 6:16pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/13 "2022-03-12T18:16:46Z")

</div>

The change has been merged with TubeTK.

TubeTK master should now compile with ITK master. However, it is now incompatible with the most recent release of ITK (v5.3rc03). Either use TubeTK v1.1 with ITKv5.3rc03, or use TubeTK master with ITK master from within the past few days.

Thanks!

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [March 12, 2022, 7:52pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/14 "2022-03-12T19:52:40Z")

</div>

> [@Stephen\_Aylward](#):
>
> I think it might be a good idea to start from an empty build directory.

Yes, thank you. One of the convenient functionalities of makepkg (the building tools of Parabola GNU/Linux) is the option to clear the building environment.

> [@Stephen\_Aylward](#):
>
> any deviations from that are at your own risk 🙂 (Ok, not really, but you’re definitely moving into uncharted territory that could have funky consequences).

I know… further, I am sorry to take your time, but many of the options are for faster or safer building. For instance, this means that I don’t have to download or recompile libraries:

```
-DITK_USE_SYSTEM_SWIG:BOOL=ON
-DITK_USE_SYSTEM_CASTXML:BOOL=ON

-DITK_USE_SYSTEM_LIBRARIES:BOOL=ON
-DITK_USE_SYSTEM_JPEG:BOOL=ON
-DITK_USE_SYSTEM_PNG:BOOL=ON
-DITK_USE_SYSTEM_ZLIB:BOOL=ON
-DITK_USE_SYSTEM_TIFF:BOOL=ON
-DITK_USE_SYSTEM_GDCM:BOOL=ON
-DITK_USE_SYSTEM_EXPAT:BOOL=ON
-DITK_USE_SYSTEM_FFTW:BOOL=ON
-DITK_USE_SYSTEM_HDF5:BOOL=ON

```

These will certainly shorten compilation time and space:

```
-DBUILD_TESTING:BOOL=OFF
-DBUILD_EXAMPLES:BOOL=OFF
-DITK_BUILD_DOCUMENTATION:BOOL=OFF

```

Regarding the compilation flags,

- **`-march=native`, `mtune=native`:** will build for my architecture and processor (faster)
- **`-D-FORTIFY-SOURCE=2`:** detect some buffer overflow
- **`-D_GLIBCXX_ASSERTIONS`:** enables extra error checking in the form of precondition assertions
- **`-fPIC`:** use relative addresses, and not absolute addresses in jump calls
- **`-fcf-protection`:** protect against Return-oriented Programming (ROP) and call/jmp-oriented programming (COP/JOP)
- **`-pipe`:** Use pipes rather than temporary files during compilation
- **`-fno-plt`:** more efficient code by eliminating PLT stubs and exposing GOT loads to optimizations
- **`-fopenmp`:** Enable handling of OpenMP directives
- **`-fstack-clash-protection`:** prevent stack clash style attacks
- **`-Werror=format-security`:** warn aboutf uses of format functions that represent possible security problems

For some years, I have been using out-of-source builds, just because it makes debugging easier and safer (`-S` and `-B`).

Then, these allow for 3D registration functionalities:

```
-DITK_WRAP_IMAGE_DIMS:STRING="2;3;4"
-DITK_WRAP_VECTOR_COMPONENTS:STRING="2;3;4"
-DITK_WRAP_float:BOOL=ON
-DITK_WRAP_vector_float:BOOL=ON

```

As for the rest, I **think** that it’s better to have `-DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON`, because I don’t know if any paths get in the way: with `makepkg`, you have a building directory, a packaging directory and then a package, which may not have the same paths. Then, `-DITK_BUILD_DEFAULT_MODULES:BOOL=ON` is more as a reminder. Finally, `-DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON` gives me a `compile_commands.json` for my IDE.

I don’t know if I express this sufficiently, but I really appreciate the support 🙂 .

---

<div class="post-metadata">

### Author: ![edgar](https://discourse.itk.org/letter_avatar_proxy/v4/letter/e/b487fb/32.png) [@edgar](https://discourse.itk.org/u/edgar)
#### Post date: [April 12, 2022, 7:20pm UTC](https://discourse.itk.org/t/compiling-tubetk-v1-1-or-v1-0-0-with-itk-5-3rc03/4853/15 "2022-04-12T19:20:57Z")

</div>

Just for (in)completeness, the Java library path **may** be affected by `-DCMAKE_SKIP_INSTALL_RPATH:BOOL=ON`. To create the package, I created a /etc/ld.so.conf.d/insight-toolkit.conf with this:

```
/usr/lib/jvm/default/lib
/usr/lib/jvm/default/lib/server

```

The alternative of LD\_LIBRARY\_PATH is also viable. A recompilation with `-DCMAKE_SKIP_INSTALL_RPATH:BOOL=OFF` would be needed to check if `RPATH` is in fact missing in the libraries and triggering my error.