[Insight-developers] linking error ITK with an installed hdf5 1.8.12 on Mac

[Arnaud Gelas]

Hi all,

I am trying to build latest ITK (master branch) with an installed version of hdf5 (installed with homebrew on Mac 10.8), and I get the following linking errors:

Linking CXX shared library ../../../../lib/libITKIOHDF5-4.6.dylib
Undefined symbols for architecture x86_64:
  "H5::H5Location::createAttribute(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::PropList const&) const", referenced from:
      itk::HDF5ImageIO::WriteScalar(std::string const&, bool const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteScalar(std::string const&, long const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteScalar(std::string const&, unsigned long const&) in itkHDF5ImageIO.cxx.o
  "H5::DataSet::read(std::string&, H5::DataType const&, H5::DataSpace const&, H5::DataSpace const&, H5::DSetMemXferPropList const&) const", referenced from:
      itk::HDF5ImageIO::ReadString(std::string const&) in itkHDF5ImageIO.cxx.o
  "H5::DataSet::write(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::DataSpace const&, H5::DSetMemXferPropList const&) const", referenced from:
      itk::HDF5ImageIO::WriteString(std::string const&, std::string const&) in itkHDF5ImageIO.cxx.o
  "H5::CommonFG::createGroup(std::string const&, unsigned long) const", referenced from:
      itk::HDF5ImageIO::WriteImageInformation() in itkHDF5ImageIO.cxx.o
  "H5::CommonFG::openDataSet(std::string const&) const", referenced from:
      itk::HDF5ImageIO::ReadString(std::string const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::ReadDirections(std::string const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::ReadImageInformation() in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::Read(void*) in itkHDF5ImageIO.cxx.o
      std::vector<double, std::allocator<double> > itk::HDF5ImageIO::ReadVector<double>(std::string const&) in itkHDF5ImageIO.cxx.o
      std::vector<unsigned long, std::allocator<unsigned long> > itk::HDF5ImageIO::ReadVector<unsigned long>(std::string const&) in itkHDF5ImageIO.cxx.o
      int itk::HDF5ImageIO::ReadScalar<int>(std::string const&) in itkHDF5ImageIO.cxx.o
      ...
  "H5::CommonFG::createDataSet(std::string const&, H5::DataType const&, H5::DataSpace const&, H5::DSetCreatPropList const&) const", referenced from:
      itk::HDF5ImageIO::WriteScalar(std::string const&, bool const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteScalar(std::string const&, long const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteScalar(std::string const&, unsigned long const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteString(std::string const&, std::string const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::WriteDirections(std::string const&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > const&) in itkHDF5ImageIO.cxx.o
      itk::HDF5ImageIO::Write(void const*) in itkHDF5ImageIO.cxx.o
      void itk::HDF5ImageIO::WriteVector<double>(std::string const&, std::vector<double, std::allocator<double> > const&) in itkHDF5ImageIO.cxx.o
      ...
  "H5::CommonFG::openGroup(std::string const&) const", referenced from:
      itk::HDF5ImageIO::ReadImageInformation() in itkHDF5ImageIO.cxx.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [lib/libITKIOHDF5-4.6.1.dylib] Error 1
make[1]: *** [Modules/IO/HDF5/src/CMakeFiles/ITKIOHDF5.dir/all] Error 2
make: *** [all] Error 2


Any clue how to solve this issue?

Thanks in advance!!

Cheers,
Arnaud