HDF5 error while compiling another library - cmake

Question

I have compiled HDF5 following these steps:
untar hdf5-xxx.tar.gz
cd hdf5-xxx
make
make install
However, while I install another library (OpenGM), which request HDF5, I give the following arguments:
HDF5_CORE_LIBRARY /Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5
HDF5_CPP_LIBRARY /Users/Florian/Documents/THESE/hdf5-1.8.7/c++
HDF5_HL_LIBRARY /Users/Florian/Documents/THESE/hdf5-1.8.7/hl
HDF5_INCLUDE_DIR /Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5/include
HDF5_Z_LIBRARY /usr/lib/libz.dylib
After using CMake and generate, I get:
WARNING: Target "example-io" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "example-io" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "external-library-daoopt" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only
to libraries. CMake is dropping the item.
WARNING: Target "external-library-daoopt" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link only to
libraries. CMake is dropping the item.
WARNING: Target "external-library-daoopt-shared" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may
link only to libraries. CMake is dropping the item.
WARNING: Target "external-library-daoopt-shared" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link
only to libraries. CMake is dropping the item.
WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to
libraries. CMake is dropping the item.
WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to
libraries. CMake is dropping the item.
WARNING: Target "_opengmcore" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "_hdf5" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "_hdf5" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link only to libraries. CMake
is dropping the item.
WARNING: Target "modelIO" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "modelIO" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hl". Targets may link only to libraries.
CMake is dropping the item.
WARNING: Target "buildFoE" requests linking to directory "/Users/Florian/Documents/THESE/hdf5-1.8.7/hdf5". Targets may link only to libraries.
CMake is dropping the item.
As those are "just" warnings, I can compile my OpenGM library:
make
But I thus end up with the following error:
Undefined symbols for architecture x86_64:
"_H5Aclose", referenced from:
void marray::hdf5::save<unsigned long>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<unsigned long, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
void marray::hdf5::save<float>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<float, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
void marray::hdf5::save<double>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<double, std::__1::allocator<unsigned long> > const&) in io_graphical_model.cxx.o
void marray::hdf5::save<long>(int const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, marray::Marray<long, std::__1::allocator<unsigned long> > const&) in io_graphical_model.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)
As both warnings and the error deal with HDF5, I suppose the main problem comes from this library.
I am using MacOSX if it can help.
**EDIT:**Add the FindHDF5.cmake file
# - Find HDF5, a library for reading and writing self describing array data.
#
FIND_PATH(HDF5_INCLUDE_DIR hdf5.h)
FIND_LIBRARY(HDF5_CORE_LIBRARY NAMES hdf5dll hdf5 )
FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hldll hdf5_hl )
FIND_LIBRARY(HDF5_CPP_LIBRARY NAMES hdf5_cppdll hdf5_cpp )
IF(WIN32 AND HDF5_CORE_LIBRARY MATCHES "dll.lib$")
SET(HDF5_CFLAGS "-D_HDF5USEDLL_")
SET(HDF5_CPPFLAGS "-D_HDF5USEDLL_ -DHDF5CPP_USEDLL")
ELSE()
SET(HDF5_CFLAGS)
SET(HDF5_CPPFLAGS)
ENDIF()
SET(HDF5_VERSION_MAJOR 1)
SET(HDF5_VERSION_MINOR 8)
set(HDF5_SUFFICIENT_VERSION FALSE)
TRY_COMPILE(HDF5_SUFFICIENT_VERSION
${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5version.c
COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DMIN_MAJOR=${HDF5_VERSION_MAJOR} -DMIN_MINOR=${HDF5_VERSION_MINOR}")
if(HDF5_SUFFICIENT_VERSION)
MESSAGE(STATUS
"Checking HDF5 version (at least ${HDF5_VERSION_MAJOR}.${HDF5_VERSION_MINOR}): ok")
else()
MESSAGE( STATUS "HDF5: need at least version ${HDF5_VERSION_MAJOR}.${HDF5_VERSION_MINOR}" )
endif()
set(HDF5_USES_ZLIB FALSE)
TRY_COMPILE(HDF5_USES_ZLIB
${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5usesCompression.c
COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DH5_SOMETHING=H5_HAVE_FILTER_DEFLATE")
if(HDF5_USES_ZLIB)
FIND_LIBRARY(HDF5_Z_LIBRARY NAMES zlib1 zlib z )
set(HDF5_ZLIB_OK ${HDF5_Z_LIBRARY})
else()
set(HDF5_ZLIB_OK TRUE)
set(HDF5_Z_LIBRARY "")
endif()
set(HDF5_USES_SZLIB FALSE)
TRY_COMPILE(HDF5_USES_SZLIB
${CMAKE_BINARY_DIR} ${CMAKE_MODULE_PATH}/checkHDF5usesCompression.c
COMPILE_DEFINITIONS "-I\"${HDF5_INCLUDE_DIR}\" -DH5_SOMETHING=H5_HAVE_FILTER_SZIP")
if(HDF5_USES_SZLIB)
FIND_LIBRARY(HDF5_SZ_LIBRARY NAMES szlibdll sz )
set(HDF5_SZLIB_OK ${HDF5_SZ_LIBRARY})
else()
set(HDF5_SZLIB_OK TRUE)
set(HDF5_SZ_LIBRARY "")
endif()
# handle the QUIETLY and REQUIRED arguments and set HDF5_FOUND to TRUE if
# all listed variables are TRUE
INCLUDE(FindPackageHandleStandardArgs)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(HDF5 DEFAULT_MSG HDF5_CORE_LIBRARY
HDF5_HL_LIBRARY HDF5_ZLIB_OK HDF5_SZLIB_OK HDF5_INCLUDE_DIR)
IF(HDF5_FOUND)
SET(HDF5_LIBRARIES ${HDF5_CORE_LIBRARY} ${HDF5_HL_LIBRARY} ${HDF5_Z_LIBRARY} ${HDF5_SZ_LIBRARY})
ELSE()
SET(HDF5_CORE_LIBRARY HDF5_CORE_LIBRARY-NOTFOUND)
SET(HDF5_HL_LIBRARY HDF5_HL_LIBRARY-NOTFOUND)
SET(HDF5_Z_LIBRARY HDF5_Z_LIBRARY-NOTFOUND)
SET(HDF5_SZ_LIBRARY HDF5_SZ_LIBRARY-NOTFOUND)
ENDIF(HDF5_FOUND)

Answer 1

The problem was solved by compiling the HDF5 library with the --with_cxx flag to build the C++ interface. In addition, I installed the HDF5 library in /usr/local so that it is automatically found when installing opengm.