[Insight-users] Install ITK on mac , HDF5 problem

[Jana Sefcikova]

Dear users,

I had tried to compile ITK with Eclipse on MAC (snow leopard) and got
following error :

Scanning dependencies of target H5detect

/usr/bin/make -f
Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/H5detect.dir/build.make
Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/H5detect.dir/build

"/Applications/CMake 2.8-7.app/Contents/bin/cmake" -E cmake_progress_report
/Developer/ITK/ITK-4.1/Build/Debug/CMakeFiles

[ 17%] Building C object
Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/H5detect.dir/H5detect.c.o

cd
/Developer/ITK/ITK-4.1/Build/Debug/Modules/ThirdParty/HDF5/src/itkhdf5/src
&& /usr/bin/gcc  -DDEBUG -DH5Z_DEBUG -DH5V_DEBUG -DH5T_DEBUG -DH5S_DEBUG
-DH5P_DEBUG -DH5O_DEBUG -DH5MM_DEBUG -DH5MF_DEBUG -DH5I_DEBUG -DH5HL_DEBUG
-DH5HG_DEBUG -DH5G_DEBUG -DH5F_DEBUG -DH5E_DEBUG -DH5D_DEBUG -DH5B_DEBUG
-DH5AC_DEBUG -Wno-uninitialized -Wno-unused-parameter -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  -w -static -std=c99
-finline-functions -fno-common -fmessage-length=0 -g
-I/Developer/ITK/ITK-4.1/Build/Debug/Modules/ThirdParty/ZLIB/src
-I/Developer/ITK/ITK-4.1/InsightToolkit-4.1.0/Modules/ThirdParty/ZLIB/src
-I/Developer/ITK/ITK-4.1/InsightToolkit-4.1.0/Modules/ThirdParty/HDF5/src
-I/Developer/ITK/ITK-4.1/Build/Debug/Modules/ThirdParty/HDF5/src
-I/Developer/ITK/ITK-4.1/Build/Debug/Modules/ThirdParty/HDF5/src/itkhdf5
-I/Developer/ITK/ITK-4.1/InsightToolkit-4.1.0/Modules/ThirdParty/HDF5/src/itkhdf5/src
-I/Developer/ITK/ITK-4.1/InsightToolkit-4.1.0/Modules/ThirdParty/HDF5/src/itkhdf5
-I/Developer/ITK/ITK-4.1/Build/Debug    -UNDEBUG -Wall -o
CMakeFiles/H5detect.dir/H5detect.c.o   -c
/Developer/ITK/ITK-4.1/InsightToolkit-4.1.0/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5detect.c

Linking C executable ../../../../../../bin/H5detect

cd
/Developer/ITK/ITK-4.1/Build/Debug/Modules/ThirdParty/HDF5/src/itkhdf5/src
&& "/Applications/CMake 2.8-7.app/Contents/bin/cmake" -E cmake_link_script
CMakeFiles/H5detect.dir/link.txt --verbose=1

/usr/bin/gcc     -Wno-uninitialized -Wno-unused-parameter -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  -w -static -std=c99
-finline-functions -fno-common -fmessage-length=0 -g
-Wl,-search_paths_first -Wl,-headerpad_max_install_names
CMakeFiles/H5detect.dir/H5detect.c.o  -o ../../../../../../bin/H5detect

ld: library not found for -lcrt0.o

collect2: ld returned 1 exit status

make[2]: *** [bin/H5detect] Error 1

make[1]: ***
[Modules/ThirdParty/HDF5/src/itkhdf5/src/CMakeFiles/H5detect.dir/all] Error
2

make: *** [all] Error 2


Do I need install HDF5 before installing ITK and how I can preset it ? I
found directory HDF5 in ThirdParty directory and read README, but did not
understand basic idea from it.

I found two variables concerning HDF5 using cmake gui :

- HDF5_BUILD_WITH_INSTALL_NAME , but I am not able to determine what is
meant by 'with install name' ??

- ITK_USE_SYSTEM_HDF5 , from this variable I would conclude that ITK has
some internal support for HDF5 but from the error I would say that it does
not have.

Besides HDF5,  I do not know how I should fill CMAKE_INSTALL_NAME_TOOL it
is set to /usr/bin/install_name_tool , what it should be ?


Does anyone have tip how to solve ?

Thanks in advance, any idea would be great.

Jana
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