[MINC-users] Problem Compiling Minc

Tue Apr 22 06:19:07 EDT 2008

Thanks Simon,

I found the problem. In the header file I have to define on linux machine 
extern "C" {// C header names} rather than the function names. I guess OSX compiler is intelligent to do it on its own.
it complies sweetly. 

Regards,
Bilal

> Date: Tue, 22 Apr 2008 11:40:50 +0200
> From: se at hst.aau.dk
> To: minc-users at bic.mni.mcgill.ca
> Subject: Re: [MINC-users] Problem Compiling Minc
> 
> Hi Bilal,
> Try putting the linker libraries at the end of the g++ statements and 
> change the order so the dependency goes from left to right (that usually 
> works with gcc):
> g++ -o MincTest MincThreshold.o MincCorrectPV.o CheckDimensions.o 
> MincTest.o -lvolume_io -lminc -lnetcdf
> 
> I have omitted the -Wl option above, as I'm not sure what you're trying 
> to pass to the linker.
> Also, in your makefile, LDFLAGS should point at the library paths, e.g. 
> -L/usr/local/mni/lib, while LIBS should hold the dynamic libraries, e.g. 
> -lvolume_io ...
> 
> And finally, newline at end of file ;)
> 
> Hope it helps,
> Simon
> 
> Bilal Abdul Mujeeb wrote:
> > Hi,
> > I am using minc library 1.5 to develop some applications. I am working simple c++ classes using minc headers. 
> > I am using them on OS X 10.5.2 with GCC 4.x.x for MAC, it works fine on my mac. But when i took the same code on a linux machine it gives me linking errors. The link libraries for minc in both mac and linux sytem are .a and .la.
> > 
> >  I have added the library path in make file as well but no use. I have tried using Extern "C" to declare function again in my code but in mac it dont give me any error but on linux its gives error of redecleration.
> > 
> > my compiler output is as follow: 
> > ------------------------------------------------------------------
> > bilal at BILAL:~/workspace/MincTest$ make
> > g++ -O2 -g -Wall -fmessage-length=0 -Wno-deprecated   -c -o MincThreshold.o MincThreshold.cpp
> > MincThreshold.cpp:172:2: warning: no newline at end of file
> > MincThreshold.cpp: In member function ‘void MincThreshold::printVolumeInfo(volume_struct*, int*)’:
> > MincThreshold.cpp:28: warning: unused variable ‘value’
> > MincThreshold.cpp: In member function ‘int MincThreshold::saveVolume(volume_struct*, char*, char*)’:
> > MincThreshold.cpp:168: warning: deprecated conversion from string constant to ‘char*’
> > g++ -O2 -g -Wall -fmessage-length=0 -Wno-deprecated   -c -o MincCorrectPV.o MincCorrectPV.cpp
> > MincCorrectPV.cpp: In member function ‘int MincCorrectPV::saveVolume(volume_struct*, char*, char*)’:
> > MincCorrectPV.cpp:82: warning: deprecated conversion from string constant to ‘char*’
> > g++ -O2 -g -Wall -fmessage-length=0 -Wno-deprecated   -c -o CheckDimensions.o CheckDimensions.cpp
> > CheckDimensions.cpp:49:2: warning: no newline at end of file
> > CheckDimensions.cpp: In member function ‘int CheckDimensions::saveVolume(volume_struct*, char*, char*)’:
> > CheckDimensions.cpp:45: warning: deprecated conversion from string constant to ‘char*’
> > g++ -O2 -g -Wall -fmessage-length=0 -Wno-deprecated   -c -o MincTest.o MincTest.cpp
> > MincTest.cpp:33:2: warning: no newline at end of file
> > g++ -lminc -lnetcdf -lvolume_io -Wl -o MincTest MincThreshold.o MincCorrectPV.o CheckDimensions.o MincTest.o
> > MincThreshold.o: In function `MincThreshold::saveVolume(volume_struct*, char*, char*)':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:168: undefined reference to `output_modified_volume'
> > MincThreshold.o: In function `MincThreshold::normalThreshold(volume_struct*, int*, double, int)':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:150: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:158: undefined reference to `set_volume_real_value'
> > MincThreshold.o: In function `MincThreshold::bandThreshold(volume_struct*, int*, double, double, int)':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:128: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:136: undefined reference to `set_volume_real_value'
> > MincThreshold.o: In function `~MincThreshold':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:12: undefined reference to `delete_volume'
> > MincThreshold.o: In function `MincThreshold::printVolumeInfo(volume_struct*, int*)':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:36: undefined reference to `get_volume_nc_data_type'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:40: undefined reference to `get_volume_n_dimensions'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:45: undefined reference to `get_volume_voxel_max'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:46: undefined reference to `get_volume_voxel_min'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:50: undefined reference to `get_volume_real_max'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:51: undefined reference to `get_volume_real_min'
> > MincThreshold.o: In function `MincThreshold::parseArguments(int, char**)':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:97: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:98: undefined reference to `get_volume_sizes'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:106: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:107: undefined reference to `get_volume_sizes'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:85: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:86: undefined reference to `get_volume_sizes'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:75: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:76: undefined reference to `get_volume_sizes'
> > MincThreshold.o: In function `~MincThreshold':
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:12: undefined reference to `delete_volume'
> > /home/bilal/workspace/MincTest/MincThreshold.cpp:12: undefined reference to `delete_volume'
> > MincCorrectPV.o: In function `MincCorrectPV::correctPV_Morphology(volume_struct*, int*, volume_struct*, int*, int, double, volume_struct*, volume_struct*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:114: undefined reference to `copy_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:122: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:123: undefined reference to `set_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:128: undefined reference to `set_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:129: undefined reference to `set_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:143: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:149: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:150: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:164: undefined reference to `get_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:166: undefined reference to `get_volume_real_value'
> > MincCorrectPV.o:/home/bilal/workspace/MincTest/MincCorrectPV.cpp:164: more undefined references to `get_volume_real_value' follow
> > MincCorrectPV.o: In function `MincCorrectPV::correctPV_Morphology(volume_struct*, int*, volume_struct*, int*, int, double, volume_struct*, volume_struct*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:173: undefined reference to `set_volume_real_value'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:167: undefined reference to `set_volume_real_value'
> > MincCorrectPV.o: In function `MincCorrectPV::saveVolume(volume_struct*, char*, char*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:82: undefined reference to `output_modified_volume'
> > MincCorrectPV.o: In function `MincCorrectPV::correct_GM_PV(char*, char*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:91: undefined reference to `copy_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:92: undefined reference to `copy_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:106: undefined reference to `delete_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:107: undefined reference to `delete_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:108: undefined reference to `delete_volume'
> > MincCorrectPV.o: In function `MincCorrectPV::checkMincRange(volume_struct*, double, double)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:75: undefined reference to `get_volume_real_min'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:75: undefined reference to `get_volume_real_max'
> > MincCorrectPV.o: In function `MincCorrectPV::praseParameters(int, char**)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:40: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:40: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:42: undefined reference to `get_volume_sizes'
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:43: undefined reference to `get_volume_sizes'
> > MincCorrectPV.o: In function `MincCorrectPV::correctPV_Morphology(volume_struct*, int*, volume_struct*, int*, int, double, volume_struct*, volume_struct*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:182: undefined reference to `delete_volume'
> > MincCorrectPV.o: In function `MincCorrectPV::correct_GM_PV(char*, char*)':
> > /home/bilal/workspace/MincTest/MincCorrectPV.cpp:109: undefined reference to `delete_volume'
> > CheckDimensions.o: In function `CheckDimensions::saveVolume(volume_struct*, char*, char*)':
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:45: undefined reference to `output_modified_volume'
> > CheckDimensions.o: In function `CheckDimensions::viewDimensions(volume_struct*, int*)':
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:31: undefined reference to `get_volume_voxel_max'
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:35: undefined reference to `set_volume_real_value'
> > CheckDimensions.o: In function `CheckDimensions::parseArguments(int, char**)':
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:18: undefined reference to `input_volume'
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:19: undefined reference to `get_volume_sizes'
> > CheckDimensions.o: In function `~CheckDimensions':
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:12: undefined reference to `delete_volume'
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:12: undefined reference to `delete_volume'
> > /home/bilal/workspace/MincTest/CheckDimensions.cpp:12: undefined reference to `delete_volume'
> > collect2: ld returned 1 exit status
> > make: *** [MincTest] Error 1
> > --------------------------------------------------------------------------------------
> > 
> > my make file......
> > 
> > LDFLAGS = -lminc -lnetcdf -lvolume_io -Wl
> > 
> > CXXFLAGS =    -O2 -g -Wall -fmessage-length=0 -Wno-deprecated
> > 
> > OBJS =        MincThreshold.o MincCorrectPV.o CheckDimensions.o MincTest.o    
> > 
> > LIBS =
> > 
> > TARGET =    MincTest
> > 
> > $(TARGET):    $(OBJS)
> >     $(CXX) $(LDFLAGS) -o $(TARGET) $(OBJS) $(LIBS)
> > 
> > all:    $(TARGET)
> > 
> > clean:
> >     rm -f $(OBJS) $(TARGET)
> > 
> > 
> > 
> > Regards,
> > Bilal
> > 
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