Undefined reference to __cxa_atexit with Matlab/CUDA MEX - matlab

I'm compiling some CUDA/C to run as a MEX library in Matlab, and I am getting the following error:
Error using mex
/usr/lib/x86_64-linux-gnu/libc_nonshared.a(atexit.oS): In function `atexit':
(.text+0x12): undefined reference to `__cxa_atexit'
collect2: error: ld returned 1 exit status
I'm assuming this means I need to link in some additional library, but what?
My current compile command is:
mex -L/usr/local/cuda/lib64 -lcudart -I./ A.cpp B.cpp C.cu D.cpp
I have several kernels to compile into mex, and interestingly some of them work and some of them don't. I don't immediately see what the difference is between them - I certainly don't call atexit anywhere in my source.
Here is the output of a verbose mex:
Verbose mode is on.
Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require the use of
-largeArrayDims and remove the -compatibleArrayDims option.
For more information:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
... Looking for compiler 'nvcc' ...
... Looking for environment variable 'MW_NVCC_PATH' ...Yes ('/usr/local/cuda-6.5/bin/nvcc').
... Looking for folder '/usr/local/cuda-6.5/bin' ...Yes.
... Looking for file '/usr/local/cuda-6.5/bin/nvcc' ...Yes.
... Executing command 'which g++' ...Yes ('/usr/bin/g++').
... Executing command 'g++ -print-file-name=libstdc++.so' ...Yes ('/usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so').
Found installed compiler 'nvcc'.
Options file details
-------------------------------------------------------------------
Compiler location: /usr/local/cuda-6.5/bin/nvcc
Options file: /home/nick/Documents/FrameLab/matlab/mex/source codes/mex_CUDA_glnxa64.xml
CMDLINE2 : /usr/bin/g++ -pthread -Wl,--no-undefined -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5 -o Atx_fan_mf.mexa64
CXX : /usr/local/cuda-6.5/bin/nvcc
DEFINES : -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE
MATLABMEX : -DMATLAB_MEX_FILE
NVCCFLAGS : -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS
CXXFLAGS : --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread
INCLUDE : -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/"
CXXOPTIMFLAGS : -O -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/g++
LDFLAGS : -pthread -Wl,--no-undefined
LDTYPE : -shared
LINKEXPORT : -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map"
LINKLIBS : -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexa64
NVCC : /usr/local/cuda-6.5/bin/nvcc
GCC : /usr/bin/g++
CPPLIB_DIR : /usr/lib/gcc/x86_64-linux-gnu/4.8/libstdc++.so
MATLABROOT : /usr/local/MATLAB/R2014a
ARCH : glnxa64
SRC : "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp";"/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp"
OBJ : /tmp/mex_86382821022260_3849/Atx_fan_mf.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o;/tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o;/tmp/mex_86382821022260_3849/find_l.o;/tmp/mex_86382821022260_3849/find_area.o
OBJS : /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o
SRCROOT : /home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf
DEF : /tmp/mex_86382821022260_3849/Atx_fan_mf.def
EXP : Atx_fan_mf.exp
LIB : Atx_fan_mf.lib
EXE : Atx_fan_mf.mexa64
ILK : Atx_fan_mf.ilk
MANIFEST : Atx_fan_mf.mexa64.manifest
TEMPNAME : Atx_fan_mf
EXEDIR :
EXENAME : Atx_fan_mf
OPTIM : -O -DNDEBUG
LINKOPTIM : -O
CMDLINE1_0 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf.o
CMDLINE1_1 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o
CMDLINE1_2 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o
CMDLINE1_3 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o
CMDLINE1_4 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o
CMDLINE1_5 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp" -o /tmp/mex_86382821022260_3849/find_l.o
CMDLINE1_6 : /usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp" -o /tmp/mex_86382821022260_3849/find_area.o
CMDLINE3_0 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf.o
CMDLINE3_1 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o
CMDLINE3_2 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o
CMDLINE3_3 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o
CMDLINE3_4 : rm -f /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o
CMDLINE3_5 : rm -f /tmp/mex_86382821022260_3849/find_l.o
CMDLINE3_6 : rm -f /tmp/mex_86382821022260_3849/find_area.o
-------------------------------------------------------------------
Building with 'nvcc'.
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_gpu_new_fb.cu" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/Atx_fan_mf_cpu_new_fb.cpp" -o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_l.cpp" -o /tmp/mex_86382821022260_3849/find_l.o
/usr/local/cuda-6.5/bin/nvcc -c -DMX_COMPAT_32 --compiler-options=-D_GNU_SOURCE,-DMATLAB_MEX_FILE -I./ -I"/usr/local/MATLAB/R2014a/extern/include" -I"/usr/local/MATLAB/R2014a/toolbox/distcomp/gpu/extern/include/" -gencode=arch=compute_30,code=\"sm_30,compute_30\" $NVCC_FLAGS --compiler-options=-ansi,-fexceptions,-fPIC,-fno-omit-frame-pointer,-pthread -O -DNDEBUG "/home/nick/Documents/FrameLab/matlab/mex/source codes/find_area.cpp" -o /tmp/mex_86382821022260_3849/find_area.o
/usr/bin/g++ -pthread -Wl,--no-undefined -shared -O -Wl,--version-script,"/usr/local/MATLAB/R2014a/extern/lib/glnxa64/mexFunction.map" /tmp/mex_86382821022260_3849/Atx_fan_mf.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_gpu_new_fb.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new.o /tmp/mex_86382821022260_3849/Atx_fan_mf_cpu_new_fb.o /tmp/mex_86382821022260_3849/find_l.o /tmp/mex_86382821022260_3849/find_area.o -lcudart -L/usr/local/cuda/lib64 -Wl,-rpath-link,/usr/local/MATLAB/R2014a/bin/glnxa64 -L"/usr/local/MATLAB/R2014a/bin/glnxa64" -lmx -lmex -lmat -lm -lmwgpu /usr/local/MATLAB/R2014a/bin/glnxa64/libcudart.so.5.5 -o Atx_fan_mf.mexa64
I'm wondering if I should try using a different version of g++ or the c++ libraries? I'm not sure how to change the CPPLIB_DIR variable...Matlab has made it more difficult to mess with mex settings in 2014a.
Thanks for any thoughts!

I got the same error using Matlab 2015 Prerelease on Ubuntu 14.04 with CUDA 6.5 and g++4.8. Thanks to Matlab support we figured out, that manually linking does the trick. Here is my compile script for the matlab mex/gpu example:
myArch = computer('arch'); pathToOpts = fullfile(matlabroot, ... 'toolbox', 'distcomp', 'gpu', ... 'extern', 'src', 'mex', myArch,'gcc',... ['mex_CUDA_' myArch '.xml']); copyfile(pathToOpts,'.','f')
mex -v -largeArrayDims mexGPUExample.cu -lstdc++ -lc

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"/usr/bin/perl.exe" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/Algorithm/AhoCorasick/XS/XS.bs 644
g++ -c -Wall -std=c++11 -DUSEIMPORTLIB -march=x86-64 -mtune=generic -O2 -pipe -DVERSION=\"0.04\" -DXS_VERSION=\"0.04\" "-I/usr/lib/perl5/core_perl/CORE" Matcher.cpp
"/usr/bin/perl.exe" "/usr/share/perl5/core_perl/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl5/core_perl/ExtUtils/typemap' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/perlobject.map' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/typemap' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/typemap' ac.xs > ac.xsc
mv ac.xsc ac.c
g++ -c -Wall -std=c++11 -DUSEIMPORTLIB -march=x86-64 -mtune=generic -O2 -pipe -DVERSION=\"0.04\" -DXS_VERSION=\"0.04\" "-I/usr/lib/perl5/core_perl/CORE" ac.c
In file included from ac.xs:11:
ppport.h:4594: warning: "WIDEST_UTYPE" redefined
4594 | # define WIDEST_UTYPE U64TYPE
|
In file included from /usr/lib/perl5/core_perl/CORE/perl.h:2753,
from ac.xs:5:
/usr/lib/perl5/core_perl/CORE/handy.h:1251: note: this is the location of the previous definition
1251 | # define WIDEST_UTYPE U64
|
In file included from /usr/lib/perl5/core_perl/CORE/perl.h:28,
from ac.xs:5:
/usr/lib/perl5/core_perl/CORE/config.h:1011:20: error: ‘sigjmp_buf’ does not name a type; did you mean ‘Sigjmp_buf’?
1011 | #define Sigjmp_buf sigjmp_buf
| ^~~~~~~~~~
/usr/lib/perl5/core_perl/CORE/cop.h:34:5: note: in expansion of macro ‘Sigjmp_buf’
34 | Sigjmp_buf je_buf; /* uninit if je_prev is NULL */
| ^~~~~~~~~~
make: *** [Makefile:341: ac.o] Error 1
What can be the problem here?
It seems like the C++ option -std=c++11 is confusing MSYS2. In Makefile.PL line #20, we have:
CCFLAGS => '-Wall -std=c++11',
if I remove -std=c++11 and save the file and recompile, it works fine:
$ make clean
$ perl Makefile.PL
$ make
cp lib/Algorithm/AhoCorasick/XS.pm blib/lib/Algorithm/AhoCorasick/XS.pm
Running Mkbootstrap for XS ()
chmod 644 "XS.bs"
"/usr/bin/perl.exe" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/Algorithm/AhoCorasick/XS/XS.bs 644
g++ -c -Wall -DUSEIMPORTLIB -march=x86-64 -mtune=generic -O2 -pipe -DVERSION=\"0.04\" -DXS_VERSION=\"0.04\" "-I/usr/lib/perl5/core_perl/CORE" Matcher.cpp
"/usr/bin/perl.exe" "/usr/share/perl5/core_perl/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl5/core_perl/ExtUtils/typemap' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/perlobject.map' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/typemap' -typemap '/home/hakon/perl/cpan-source/Algorithm-AhoCorasick-XS-0.04/typemap' ac.xs > ac.xsc
mv ac.xsc ac.c
g++ -c -Wall -DUSEIMPORTLIB -march=x86-64 -mtune=generic -O2 -pipe -DVERSION=\"0.04\" -DXS_VERSION=\"0.04\" "-I/usr/lib/perl5/core_perl/CORE" ac.c
In file included from ac.xs:11:
ppport.h:4594: warning: "WIDEST_UTYPE" redefined
4594 | # define WIDEST_UTYPE U64TYPE
|
In file included from /usr/lib/perl5/core_perl/CORE/perl.h:2753,
from ac.xs:5:
/usr/lib/perl5/core_perl/CORE/handy.h:1251: note: this is the location of the previous definition
1251 | # define WIDEST_UTYPE U64
|
g++ -c -Wall -DUSEIMPORTLIB -march=x86-64 -mtune=generic -O2 -pipe -DVERSION=\"0.04\" -DXS_VERSION=\"0.04\" "-I/usr/lib/perl5/core_perl/CORE" test.c
rm -f blib/arch/auto/Algorithm/AhoCorasick/XS/XS.dll
g++ --shared -Wl,--enable-auto-import -Wl,--export-all-symbols -Wl,--enable-auto-image-base -fstack-protector-strong Matcher.o ac.o test.o -o blib/arch/auto/Algorithm/AhoCorasick/XS/XS.dll \
/usr/lib/perl5/core_perl/CORE/msys-perl5_32.dll \
chmod 755 blib/arch/auto/Algorithm/AhoCorasick/XS/XS.dll
Manifying 1 pod document
$ make test
"/usr/bin/perl.exe" -MExtUtils::Command::MM -e 'cp_nonempty' -- XS.bs blib/arch/auto/Algorithm/AhoCorasick/XS/XS.bs 644
PERL_DL_NONLAZY=1 "/usr/bin/perl.exe" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/basic.t ....... ok
t/details.t ..... ok
t/edge_cases.t .. ok
t/utf8.t ........ ok
t/variation.t ... ok
All tests successful.
Files=5, Tests=1624, 2 wallclock secs ( 0.14 usr 0.06 sys + 0.64 cusr 0.85 csys = 1.69 CPU)
Result: PASS
See also this question.

Why make utility cannot find header file?

I have been working in Eclipse based IDE called Vitis (IDE from Xilinx).
I have an automatically generated software project containing three automatically
generated Makefiles. Organization of the project is following:
zynq_fsbl
-Makefile_level_01
-main.c
-zynq_fsbl_bsp
-Makefile_level_02
-ps7_cortexa9_0
-code
-include
-Config.h
-lib
-libsrc
-peripheral_01
-src
-driver_peripheral_01.c
-driver_peripheral_01.h
-Makefile_level_03_01
-peripheral_02
-src
-driver_peripheral_02.c
-driver_peripheral_02.h
-Makefile_level_03_02
- ... same pattern repeats for other perpherals
Makefile_level_01 contains:
# Auto Generated by Xilinx generate_app. Modify at your own risk
CC := arm-none-eabi-gcc
CC_FLAGS := -MMD -MP -mcpu=cortex-a9 -mfpu=vfpv3 -mfloat-abi=hard
CFLAGS :=
LN_FLAGS := -mcpu=cortex-a9 -mfpu=vfpv3 -mfloat-abi=hard -Wl,-build-id=none -specs=Xilinx.spec -lrsa -Wl,--start-group,-lxil,-lgcc,-lc,--end-group -Wl,--start-group,-lxilffs,-lxil,-lgcc,-lc,--end-group -Wl,--start-group,-lrsa,-lxil,-lgcc,-lc,--end-group -Wl,--gc-sections
c_SOURCES := $(wildcard *.c)
S_SOURCES := $(wildcard *.S)
INCLUDES := $(wildcard *.h)
OBJS := $(patsubst %.c, %.o, $(c_SOURCES))
OBJS += $(patsubst %.S, %.o, $(S_SOURCES))
LSCRIPT := -Tlscript.ld
CURRENT_DIR = $(shell pwd)
DEPFILES := $(patsubst %.o, %.d, $(OBJS))
LIBS := zynq_fsbl_bsp/ps7_cortexa9_0/lib/libxil.a
EXEC := executable.elf
INCLUDEPATH := -Izynq_fsbl_bsp/ps7_cortexa9_0/include -I.
LIBPATH := -Lzynq_fsbl_bsp/ps7_cortexa9_0/lib -L./
all: $(EXEC)
$(EXEC): $(LIBS) $(OBJS) $(INCLUDES)
$(CC) -o $# $(OBJS) $(CC_FLAGS) $(CFLAGS) $(LN_FLAGS) $(LIBPATH) $(LSCRIPT)
$(LIBS):
$(MAKE) -C zynq_fsbl_bsp
%.o:%.c
$(CC) $(CC_FLAGS) $(CFLAGS) -c $< -o $# $(INCLUDEPATH)
%.o:%.S
$(CC) $(CC_FLAGS) $(CFLAGS) -c $< -o $# $(INCLUDEPATH)
%.o:%.s
$(CC) $(CC_FLAGS) $(CFLAGS) -c $< -o $# $(INCLUDEPATH)
clean:
rm -rf $(OBJS) $(LIBS) $(EXEC) *.o
-include $(DEPFILES)
Makefile_level_02 contains:
# Makefile generated by Xilinx.
PROCESSOR = ps7_cortexa9_0
LIBRARIES = ${PROCESSOR}/lib/libxil.a
BSP_MAKEFILES := $(wildcard $(PROCESSOR)/libsrc/*/src/Makefile)
SUBDIRS := $(patsubst %/Makefile, %, $(BSP_MAKEFILES))
ifneq (,$(findstring win,$(RDI_PLATFORM)))
SHELL = CMD
endif
all: libs
#echo 'Finished building libraries'
include: $(addsuffix /make.include,$(SUBDIRS))
libs: $(addsuffix /make.libs,$(SUBDIRS))
clean: $(addsuffix /make.clean,$(SUBDIRS))
$(PROCESSOR)/lib/libxil.a: $(PROCESSOR)/lib/libxil_init.a
cp -f $< $#
%/make.include: $(if $(wildcard $(PROCESSOR)/lib/libxil_init.a),$(PROCESSOR)/lib/libxil.a,)
#echo "Running Make include in $(subst /make.include,,$#)"
$(MAKE) -C $(subst /make.include,,$#) -s include "SHELL=$(SHELL)" "COMPILER=arm-none-eabi-gcc" "ASSEMBLER=arm-none-eabi-as" "ARCHIVER=arm-none-eabi-ar" "COMPILER_FLAGS= -O2 -c" "EXTRA_COMPILER_FLAGS=-mcpu=cortex-a9 -mfpu=vfpv3 -mfloat-abi=hard -nostartfiles -g -Wall -Wextra"
%/make.libs: include
#echo "Running Make libs in $(subst /make.libs,,$#)"
$(MAKE) -C $(subst /make.libs,,$#) -s libs "SHELL=$(SHELL)" "COMPILER=arm-none-eabi-gcc" "ASSEMBLER=arm-none-eabi-as" "ARCHIVER=arm-none-eabi-ar" "COMPILER_FLAGS= -O2 -c" "EXTRA_COMPILER_FLAGS=-mcpu=cortex-a9 -mfpu=vfpv3 -mfloat-abi=hard -nostartfiles -g -Wall -Wextra"
%/make.clean:
$(MAKE) -C $(subst /make.clean,,$#) -s clean
clean:
rm -f ${PROCESSOR}/lib/libxil.a
Makefile_level_03 for peripheral_01 contains:
COMPILER=
ARCHIVER=
CP=cp
COMPILER_FLAGS=
EXTRA_COMPILER_FLAGS=
LIB=libxil.a
LEVEL=0
RELEASEDIR=../../../lib
INCLUDEDIR=../../../include
INCLUDES=-I./. -I${INCLUDEDIR}
INCLUDEFILES=*.h
LIBSOURCES=*.c
OUTS = *.o
libs:
echo "Compiling driver_peripheral_01 ..."
$(COMPILER) $(COMPILER_FLAGS) $(EXTRA_COMPILER_FLAGS) $(INCLUDES) $(LIBSOURCES)
$(ARCHIVER) -r ${RELEASEDIR}/${LIB} ${OUTS}
make clean
include:
${CP} $(INCLUDEFILES) $(INCLUDEDIR)
clean:
rm -rf ${OUTS}
My problem is that I am not able to compile the driver_peripheral_01.c module due to the problem with
Config.h header file inclusion. The "fatal error: Config.h: No such file or directory" is being invoked despite the fact that I have copied the header file in question into the include subdirectory in project directory structure. Does anybody have any idea why the make cannot find the Config.h header file? Thanks for any suggestions.

Matlab mex code not compiling using a Makefile - Undefined Reference

I have a matlab mex extension which I want to compile using a Makefile. The Linker does not seem to find the mex libraries. Here is the Makefile:
MEXSUFFIX = mexa64
IX = mexa64
MATLABHOME = /usr/local/MATLAB/R2013b
MEX = g++
MEXCXX = echo
CXX = g++
CFLAGS = -fPIC -pthread -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -O3 -DNDEBUG
LIBS = -lm
INCLUDE = -I$(MATLABHOME)/extern/include -Icommon
#g++
MEXFLAGS = -shared -Wl,--no-undefined -Wl,-rpath-link,$(MATLABHOME)/bin/glnxa64 -L$(MATLABHOME)/bin/glnxa64 -lmx -lmex -lmat -lm
PROJECTS = residualfm
MEXDIR = ..
all: $(PROJECTS)
residualfm: residualfm/functions.o
$(MEX) $(MEXFLAGS) $(LIBS) -o $(MEXDIR)/$#.$(MEXSUFFIX) $^
.cpp.o:
$(CXX) -c -o $# $< $(CFLAGS) $(INCLUDE)
clean:
rm -f common/*.o
for proj in $(PROJECTS); do \
rm -f $$proj/*.o; \
rm -f $(MEXDIR)/$$proj.$(MEXSUFFIX); \
done
and here my filestructure:
$ ls *
Makefile mex.kdev4 sfr_mex.sln sfr_mex.suo sfr_mex.v11.suo
residualfm:
DllMain.cpp residualfm_variant.def stdafx.h
functions.cpp residualfm_variant.vcxproj timing.cpp
functions.o residualfm_variant.vcxproj.user
maxflow_classic_boykov stdafx.cpp
Here is the error:
$ make
g++ -shared -Wl,--no-undefined -Wl,-rpath-link,/usr/local/MATLAB/R2013b/bin/glnxa64 -L/usr/local/MATLAB/R2013b/bin/glnxa64 -lmx -lmex -lmat -lm -lm -o ../residualfm.mexa64 residualfm/functions.o
residualfm/functions.o: In function `mexFunction':
functions.cpp:(.text+0x27b): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x2a0): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x2c7): undefined reference to `mxGetClassID'
functions.cpp:(.text+0x2e5): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x301): undefined reference to `mxGetNumberOfDimensions'
functions.cpp:(.text+0x320): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x341): undefined reference to `mxGetData'
functions.cpp:(.text+0x350): undefined reference to `mxGetDimensions'
functions.cpp:(.text+0x371): undefined reference to `mxGetNumberOfElements'
functions.cpp:(.text+0x390): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x3aa): undefined reference to `mxGetScalar'
functions.cpp:(.text+0x3c5): undefined reference to `mxGetNumberOfElements'
functions.cpp:(.text+0x3e4): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0x3fe): undefined reference to `mxGetScalar'
functions.cpp:(.text+0x4f5): undefined reference to `mexErrMsgTxt'
functions.cpp:(.text+0xdd3): undefined reference to `mxCreateNumericArray'
functions.cpp:(.text+0xdde): undefined reference to `mxGetData'
functions.cpp:(.text+0xefe): undefined reference to `mxGetScalar'
functions.cpp:(.text+0xf9d): undefined reference to `mxCreateNumericArray'
functions.cpp:(.text+0xfa8): undefined reference to `mxGetData'
functions.cpp:(.text+0x11dc): undefined reference to `mxCreateSparse'
functions.cpp:(.text+0x11e7): undefined reference to `mxGetJc'
functions.cpp:(.text+0x11f2): undefined reference to `mxGetIr'
functions.cpp:(.text+0x11fd): undefined reference to `mxGetPr'
residualfm/functions.o: In function `visit_backwards(Node*, Node*, double*, int)':
functions.cpp:(.text+0x232): undefined reference to `mexErrMsgTxt'
collect2: error: ld returned 1 exit status
make: *** [residualfm] Error 1
Compiling from matlab using mex functions.cpp works fine
edit:
Thanks for the hints!
Solved (but not understood):
Changing the order in residualfm: residualfm/functions.o from:
$(MEX) $(MEXFLAGS) $(LIBS) -o $(MEXDIR)/$#.$(MEXSUFFIX) $^
to
$(MEX) -o $(MEXDIR)/$#.$(MEXSUFFIX) $^ $() $(MEXFLAGS) $(LIBS)
solved the problem. Can someone explain this?
(Solved in the comments and edits. See Question with no answers, but issue solved in the comments (or extended in chat) )
#Amro wrote:
Linked libraries must come after the file being compiled in the command-line
The OP wrote:
Changing the order in residualfm: residualfm/functions.o from:
$(MEX) $(MEXFLAGS) $(LIBS) -o $(MEXDIR)/$#.$(MEXSUFFIX) $^
to
$(MEX) -o $(MEXDIR)/$#.$(MEXSUFFIX) $^ $() $(MEXFLAGS) $(LIBS)
solved the problem.

CMake output in Eclipse CDT console

Making project through command line behaves as expected and provides neat and colored output:
However, when invoking make through Eclipse - I get the following garbage:
**** Build of configuration Debug for project New2 ****
make -C debug -j all
make: Entering directory `/d/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug'
/D/Software/CMake/bin/cmake.exe -H"/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2" -B"/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug" --check-build-system CMakeFiles/Makefile.cmake 0
/D/Software/CMake/bin/cmake.exe -E cmake_progress_start "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles/progress.marks"
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/d/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug'
make -f CMakeFiles/go.dir/build.make CMakeFiles/go.dir/depend
make[2]: Entering directory `/d/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug'
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 8
[ 12%] [34m[1mGenerating moc_GLWidget.cxx
[0m/D/Software/Qt/4.8.0/bin/moc.exe #moc_GLWidget.cxx_parameters
/D/Software/CMake/bin/cmake.exe -E cmake_depends "MSYS Makefiles" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug" "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles/go.dir/DependInfo.cmake" --color=
make[2]: Leaving directory `/d/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug'
make -f CMakeFiles/go.dir/build.make CMakeFiles/go.dir/build
make[2]: Entering directory `/d/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug'
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 1
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 2
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 3
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 4
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 5
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 6
/D/Software/CMake/bin/cmake.exe -E cmake_progress_report "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/CMakeFiles" 7
[ 25%] [ 37%] [ 50%] [ 62%] [ 75%] [ 87%] [100%] [32mBuilding CXX object CMakeFiles/go.dir/Perfomance.cpp.obj
[0m[32mBuilding CXX object CMakeFiles/go.dir/Camera.cpp.obj
[0m/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/Perfomance.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/Perfomance.cpp"
[32mBuilding CXX object CMakeFiles/go.dir/main.cpp.obj
[0m[32mBuilding CXX object CMakeFiles/go.dir/moc_GLWidget.cxx.obj
[0m[32mBuilding CXX object CMakeFiles/go.dir/Milliseconds.cpp.obj
[0m[32mBuilding CXX object CMakeFiles/go.dir/Keyboard.cpp.obj
[0m[32mBuilding CXX object CMakeFiles/go.dir/Seconds.cpp.obj
[0m/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/Camera.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/Camera.cpp"
/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/moc_GLWidget.cxx.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/debug/moc_GLWidget.cxx"
/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/Keyboard.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/Keyboard.cpp"
/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/main.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/main.cpp"
/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/Seconds.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/Seconds.cpp"
/D/Software/MinGW/bin/g++.exe -DQT_DLL -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_DLL -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_HAVE_MMX -DQT_HAVE_3DNOW -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_THREAD_SUPPORT -DQT_DEBUG -fmessage-length=0 -mfpmath=sse -msse2 -msse3 -mssse3 -msse4 -fopenmp -g #CMakeFiles/go.dir/includes_CXX.rsp -o CMakeFiles/go.dir/Milliseconds.cpp.obj -c "/D/Users/Haroogan/Development/Eclipse CDT/Workspace/New2/Milliseconds.cpp"
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There is no coloring, but that's understandable. However, the output structure is completely messed up and appears to be grouped in a wrong way. Furthermore, this "[0m[32" garbage is the most annoying feature :)
Any suggestions?
Try to configure/generate your project with -DCMAKE_COLOR_MAKEFILE=OFF.