Standard C libraries not found when compiling mex files in Matlab

Question

Update: I installed XCode and changed SDKROOT in mexopts.sh to reflect the actual path as described here, but I still get this error when I include mex.h:

In file included from /Applications/MATLAB_R2012b.app/extern/include/matrix.h:294,
                 from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
                 from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:61:21: error: float.h: No such file or directory

    mex: compile of ' "test.c"' failed.

I'm trying to compile a trivial C file for use in Matlab through mex, but it seems to never find default libraries that I know are installed. For instance, trying to compile the following:

#include <string.h>
int main() {
    return 0;
}

gives me the error:

test.c:1:20: error: string.h: No such file or directory
mex: compile of ' "test.c"' failed.

even though it compiles fine using gcc. Worse, when I try to include mex.h like so:

#include "mex.h"
int main() {
    return 0;
}

I get the following error:

In file included from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
                 from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:293:20: error: stddef.h: No such file or directory
In file included from /Applications/MATLAB_R2012b.app/extern/include/matrix.h:294,
                 from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
                 from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:43:20: error: limits.h: No such file or directory
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:46:21: error: stdbool.h: No such file or directory
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:61:21: error: float.h: No such file or directory
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:777:2: error: #error "This code must be compiled using a 2's complement representation for signed integer values"
In file included from /Applications/MATLAB_R2012b.app/extern/include/matrix.h:294,
                 from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
                 from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/tmwtypes.h:823: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'CHAR16_T'
In file included from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
                 from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:319: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mxChar'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:375: error: expected ')' before 'n'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:383: error: expected ')' before 'n'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:397: error: expected declaration specifiers or '...' before 'size_t'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:590: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mxGetNumberOfElements'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:632: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:688: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mxGetM'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:700: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mxGetN'
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:750: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'mxGetElementSize'
In file included from /Applications/MATLAB_R2012b.app/extern/include/mex.h:58,
             from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:851:20: error: stdlib.h: No such file or directory
/Applications/MATLAB_R2012b.app/extern/include/matrix.h:1072: error: expected ')' before 'm'
In file included from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/mex.h:91: error: expected specifier-qualifier-list before 'size_t'
In file included from test.c:2:
/Applications/MATLAB_R2012b.app/extern/include/mex.h:161:19: error: stdio.h: No such file or directory

    mex: compile of ' "test.c"' failed.

I assume mex isn't looking in the right place for these libraries, or the installation is corrupt somehow, but I have no idea how to fix it.

Mac OSX Mountain Lion + XCode 4.5.2, Matlab R2012b, gcc 4.2.1

It compiles fine if I don't include any libraries, and remove any reference to mex-specific types like mxArray. — David Pfau

barnie82 barnie82 · Accepted Answer · 2012-11-18T06:09:19

The include file(s) need to be in your PATH (type path to show these folders) unless you specifically include them using mex -Ipathname. You can click 'File->Set Path' and add the folder containing your string.h.

Standard C libraries not found when compiling mex files in Matlab

3 Answers