mex cannot find gfortran compiler (Mac OS)

 gfortran works from Terminal on MacOS
( which gfortran
/usr/local/bin/gfortran
)
 but doesn't from inside MATLAB
 mex -v timestwo.F
 **************************************************************************
  Warning: 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, see:
           http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html
**************************************************************************
 -> mexopts.sh sourced from directory (DIR = $PREF_DIR)
   FILE = /Users/murphy/.matlab/R2013a/mexopts.sh
----------------------------------------------------------------
->    MATLAB                = /Applications/MATLAB_R2013a.app
->    CC                    = xcrun  -sdk macosx10.7  clang
->    CC flags:
         CFLAGS             = -fno-common -arch x86_64 -isysroot  -mmacosx-version-min=10.7  -fexceptions
         CDEBUGFLAGS        = -g
         COPTIMFLAGS        = -O2 -DNDEBUG
         CLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    CXX                   = xcrun  -sdk macosx10.7  clang++
->    CXX flags:
         CXXFLAGS           = -fno-common -fexceptions -arch x86_64 -isysroot  -mmacosx-version-min=10.7
         CXXDEBUGFLAGS      = -g
         CXXOPTIMFLAGS      = -O2 -DNDEBUG
         CXXLIBS            = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    FC                    = gfortran
->    FC flags:
         FFLAGS             = -fexceptions -m64 -fbackslash
         FDEBUGFLAGS        = -g
         FOPTIMFLAGS        = -O
         FLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L -lgfortran -L -lgfortranbegin
         arguments          =  -DMX_COMPAT_32
->    LD                    = xcrun -sdk macosx10.7 clang
->    Link flags:
         LDFLAGS            = -arch x86_64 -Wl,-syslibroot, -mmacosx-version-min=10.7 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/fexport.map
         LDDEBUGFLAGS       = -g
         LDOPTIMFLAGS       = -O
         LDEXTENSION        = .mexmaci64
         arguments          = 
->    LDCXX                 = 
->    Link flags:
         LDCXXFLAGS         = 
         LDCXXDEBUGFLAGS    = 
         LDCXXOPTIMFLAGS    = 
         LDCXXEXTENSION     = 
         arguments          = 
----------------------------------------------------------------
 -> gfortran -c  -I/Applications/MATLAB_R2013a.app/extern/include -I/Applications/MATLAB_R2013a.app/simulink/include -fexceptions -m64 -fbackslash  -DMX_COMPAT_32 -O  "timestwo.F"
 /Applications/MATLAB_R2013a.app/bin/mex: line 1343: gfortran: command not found
    mex: compile of ' "timestwo.F"' failed.
 Error using mex (line 206)
Unable to complete successfully.

Answer 1

[Ken Atwell]

The PATH as set by the Terminal application may be different than as set by launch an application from the Dock. Try this in MATLAB:

 getenv('PATH')

Is /usr/local/bin there?

Now try launching MATLAB from the Terminal window (where gfortran is on the path):

 /Applications/MATLAB_R2013a.app/bin/matlab

My guess is that MEX will work if you launch MATLAB this second way.

[Robert]

 Thanks, that helped.  I put 
    setenv('PATH', [getenv('PATH') ':/usr/local/bin']);
 into startup.m.  However, now I get
 >> getenv('PATH')

 ans =

 /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

 >> mex -v timestwo.F

 **************************************************************************
  Warning: 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, see:
           http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html
 **************************************************************************

 -> mexopts.sh sourced from directory (DIR = $PREF_DIR)
   FILE = /Users/murphy/.matlab/R2013a/mexopts.sh
 ----------------------------------------------------------------
->    MATLAB                = /Applications/MATLAB_R2013a.app
->    CC                    = xcrun  -sdk macosx10.7  clang
->    CC flags:
         CFLAGS             = -fno-common -arch x86_64 -isysroot  -mmacosx-version-min=10.7  -fexceptions
         CDEBUGFLAGS        = -g
         COPTIMFLAGS        = -O2 -DNDEBUG
         CLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    CXX                   = xcrun  -sdk macosx10.7  clang++
->    CXX flags:
         CXXFLAGS           = -fno-common -fexceptions -arch x86_64 -isysroot  -mmacosx-version-min=10.7
         CXXDEBUGFLAGS      = -g
         CXXOPTIMFLAGS      = -O2 -DNDEBUG
         CXXLIBS            = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    FC                    = gfortran
->    FC flags:
         FFLAGS             = -fexceptions -m64 -fbackslash
         FDEBUGFLAGS        = -g
         FOPTIMFLAGS        = -O
         FLIBS              = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.8.2/../../.. -lgfortran -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.8.2 -lgfortranbegin
         arguments          =  -DMX_COMPAT_32
->    LD                    = xcrun -sdk macosx10.7 clang
->    Link flags:
         LDFLAGS            = -arch x86_64 -Wl,-syslibroot, -mmacosx-version-min=10.7 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/fexport.map
         LDDEBUGFLAGS       = -g
         LDOPTIMFLAGS       = -O
         LDEXTENSION        = .mexmaci64
         arguments          = 
->    LDCXX                 = 
->    Link flags:
         LDCXXFLAGS         = 
         LDCXXDEBUGFLAGS    = 
         LDCXXOPTIMFLAGS    = 
         LDCXXEXTENSION     = 
         arguments          = 
----------------------------------------------------------------

 -> gfortran -c  -I/Applications/MATLAB_R2013a.app/extern/include -I/Applications/MATLAB_R2013a.app/simulink/include -fexceptions -m64 -fbackslash  -DMX_COMPAT_32 -O  "timestwo.F"

 -> xcrun -sdk macosx10.7 clang -O -arch x86_64 -Wl,-syslibroot, -mmacosx-version-min=10.7 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/fexport.map -o  "timestwo.mexmaci64"  timestwo.o  -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.8.2/../../.. -lgfortran -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.8.2 -lgfortranbegin

 xcodebuild: error: SDK "macosx10.7" cannot be located.
xcrun: error: unable to find utility "clang", not a developer tool or in PATH

    mex: link of ' "timestwo.mexmaci64"' failed.

 Error using mex (line 206)
 Unable to complete successfully.

[Ken Atwell]

This is almost certainly an unrelated problem with Xcode 5 no longer shipping the 10.7 SDK (R2013a was released before Xcode 5). For a work-around, see:

http://www.mathworks.com/matlabcentral/answers/103904

Answer 2

[Zhong Hao]

Upon setenv('PATH', [getenv('PATH') ':/usr/local/bin']);

I managed to successfully compile timestwo.F

However I got an error while trying to compile yprimefg.F

****************************************************************************************

>> mex -v yprimefg.F

**************************************************************************
  Warning: 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, see:
           http://www.mathworks.com/help/techdoc/matlab_external/bsflnue-1.html
**************************************************************************

-> mexopts.sh sourced from directory (DIR = $PREF_DIR)
   FILE = /Users/neozhonghao/.matlab/R2012a/mexopts.sh
----------------------------------------------------------------
->    MATLAB                = /Applications/MATLAB_R2012a.app
->    CC                    = llvm-gcc
->    CC flags:
         CFLAGS             = -fno-common -no-cpp-precomp -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/ -mmacosx-version-min=10.5  -fexceptions
         CDEBUGFLAGS        = -g
         COPTIMFLAGS        = -O2 -DNDEBUG
         CLIBS              = -L/Applications/MATLAB_R2012a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    CXX                   = llvm-g++
->    CXX flags:
         CXXFLAGS           = -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/ -mmacosx-version-min=10.5
         CXXDEBUGFLAGS      = -g
         CXXOPTIMFLAGS      = -O2 -DNDEBUG
         CXXLIBS            = -L/Applications/MATLAB_R2012a.app/bin/maci64 -lmx -lmex -lmat -lstdc++
         arguments          =  -DMX_COMPAT_32
->    FC                    = gfortran
->    FC flags:
         FFLAGS             = -fexceptions -m64 -fbackslash
         FDEBUGFLAGS        = -g
         FOPTIMFLAGS        = -O
         FLIBS              = -L/Applications/MATLAB_R2012a.app/bin/maci64 -lmx -lmex -lmat -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.9.0/../../.. -lgfortran -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.9.0 -lgfortranbegin
         arguments          =  -DMX_COMPAT_32
->    LD                    = llvm-gcc
->    Link flags:
         LDFLAGS            = -Wl,-twolevel_namespace -undefined error -arch x86_64 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/ -mmacosx-version-min=10.5 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2012a.app/extern/lib/maci64/fexport.map
         LDDEBUGFLAGS       = -g
         LDOPTIMFLAGS       = -O
         LDEXTENSION        = .mexmaci64
         arguments          = 
->    LDCXX                 = 
->    Link flags:
         LDCXXFLAGS         = 
         LDCXXDEBUGFLAGS    = 
         LDCXXOPTIMFLAGS    = 
         LDCXXEXTENSION     = 
         arguments          = 
----------------------------------------------------------------

    -> gfortran -c  -I/Applications/MATLAB_R2012a.app/extern/include -I/Applications/MATLAB_R2012a.app/simulink/include -fexceptions -m64 -fbackslash  -DMX_COMPAT_32 -O  "yprimefg.F"

    -> llvm-gcc -O -Wl,-twolevel_namespace -undefined error -arch x86_64 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/ -mmacosx-version-min=10.5 -bundle -Wl,-exported_symbols_list,/Applications/MATLAB_R2012a.app/extern/lib/maci64/fexport.map -o  "yprimefg.mexmaci64"  yprimefg.o  -L/Applications/MATLAB_R2012a.app/bin/maci64 -lmx -lmex -lmat -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.9.0/../../.. -lgfortran -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin13/4.9.0 -lgfortranbegin

    Undefined symbols for architecture x86_64:
      "_yprime_", referenced from:
          _mexfunction_ in yprimefg.o
    ld: symbol(s) not found for architecture x86_64
    clang: error: linker command failed with exit code 1 (use -v to see invocation)

        mex: link of ' "yprimefg.mexmaci64"' failed.

    Error using mex (line 206)
    Unable to complete successfully.