How to configure the mexopts.sh file in MAC 10.12.6 El Capitan

I could not compile the c code in MATLAB 2012b on my MAC 10.12.6. When I implement the command: mex hello.c, it releases an error like:

gcc-5.3.0: command not found.

I had tried many ways to fix that problem but I failed. I have known that gcc (version 5.3.0) is existed on my MAC, but it seems to me that the MATLAB couldn't link to the gcc. I guess that the configuration in the mexopts.sh is wrong. Below is a part of the mexopts.sh file:

C='gcc-5.3.0'
SDKROOT='Applications/Xcode/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk'
MACOSX_DEPLOYMENT_TARGET='10.5'
ARCHS='x86_64'
CFLAGS="-fno-common -no-cpp-precomp -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
CFLAGS="$CFLAGS  -fexceptions"
CLIBS="$MLIBS"
COPTIMFLAGS='-O2 -DNDEBUG'
CDEBUGFLAGS='-g'
#
CLIBS="$CLIBS -lstdc++"
# C++keyName: GNU C++
# C++keyManufacturer: GNU
# C++keyLanguage: C++
# C++keyVersion:
# C++keyLinkerName:
# C++keyLinkerVersion:
CXX=g++-5.3.0
CXXFLAGS="-fno-common -no-cpp-precomp -fexceptions -arch $ARCHS -isysroot $SDKROOT -mmacosx-version-min=$MACOSX_DEPLOYMENT_TARGET"
CXXLIBS="$MLIBS -lstdc++"
CXXOPTIMFLAGS='-O2 -DNDEBUG'
CXXDEBUGFLAGS='-g'

Could anyone please let me know how to solve that problem. Thank you!

Answer 1

[Walter Roberson]

Your gcc-5.3 is probably not on your path. If you are calling mex from within MATLAB then first set the PATH environment variable to include the directory that your gcc-5.3 is in. For example,

   setenv('PATH', strcat(getenv('PATH'), ':/usr/local/bin'))

[Marsge]

Thank you for your reply. I tried but failed. I have done:

1. Found the gcc folder: by !which gcc and get:

/usr/bin/gcc

2. I modified the environment variable, the results is

PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/munki:/usr/bin/gcc:/bin/gcc:/gcc

But when I compile the .c file, it releases the same errors

/Applications/MATLAB_R2012b.app/bin/mex: line 305: gcc-5.3: command not found
/Applications/MATLAB_R2012b.app/bin/mex: line 1326: gcc-5.3: command not found

Could you plz give me some more advices. Thank you.

[Walter Roberson]

You need to find gcc-5.3 specifically, not just gcc

/usr/bin/gcc is an executable or a shell script, not a directory, so you should not be adding it to your PATH.

[Marsge]

Sorry for my dumb. I'm really confused because I have realised that there many version of gcc in my MAC.

The below image shows the organisation in the /usr/ folder which includes both gcc-6.1.0 and gcc-5.3.0 in the different location.

However, I found that in the path /opt/local/, there are some other versions of gcc that don't match to the versions in /usr/.

I have tried configure the mexopts.sh with all the versions but still failed. Could guys plz help me.

[Walter Roberson]

At your Linux command prompt,

find / -type f -perm -o+x \( -name gcc -o -name gcc-5.3\* \) -print0 2>/dev/null | xargs -L1 -0 -t -J % % --version

to try to find the path to your gcc 5.3 executable.

This might take some time to execute. You might want to search /usr or /opt instead of all of / and you might have reason to use the -mount option . For example,

    find /usr -mount -type f -perm -o+x \( -name gcc -o -name gcc-5.3\* \) -print0 2>/dev/null | xargs -L1 -0 -t -J % % --version

[Marsge]

Hi Walter Roberson,

Thank you very much for your help.

Could you please look at the results of when I implemented the 1st prompt command.

/Applications/Xcode.app/Contents/Developer/usr/bin/gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/Library/Developer/CommandLineTools/usr/bin/gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/bin/gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/local/bin/gcc --version
gcc (GCC) 5.3.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

The result of the second prompt command:

/usr/bin/gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 8.0.0 (clang-800.0.42.1)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
/usr/local/bin/gcc --version
gcc (GCC) 5.3.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

The gcc version is not the same in the paths. I tried to add the /usr/local/bin/gcc into the PATH environment, but it's still failed :(

[Walter Roberson]

Add /usr/local/bin to the PATH, and make sure it is earlier on the path than /usr/bin is.

[Marsge]

It didn't work :(

[Walter Roberson]

Did you install XCode? If you did, then which version?

In mexopts.sh you can change

CC = gcc-5.3

to

CC = /usr/local/bin/gcc-5.3

[Marsge]

My Xcode version is 8.1 (Build version 8B62). Hi Walter, When I try to specify CC='/usr/local/bin/gcc' (because there is no gcc-5.3 file in the gcc folder), it release another error:

gcc: error: unrecognized command line option '-no-cpp-precomp'