Kamil - I observed the same error when running Make (from the terminal window, in the folder /Users/geoff/.../svm-struct-matlab-1.0) as make ARCH=maci64
...
Building with 'Xcode with Clang'.
clang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk'
/Users/geoff/...
found #include <stdio.h>
...
The Makefile has the following lines (of interest)
# Mac OS X Intel 32
ifeq ($(ARCH),maci)
SDKROOT ?= /Developer/SDKs/MacOSX10.6.sdk
This folder doesn't exist on my computer (OS X 10.8.5). Since MEX has been configured to use 'Xcode with Clang', the equivalent SDKs directory is
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
Within this directory, I have
MacOSX10.8.sdk
MacOSX10.9.sdk
So I changed the line in the Makefile from the
SDKROOT ?= /Developer/SDKs/MacOSX10.6.sdk
to
SDKROOT ?= /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk
and then re-ran make ARCH=maci64 and the svm_struct_learn.mexmaci64 file was built. (Running, in the Command Window of MATLAB, test_svm_struct_learn was successful).
I suggest you try updating the Makefile, in a similar manner as described above, with the appropriate MacOSX10.X.sdk.
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