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Previously we used gcc compiler and libstd++ for OpenCV iOS framework. So you should comment the following strings for using clang compiler:
CMAKE_FORCE_C_COMPILER (gcc gcc)
CMAKE_FORCE_CXX_COMPILER (g++ g++)
in the both toolchain files (e.g. https://github.com/Itseez/opencv/blob/master/ios/cmake/Toolchains/Toolchain-iPhoneOS_Xcode.cmake).
Or you can download the latest OpenCV code. Today we updated it for using clang compiler and libc++. The second problem with atomicity was fixed too(https://github.com/Itseez/opencv/pull/126).