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Here in the script, the toolchains for each ABI are set. You have to change gcc to clang, for example:

arm-linux-androideabi-4.8 --> arm-linux-androideabi-clang3.5

Here is the list of supported toolchains.

Or you can disable manual toolchain selection by removing line 136 from the script, but in this case there can be problems with cmake scripts as they have not been adapted to the latest NDKs.