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clang has dropped support for this warning and therefore emits warnings when it is used as a compiler flag. configure now uses AX_CHECK_COMPILE_FLAG[0] to check for compiler support. [0] http://www.gnu.org/software/autoconf-archive/ax_check_compile_flag.html Because local m4 macros are located in the sub-directory m4, autogen.sh must not remove that directory but only clean the libtool-generated files.