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The question is in the title. Using GCC version 3.4.5 on Windows Vista and a recent version of the Eclipse C/C++ IDE (not sure what version exactly because it’s hard to figure out which version is the one for the whole IDE, but I downloaded it two weeks ago so it can’t be that old).
This depends on the build system you use, but you can always try adding the “CFLAGS=-std=c99” as a build and/or environment variable the the builder.