Compiling doxygen with GCC 4 and -O3 causes doxygen to behave improperly. Could verify it myself with app-doc/doxygen-1.4.[347], gcc-4.1.1 and CFLAGS="-march=athlon-xp -O3 -mfpmath=sse -msse". Setting optimization level down to -O2 made the problem disappear, so it might be a problem with GCC. Still the ebuild might want to check for affected versions of gcc and perform some actions to avoid the problem, or whatever is more suitable.
Created attachment 96784 [details] Output of emerge info
Yes, -O3 still produces incorrect optimizations. In general, it's best not to try to over-optimze code with gcc; not just because -O3 is buggy, but also because in the majority of cases, gcc is way smarter about it. It will automatically enable the stuff that works, including mmx, sse, etc, when it can. Forcing things OTOH, breaks packages more often than not. I would just use -O2, along with a few other safe things, and not worry about it...
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