I'm trying to build a shell version of hyphy in linux, but for some reason the version of gcc on this machine doesn't like the -fnonnull-objects flag.  I modified the build.sh script so that the source files compiled with gcc (as opposed to g++) have a different set of compiler flags, namely all the default ones except for -fnonnull-objects.  It compiles fine this way, and the binary seems to run fine, but since i don't know what -fnonnull-objects does, I wanted to make sure that it wasn't something crucial.

best,
Dan

My linux machine has gcc (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-49). 

On the other hand, it builds fine with the -fnonnull-objects flag in os x using gcc (GCC) 3.3 20030304 (Apple Computer, Inc. build 1666)

And even with the older gcc, it only seems to be a problem with the code compiled with gcc, not the stuff that uses g++.