PS: Even on x86_64, a command such as
gcc -mtune=core2 -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D
SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb
-fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3
-fmessage-length=0 -c -o core.o core.c
gcc -mtune=core2 -O9 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D
SUBREAD_VERSION=\""1.4.6-p2"\" -D_FILE_OFFSET_BITS=64 -ggdb
-fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3
-fmessage-length=0 -c -o core-junction.o core-junction.c
looks suspicious.
