Architecture change using autotools?

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I wasn't going to ask this because I thought it was peculiar to my
custom build environment, but I discovered this is no longer true.

If I manually call gcc to compile a file that uses the atomic built-in
__sync_add_and_fetch, it compiles and links fine. But if I use it in
an autotool'd project, linking will fail complaining that
__sync_add_and_fetch doesn't exist. No custom march or cflags are
being set. How is this possible? O_o Is there anyway that GCC will
choose to compile with atomic builtins disabled without specifying a
march flag?

I've tried the manual compile with/without -D_REENTRANT, -g, and -O2
and it makes no difference. Always succeeds. The only other thing I
can think of is that somehow what is *linked* against can cause GCC to
drop atomic builtins. Is this known to happen? The implication is my
configure test for the presence of __sync_add_and_fetch always
succeeds even though my app won't build, defeating its point.

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