configure vs. build with different switches leads to breaks

[Jay]

Guile failed to build for me, I forget what system, either Irix or OpenBSD, for
the following reason.

It goes and looks for some functions, like isnan or isnanf I think,
with autoconf:

compiles this program:

#include 
int main()
{
  do something with isnan
}

it compiles ok.

Later on it builds some similar code of its own, but this time with -Werror and
either -Wall or -Wmissing-prototypes. The function in question is not prototyped
in math.h, nor whatever else is #included.

I worked around by removing -Werror from the Makefile.

This seems like a general class of bug -- configure one way, build another.
(That sounds like a user error, but isn't, it is what is done automatically.)

Later on the build core dumps.
I haven't figured out why.

 - Jay