Compiling code on OS X using autotools yields a linker error

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I keep encountering this weird linker error when compiling things on OS X using autotools. The error is this:

ld: symbol(s) not found for architecture x86_64

I tried looking this up, and everything I've found shows the user set something up wrong in their Xcode project and clang gets messed up, but I'm not using Xcode, so autoconf is failing somewhere. This happened to me with gcc-5.1, binutils, lame, and a few other stuff. What am I missing?

Here's an example, trying to compile binutils for a different target.

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