The configure script sets rpath for external libraries
I tried to update my flint-arb package in Debian and was notified that it used rpath.
As far as I know, rpath is a way to point to internal sublibraries, and using it for external libraries means something might be wrong somewhere else : at build-time libs should be found using -L and at runtime, the linker should find the libraries without help.
It tried to compile flint-arb removing completely the offending line, and it worked, so are you sure you can't get rid of it?
@videlec added this line
Let's wait for his comment then : as far as I know that line can only have negative consequences.
Notice that calcium removed this line without issues, and the Debian package is patched to remove it too, so perhaps it can go?