When I cross compile pinentry on Gentoo it fails because gpg-error.m4 and libassuan.m4 both look in ${SYSROOT}/bin for their config programs instead of ${SYSROOT}/usr/bin where they actually are. The result is a fallback to searching for those programs in $PATH. It does find the versions of those programs on the build system in /usr/bin. But they say --libdir is /usr/lib64 so that gets added as an linker option. As a result none of the libraries are found since adding /usr/lib64 makes the compiler not look in /usr/lib.

Actually, I think the same problem exists for fltk, but as you can see in the Gentoo bug report I worked around that by disabling that optional feature. If I recall correctly the logic looking for fltk config was not even looking in SYSROOT and the solution would not have been so simple as the patches I made to gpg.error.m4 and libassuan.m4 to work around the problem.