I was able to build this package on arm64 by disabling the "JIT" as follows. Please implement something similar in the next upload.
--- libretro-desmume-0.9.11+git20160819+dfsg1.orig/debian/rules +++ libretro-desmume-0.9.11+git20160819+dfsg1/debian/rules @@ -12,11 +12,15 @@ PLATFORM=platform="armv hardfloat" endif +ifneq (,$(filter-out amd64 armhf i386 %-amd64 %-i386 x32, $(ARCH))) + NO_JIT=DESMUME_JIT=0 +endif + %: dh $@ --sourcedirectory=desmume/ override_dh_auto_build: - dh_auto_build -- -f Makefile.libretro $(PLATFORM) + dh_auto_build -- -f Makefile.libretro $(PLATFORM) $(NO_JIT) override_dh_auto_clean: dh_auto_clean -- -f Makefile.libretro