I encountered the exact same issue. I added a LIBTOOLFLAGS line into modules/video_filter/Modules.am: if HAVE_NEON libdeinterlace_plugin_la_SOURCES += deinterlace/merge_arm.S libdeinterlace_plugin_la_CFLAGS += -DCAN_COMPILE_ARM libdeinterlace_plugin_la_LIBTOOLFLAGS = --tag=CC endif and now it compil...