I was stuck because of ffmpeg 4.4 too
Trying again to compile vkdt gave me the opportunity to see what was holding back the ffmpeg upgrade and it was … video cd support on gst-plugins (dragging libquicktime) maybe it’s time to get rid of this 
CR3 support seems broken though
[i-raw] (/home/clind/vkdt/J12A0599.CR3) virtual void rawspeed::Cr3Decoder::checkSupportInternal(const CameraMetaData *), line 603: CR3 compressor version (CNCV: CanonCR3_001/00.11.00/00.00.00) is not supported
Raw from this thread Another try in vkdt