diff -up siril-0.99.6/configure.ac.opencv_flann siril-0.99.6/configure.ac
--- siril-0.99.6/configure.ac.opencv_flann	2020-09-22 22:01:48.000000000 +0200
+++ siril-0.99.6/configure.ac	2020-10-21 10:27:10.271118853 +0200
@@ -160,7 +160,7 @@ if test -n "$CXX" && ( test "X$CXX" != "
 	dnl http://nerdland.net/2009/07/detecting-c-libraries-with-autotools/ solution 2
 	dnl we handle 2 opencv versions because of a debian bug with opencv2 and GTK3
 	PKG_CHECK_MODULES([OPENCV], [opencv >= 3.0],
-			[OPENCV_LIBS="-lopencv_core -lopencv_imgproc -lopencv_calib3d"],
+			[OPENCV_LIBS="-lopencv_core -lopencv_imgproc -lopencv_calib3d -lopencv_flann"],
 			[PKG_CHECK_MODULES([OPENCV], [opencv >= 2.0],
 					[OPENCV_LIBS="-lopencv_core -lopencv_imgproc"],
 					[PKG_CHECK_MODULES([OPENCV], [opencv4],