diff --git a/gtsam/CMakeLists.txt b/gtsam/CMakeLists.txt
index 42a5d2599..3b6db78cb 100644
--- a/gtsam/CMakeLists.txt
+++ b/gtsam/CMakeLists.txt
@@ -127,8 +127,8 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     
     # Choose include flags depending on build process
 	set(MEX_INCLUDE_ROOT ${GTSAM_SOURCE_ROOT_DIR})
-	set(MEX_LIB_ROOT ${CMAKE_BINARY_DIR})
-	set(GTSAM_LIB_DIR ${MEX_LIB_ROOT}/gtsam)
+	set(MEX_LIB_ROOT ${CMAKE_BINARY_DIR})    # FIXME: is this used?
+	set(GTSAM_LIB_DIR ${MEX_LIB_ROOT}/gtsam) # FIXME: is this used?
     
     # Generate, build and install toolbox
     set(mexFlags ${GTSAM_BUILD_MEX_BINARY_FLAGS} -I${MEX_INCLUDE_ROOT} -I${Boost_INCLUDE_DIR})
diff --git a/gtsam_unstable/CMakeLists.txt b/gtsam_unstable/CMakeLists.txt
index 400a77e84..cd209ea95 100644
--- a/gtsam_unstable/CMakeLists.txt
+++ b/gtsam_unstable/CMakeLists.txt
@@ -88,9 +88,9 @@ if (GTSAM_INSTALL_MATLAB_TOOLBOX)
     # TODO: generate these includes programmatically
     # Choose include flags depending on build process
 	set(MEX_INCLUDE_ROOT ${GTSAM_SOURCE_ROOT_DIR})
-	set(MEX_LIB_ROOT ${CMAKE_BINARY_DIR})
-	set(GTSAM_LIB_DIR ${MEX_LIB_ROOT}/gtsam)
-	set(GTSAM_UNSTABLE_LIB_DIR ${MEX_LIB_ROOT}/gtsam_unstable)
+	set(MEX_LIB_ROOT ${CMAKE_BINARY_DIR})    # FIXME: is this used?
+	set(GTSAM_LIB_DIR ${MEX_LIB_ROOT}/gtsam) # FIXME: is this used?
+	set(GTSAM_UNSTABLE_LIB_DIR ${MEX_LIB_ROOT}/gtsam_unstable) # FIXME: is this used?
     
     # Generate, build and install toolbox
     set(mexFlags -I${MEX_INCLUDE_ROOT} -I${Boost_INCLUDE_DIR})