Problem building workspace with 'non-catkin pkgs'.

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Hello,

I'm having a problem with catkin_make command in my workspace. This happened after I used catkin_build while trying to install mavros. I ran "catkin_make_isolated" and it runs without any error but I don't know how to identify which files are "non-catkin packages". If I remove these "non-catkin packages" would it fix the problem? I've looked in the CMakeOutput.log and CMakeError.log but I don't know what I should be looking for. Thank you in advance.

Base path: /home/jtu/catkin_ws
Source space: /home/jtu/catkin_ws/src
Build space: /home/jtu/catkin_ws/build
Devel space: /home/jtu/catkin_ws/devel
Install space: /home/jtu/catkin_ws/install
####
#### Running command: "make cmake_check_build_system" in "/home/jtu/catkin_ws/build"
####
-- Using CATKIN_DEVEL_PREFIX: /home/jtu/catkin_ws/devel
-- Using CMAKE_PREFIX_PATH: /home/jtu/catkin_ws/devel;/opt/ros/indigo
-- This workspace overlays: /home/jtu/catkin_ws/devel;/opt/ros/indigo
-- Using PYTHON_EXECUTABLE: /usr/bin/python
-- Using Debian Python package layout
-- Using empy: /usr/bin/empy
-- Using CATKIN_ENABLE_TESTING: ON
-- Call enable_testing()
-- Using CATKIN_TEST_RESULTS_DIR: /home/jtu/catkin_ws/build/test_results
-- Found gtest sources under '/usr/src/gtest': gtests will be built
-- Using Python nosetests: /usr/bin/nosetests-2.7
-- catkin 0.6.19
-- BUILD_SHARED_LIBS is on
-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- ~~  traversing 21 packages in topological order:
-- ~~  - ardrone_tutorials
-- ~~  - image_pipeline (metapackage)
-- ~~  - mavlink (plain cmake)
-- ~~  - libmavconn
-- ~~  - nmea_navsat_driver
-- ~~  - mavros_msgs
-- ~~  - beginner_tutorials
-- ~~  - camera_calibration
-- ~~  - image_proc
-- ~~  - image_publisher
-- ~~  - image_view
-- ~~  - stereo_image_proc
-- ~~  - depth_image_proc
-- ~~  - mavros
-- ~~  - ardrone_autonomy
-- ~~  - eagle_one_test
-- ~~  - image_rotate
-- ~~  - learning_tf
-- ~~  - turtlesim_cleaner
-- ~~  - mavros_extras
-- ~~  - test_mavros
-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CMake Error at /opt/ros/indigo/share/catkin/cmake/catkin_workspace.cmake:95 (message):
  This workspace contains non-catkin packages in it, and catkin cannot build
  a non-homogeneous workspace without isolation.  Try the
  'catkin_make_isolated' command instead.
Call Stack (most recent call first):
  CMakeLists.txt:63 (catkin_workspace)


-- Configuring incomplete, errors occurred!
See also "/home/jtu/catkin_ws/build/CMakeFiles/CMakeOutput.log".
See also "/home/jtu/catkin_ws/build/CMakeFiles/CMakeError.log".
make: *** [cmake_check_build_system] Error 1
Invoking "make cmake_check_build_system" failed