catkin_make failing with custom source directory

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Hey guys,

I started having problems with catkin_make while using a custom location for the src directory after I updated a few ros packages. I currently have the following file structure (still in the process of migrating to catkin):

• main_ws/
  • rosbuild_package_1/
  • rosbuild_package_2/
  • ...
  • catkin_ws
    • catkin_package_1/
    • catkin_package_2/
    • ...

Each directory under main_ws is a different repository. If I checkout everything, go to the catkin_ws directory and run catkin_make --source ., it detects everything fine and generates the following:

• main_ws/
  • ...
  • catkin_ws/
    • build/
    • devel/
    • CMakeLists.txt
    • catkin_package_1/
    • catkin_package_2/
    • ...

After running catkin the first time, every time I try to run catkin_make --source . (with or without specifying source location), I get the following message:

The specified base path "/opt/main_ws/catkin_ws/" contains a CMakeLists.txt but "catkin_make" must be invoked in the root of workspace.

It seems like something changed in the way catkin_make works, and now every time I need to compile the catkin packages I have to remove the CMakeLists.txt file generated previously. This happens in 4 different machines that have the latest catkin packages, but not in another machine that has been last updated in the end of January.

Any clues about what could be causing this problem?

Felipe