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I am having the exact same problem on ROS Indigo on Ubuntu 14.04! Even on very simple URDF files. I am not sure if this is related, but as an alternative I also tried to convert the URDF to DAE in code, as follows:

#include <collada_urdf/collada_urdf.h>

boost::shared_ptr<DAE> dom;
if (!collada_urdf::colladaFromUrdfFile("waiterbot.urdf", dom)) {
    ROS_ERROR("Failed to construct COLLADA DOM");
    return false;
}
collada_urdf::colladaToFile(dom, "waiterbot.dae");

But this gives the following build error:

In file included from /home/waiterbot/catkin_ws/src/waiterbot_description/src/collada_urdf.cpp:1:0:
/opt/ros/indigo/include/collada_urdf/collada_urdf.h:42:17: fatal error: dae.h: No such file or directory
 #include <dae.h>
                 ^
compilation terminated.

I installed ROS as ros-indigo-desktop-full and it appears that there is something deeply wrong in the way the packages are set up. My knowledge in CMake and catkin isn't deep enough to find the problem. I have already wasted 4 hours on this with no success. Any help would be greatly appreciated.