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Executables not found and autocompletion not working with meta-ros

I have a many systems running meta-ros according to instructions. In all of them, ROS seems to work OK. However, one of them cannot find nodes executables. For instance, the joy package is correctly installed and I can run by doing /opt/ros/indigo/lib/joy/joy_node. However, if I try rosrun joy joy_node the output is:

[rosrun] Couldn't find executable named joy_node below /opt/ros/indigo/share/joy

The executable is actually in /opt/ros/indigo/lib/joy.

I have compared both systems, and all the environment variables are the same. However, this one in which it does not work does not have /opt/ros/indigo/include folder for instance. That is the only difference I can find, apart from some different packages.

I have also run rospack profile

Do you have any suggestion on what to try? Thanks a lot!