I had the same problem after rooting my device and another answer did not resolve it. When I ran the adb run-as command in the terminal, I kept getting
Could not set Capabilities: operation not permitted.
This is a permissions issue. You must change the permissions for the run-as file in the / system / bin folder. This resolved this for me (need root access):
1. remount /system rw
2. chmod 4750 /system/bin/run-as
3. remount /system ro
When performing custom recovery:
1. reboot to recovery
2. find the mount system and check it (make sure 'mount system as read-only' is unchecked)
3. open a terminal and type: adb shell
4. type: chmod 4750 /system/bin/run-as
5. uncheck the System mount and reboot!
. 58373: https://code.google.com/p/android/issues/detail?id=58373