Root access via adb only, not any Android applications I'm running a stock Android 4.2.2 on a Nexus 4 device. After following some instructions on how to root it, I managed to get a partially rooted phone. Now on adb shell I can do:

shell@android:/ $ su
shell@android:/ # whoami
whoami: unknown uid 0


With adb shell I can get access to /data/data, etc. No problem. And my SuperSU.apk automatically grants it super user permission. However, nothing else gets super-user permission, not even SuperSU itself. No notification/prompt ever comes. Even after setting SuperSU to default to allowing access after timeout.

Any ideas on possible causes? Any suggestions?

Flashed this zip from (http://download.chainfire.eu/282/SuperSU/).

 4c3054dfecb6d21dc6a01d67c25588af CWM-SuperSU-v0.98.zip
You must go in Settings -> Developer Options and there must be an option called "Root Access". Set it to ADB + Apps.