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It also wipes out root if you are rooted on 4.1.1 unless you have an app installed to prevent OTA from unrooting you. I have been unable to regain root since the upgrade. WugFresh's stuff is no help to me here.
I apologize. I did not intend to make an ignorant statement. The problem I am having is this with Version 1.5.4. I check the root box with custom recovery either checked or unchecked. The scripts seem to work just fine but at the end when I run SuperSU it shows no apps configured and no logs available and it does not prompt to change the binaries. When I run Root Checker it says I am not rooted. That's why I made the ignorant statement. I got unrooted when I upgraded to 4.1.2 from 4.1.1 because I had not installed to OTA app that prevents unrooting. It was not my intent to offend anyone or diminish the efforts of those who I agree have been helpful. The reason I made my statement is because the scripts all seemed to work (no errors) yet when I ran SuperSU as prescribed at the end of the scripts it does not prompt me to update the binaries.In SuperSU settings I have Superuser enabled, Re-authentication and Show notifications checked. v0.96.