In an attempt to make Android devices safer, Google might add new security warnings to its Nexus lineup, which will warn users in case their devices have been compromised.

Google has just updated its support page with with a list of new operating system safety warning, which will act as a boot verification system that checks the integrity of a phone or tablet's software during each startup.
Depending on how bad your operating system has been compromised, you might see a yellow, orange or red safety warning being displayed on your screen during the boot up.
Here is what it means. If the message is yellow, then “your devices has loaded a different operating system.” This might appear in case of rooted devices as well, so if you know why this is showing up then you shouldn't be worried at all.
The orange message displaying on the screen of your Nexus smartphone or tablet could means that “your device software can't be checked for corruption.” According to Google, the best course of action is to lock the bootloader.
Last but not least, if a red operating system safety warning is showing up on your screen during boot then things are really, really bad. Google says that “your device is corrupt” and that “it can be trusted and may not work properly.”

Messages will go away by themselves after 10 seconds

In this case Google recommends that you should not use the device in its current state and that you should restore it to the original operating system.
If you don't know how to do it, you might want to contact your device manufacturer's support center to help you with that.
However, if you know that you have modified the operating system on purpose, then you can continue to use your device, but rest assure that your device might not work properly and data can be exposed to corruption and security risks.
These safety warnings can't be dismissed from the screen, but they will go away after about 10 seconds and your device will continue the boot process.
While these messages haven't been implemented yet, they could be part of the Android M, which is expected to be released sometime this fall.