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Just because a battery reads 12V or more at the posts, does not mean it is good. Batteries lose their current capacity long before they fail to hold a voltage. Voltage is nothing more than the potential between the + and - posts, which will exist as long as the plates inside exist and their is any electrolyte between them to cause a chemical reaction. The ability to hold a charge (volts) is one measure frequently used, but in today's electronically controlled engines, it is not the best measure.

The real measure of a battery's condition is its capacity, in the form of Amps current it can produce. If the plates inside the battery have broken down from age, heat, charge cycles, drying out, etc... the first thing that goes is their current capacity. This is true in all lead acid batteries, but most prevalent in small batteries used in motorcycles. As current loss occurs, the battery's ability to feed the systems connected and accept a charge also falls off. This is most readily noted when the starter relay clatters or clicks, but does not turn over. The reason for this is that the current remaining in the battery is just not enough to move the motor. Since voltage drops under load, and motor (starter) demand is based on volts x amps, a loss of amps leads to a high voltage drop, and the starter fails to move.

There are issues with losing battery current in electronic ignition, electronic fuel pump, ECU controlled engines, that often cascade - resulting in multiple system failures, blown fuses, loss of instrument display, low power output, missing, stuttering, and slow starting when cold.

To this end, the best practice is to replace the battery before it droops (loses enough current capacity that it can't effectively run connected systems). The AGM (maintenance free, Absorbed Glass Matt) battery in the R3 will last 5 years if its kept from freezing and not abused.

To check where it's at in its life, connect a voltmeter and check standing voltage with no load. It should be no lower than 12.7V
Now, turn on the ignition. The voltage should not drop more than 0.1V, as the electronics at this moment are not creating much demand.
Now see what happens when you try to start the bike. The voltage should not drop below 9.6V under starter load for as many as 10 seconds.
If the battery is too weak to start the bike, you will see this voltage drop to below 10V as the relay begins to click or buzz. Try to charge it back to 12.7V and see if the problem repeats itself.
Finally, with the bike running (if it starts), the voltage should read between 13V and 15.5V, often going up and down as the regulator works to keep from over-charging the battery.

So, if the battery is more than 5 years old, OR standing voltage is <12.7V, OR the battery drops below 9.6V when the starter is engaged (even if the bike starts), OR the charging voltage is not at least 13V - it is time to replace the battery, even if the bike starts and runs. Anything less than these minimums means you are riding on borrowed time, and will likely be stranded at some point, as batteries have the most annoying habit of being good... then not, as they pass their useful life.

You should check these conditions any time the bike acts poorly, as electronics running at low voltage or not being supported with proper current, will produce any number of failures. Further, clicking relays are not happy relays, and can fail from being abused.
 
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