Why is one of Madera Municipal's runways labelled with only "R" on both sides?
R is for Restricted. From the chart supplement (formerly AF/D) that runway (8-26) is restricted for agricultural use only.

It's non-standard, both internationally (ICAO) and on the FAA level for Part 139 airports (see AC 150/5340-1M). Note that the airport is neither international nor Part 139, so standards may not apply.




(via skyvector.com)

Beyond the meaning of the non-standard R, the Madera County's website offers this (PDF; Sep 2015):


  Future abandonment of Runway 8/26 when the agricultural aerial applicator lease expires in 2019.


This hints at a legal agreement with a local agricultural operation. Perhaps someone who is familiar with the local government there can offer more insight.