Batter-Runner Misses First Base on Walk

 
With two outs and a runner on third base (R3), the 3-0 pitch to the batter (B1) is wild and goes to the backstop. R3 holds at 3rd base while B1 sprints for 1st base. The first base coach instructs B1 to keep running and to head for 2nd base. B1 does so, but steps over 1st base and does not touch the base on his way to 2nd base.
 
The catcher retrieves the wild pitch and attempts to put out B1 at 2nd base. B1 is safe at 2nd base as R3 runs home and scores.
 
After the actions stops, the defense calls "time" and appeals that B1 missed first base on his walk and on his way to 2nd base.
 
What does the umpire do with B1 and R3?
 
Call
If runners do not properly touch their bases, they are at risk of being called out upon proper appeal by the defense. This holds true even for bases that are awarded.
 
In the situation below, B1 did not properly touch 1st base on his way to 2nd base. The defense properly appealed, so B1 is out. Since this is the 3rd out, and B1 failed to reach first base, R3's run does not count (NF 9-1-1).