Updates to fix the marker at the end of the last chromosome bug

Hey Karl,

I started working again on the MQM code, and bug reports:

1) commited some code clean ups to make the code more readable. 
2) Fixed a couple of unused variable warnings.
3) Changes in compiler switches of R, broke the mqm.h file
4) Fix for bugreport: Scott A. Woolbright, last marker always included as cofactor under some circumstances
5) Updating the unittest to use R 3.1.0 (32 bit version)
6) Some R functions were erroneously called in standalone mode

Gr,
Danny