The warning messages are due to the implementation of the KS test in R, which expects a continuous distribution and thus there should not be any identical values in the two datasets i.e. ties.

The presence of ties always generates a warning, since continuous distributions do not generate them. If the ties arose from rounding the tests may be approximately valid, but even modest amounts of rounding can have a significant effect on the calculated statistic.

ref:

http://www.cookbook-r.com/Graphs/

http://stat.ethz.ch/R-manual/R-devel/library/stats/html/ks.test.html

http://davetang.org/muse/2012/04/17/comparing-different-distributions/

In ks.test(x, y) : p-value will be approximate in the presence of ties