Remove conversions to data frames

For the input data `x`, we're not trying to respect the class of the
input value to accommodate other data types such as sparse matrices.

There are some complications though; for pre-processing we throw a
warning if the data are not simple matrices or data frames since there
is some infrastructure that does not exist for other classes( e.g.
`complete.cases`). We also throw a warning if `returnData <- TRUE` and
it cannot be converted to a data frame.
updated for new x data types
added verbose switch
updated to move test results outside of github path
fixed a bug in test case
decided not to put this model into the package

It depends on a second predictor matrix `z` which would be hard to pass
via `train`
added Rhistory and source tar ball