Stage 1 of fixing R CMD check warnings with current R

Removes tens of  warnings of "no visible definition" for
external packages, but still leaves this one warning:

* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘MASS’ ‘cluster’ ‘rgl’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.

Wording is not clear, but I assume require(MASS) should *not*
be used (like it is done now), but we need MASS::isoMDS().
vegan Depends on R >= 2.15.0: remove hack for R < 2.13.0
forgot to import mgcv::gam
passes more anal tests in modern R

Tested with
R Under development (unstable) (2014-09-01 r66505) -- "Unsuffered Consequences"
explicit mgcv::plot.gam needed in example

-- or perhaps require(mgcv)
change mgcv::plot.gam to library(mgcv);plot.gam
use selective importFrom(MASS, ...)
remove commented out ##require()
missed one ##require and fixed a bug introduced with adding ##
Merge pull request #28 from jarioksa/R-CMD-check-import-fix

R cmd check import fix