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One thing the Java standard library doesn't do is units. As in, when you divide a distance by a duration you get a velocity. It doesn't do calculus like derivatives or reversing functions. There are no classes for the algebraic structures like polynomials or vector spaces. And that is not even the "special" things. There may be libraries to do all those things; Scala Squants and Spire might work from Java. You might not be needing most of that (although you can never go wrong with typing your units, lest you loose Mars lander). But no, nothing in the world perfect and so that is true for the Java standard library.
MATLAB and R is good for math