Z3: replace CRLF patch with inreplace
R: RStudio can find R installed via homebrew

This caveat is no longer true.
See https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R

Closes #736.
vcftools 0.1.12

Closes #734.
bcftools, htslib: Add version to compile

bcftools and htslib do not correctly determine the version, reporting
0.0.1 on the command line. These correctly write out the version
information.

Closes #733.
fastx_toolkit: Fix the build on Mountain Lion

clang build fails on Mountain Lion, but works on Mavericks.

Closes #620
Armadillo: update to 4.100.2

Closes #738.
biopieces 2291: New formula

The Biopieces are a collection of bioinformatics tools that can be
pieced together in a very easy and flexible manner to perform both
simple and complex tasks.
opencv: make Java bindings optional

Prevents forcing the :ant dependency on users without Java installed
and disables Java bindings by default.