R: use brewed gettext

On clean install, update.packages() was failing with:
In file included from R_systat.c:23:
./foreign.h:33:10: fatal error: 'libintl.h' file not found

Closes #676.
Add switches to x11 and Tcl/Tk

Two switches are added to allow users turn off non-crucial components, namely x11 and Tcl/Tk.

Closes #729.
openni: create and install pkg-config file

Closes #728.
R: fix args for configure

`--without-x` is missing from #133a72a and therefore configure
will not really disable x11.

Closes #730.
R: use RStudio CDN as primary download url
nco 4.4.2

Depends on newer texinfo.

Closes #725.
bedops: improve build process

Fixed optimization flags, removed unused links to libxml2 and
OpenGL libraries, other fixes

Closes #726.
MLPACK: new formula.

MLPACK is a library of machine learning algothms,
see http://mlpack.org for further information.

Closes #715.
Z3 theorem prover: new formula

Closes #289.
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.
bowtie: bump fails_with :clang version
bedtools 2.19.1

Closes #742.
Suite Sparse: refactor formula.

Several make variables are defined multiple times in
SuiteSparse_config_Mac.mk and sometimes with leading blanks. This caused
change_make_var to only change some of them and led to a bug where
SuiteSparse uses Accelerate even if the user selects OpenBLAS.

This update removes change_make_var entirely. See also:
https://github.com/Homebrew/homebrew/pull/27483