stacks: fails with clang

Fixes #955.
cantera: migrate from Homebrew core

Closes #948.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
gromacs: migrate from Homebrew core

Closes #947.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
sundials: migrate from Homebrew core

Closes #946.

Signed-off-by: Mike McQuaid <mike@mikemcquaid.com>
gromacs 4.6.5

Perform build-time tests.

Closes #959.
nfft 3.2.3: new Formula

Closes #396.
plink: Patch to fix build, add test

Closes #958.
hypre 2.9.0b

Hypre is a library of high performance preconditioners that features
parallel multigrid methods for both structured and unstructured grid
problems.

Closes #906.
megam 0.9.2: Maximum entropy machine learning package

megam and megam.opt (the optimized version) are machine learning commandline tools
used by Python NLP Toolkit (nltk) if the built in libraries are too slow.

Closes #949.
Use File.exist? instead of File.exists?

File.exists? is deprecated in Ruby 2.1+.
ASL: option to build Matlab interface.
Bump gal-sim to release 1.1.0

Closes #960.
cube: Fails to build with clang

Undefined symbols for architecture x86_64:
"cube::Cube::def_mirror(std::string const&)", referenced from:
MainWidget::readFile(QString) in cube-MainWidget.o
R: Fix head build.

Closes #405.
blasr: Specify the path to hdf5

Closes #932
sundials: add features

- add serial tests for C bindings
- add patches from mailing list since 2.5.0 release
- add openblas support
- add Fortran support
- add serial Fortran tests
- add mpi support
- add parallel tests for C bindings
- add parallel tests for Fortran bindings
- add patches (submitted upstream) to fix additioanl bugs
- add Argonne PETSc project mirror

Closes #962.
Healpix version 3.11

See http://healpix.jpl.nasa.gov/

HEALPix is an acronym for Hierarchical Equal Area isoLatitude
Pixelization of a sphere. As suggested in the name, this pixelization
produces a subdivision of a spherical surface in which each pixel
covers the same surface area as every other pixel.  Healpix is used
extensively in astronomy to produce maps of data on the sky.

Closes #169.
qcl: 0.6.4: a language for quantum computers

Wikipedia lists QCL as one of the first quantum programming languages. This formula downloads and installs the latest version of QCL from the maintainer's website. In addition, the formula copies the standard QCL library so that the interpreter is able to run properly.

Closes #288.
mafft: fix build error on 10.6

Closes #313.
ropebwt2 r181

Add a link to the PDF on arXiv.