Moved to homebrew/science Octave, OpenCV, VTK, ...

35 files changed, 0 insertions, 1352 deletions

diff --git a/Library/Formula/adol-c.rb b/Library/Formula/adol-c.rb
deleted file mode 100644
index a936de05c..000000000
--- a/Library/Formula/adol-c.rb
+++ /dev/null
@@ -1,33 +0,0 @@
-require 'formula'
-
-class AdolC < Formula
-  homepage 'https://projects.coin-or.org/ADOL-C'
-  url 'http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.3.0.tgz'
-  sha1 'd9124ce0b199cb8b841a9a9ec10d1fb31ed11b49'
-
-  head 'https://projects.coin-or.org/svn/ADOL-C/trunk/', :using => :svn
-
-  depends_on 'colpack'
-
-  def install
-    # Make our own realpath script
-    (buildpath/'realpath').write <<-EOS.undent
-      #!/usr/bin/python
-      import os,sys
-      print os.path.realpath(sys.argv[1])
-    EOS
-    system "chmod +x ./realpath"
-
-    # Configure may get automatically regenerated.  So patch configure.ac also.
-    inreplace %w(configure configure.ac) do |s|
-      s.gsub! "readlink -f", "/#{buildpath}/realpath"
-      s.gsub! "lib64", "lib"
-    end
-
-    system "./configure", "--prefix=#{prefix}",
-                          "--enable-sparse",
-                          "--with-colpack=#{HOMEBREW_PREFIX}"
-    system "make install"
-    system "make test"
-  end
-end
diff --git a/Library/Formula/ann.rb b/Library/Formula/ann.rb
deleted file mode 100644
index 14e5d6f78..000000000
--- a/Library/Formula/ann.rb
+++ /dev/null
@@ -1,18 +0,0 @@
-require 'formula'
-
-class Ann < Formula
-  homepage 'http://www.cs.umd.edu/~mount/ANN/'
-  url 'http://www.cs.umd.edu/~mount/ANN/Files/1.1.2/ann_1.1.2.zip'
-  sha1 '622be90314a603ef9b2abadcf62379f73f28f46c'
-
-  def install
-    system "make", "macosx-g++"
-    prefix.install "bin", "lib", "sample", "doc", "include"
-  end
-
-  def test
-    cd "#{prefix}/sample" do
-      system "#{bin}/ann_sample", "-df", "data.pts", "-qf", "query.pts"
-    end
-  end
-end
diff --git a/Library/Formula/armadillo.rb b/Library/Formula/armadillo.rb
deleted file mode 100644
index 18dbc70ec..000000000
--- a/Library/Formula/armadillo.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Armadillo < Formula
-  homepage 'http://arma.sourceforge.net/'
-  url 'http://sourceforge.net/projects/arma/files/armadillo-3.800.2.tar.gz'
-  sha1 '9e2b33574ff577b1870dc8fdfff7d4ec88648576'
-
-  depends_on 'cmake' => :build
-  depends_on 'boost'
-
-  def install
-    system "cmake", ".", *std_cmake_args
-    system "make install"
-  end
-end
diff --git a/Library/Formula/bact.rb b/Library/Formula/bact.rb
deleted file mode 100644
index 631df641a..000000000
--- a/Library/Formula/bact.rb
+++ /dev/null
@@ -1,13 +0,0 @@
-require 'formula'
-
-class Bact < Formula
-  homepage 'http://chasen.org/~taku/software/bact/'
-  url 'http://chasen.org/~taku/software/bact/bact-0.13.tar.gz'
-  sha1 'cdc8815e9258868699d98449598058011e993218'
-
-  def install
-    system "make"
-    system "make test"
-    bin.install "bact_learn", "bact_classify","bact_mkmodel"
-  end
-end
diff --git a/Library/Formula/bali-phy.rb b/Library/Formula/bali-phy.rb
deleted file mode 100644
index 20060314d..000000000
--- a/Library/Formula/bali-phy.rb
+++ /dev/null
@@ -1,26 +0,0 @@
-require 'formula'
-
-class BaliPhy < Formula
-  homepage 'http://www.biomath.ucla.edu/msuchard/bali-phy/'
-  url 'http://www.biomath.ucla.edu/msuchard/bali-phy/bali-phy-2.1.1.tar.gz'
-  sha1 'e72073a1c5b05c797668e476bfd8517594f074e6'
-
-  depends_on 'gsl'
-
-  fails_with :clang do
-    build 318
-    cause <<-EOS.undent
-      io.H:25:31: error: use of undeclared identifier 'push_back'
-      void operator()(const T& t){push_back(t);}
-      EOS
-  end
-
-  def install
-    mkdir 'macbuild' do
-      system "../configure", "--disable-debug", "--disable-dependency-tracking",
-                             "--prefix=#{prefix}",
-                             "--enable-cairo"
-      system "make install"
-    end
-  end
-end
diff --git a/Library/Formula/bedtools.rb b/Library/Formula/bedtools.rb
deleted file mode 100644
index aa4184467..000000000
--- a/Library/Formula/bedtools.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Bedtools < Formula
-  homepage 'http://code.google.com/p/bedtools/'
-  url 'http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz'
-  sha1 '1b1de3c35394a423f9ad98a9957a8853b426a578'
-
-  head 'https://github.com/arq5x/bedtools.git'
-
-  def install
-    system "make all"
-    prefix.install 'bin'
-  end
-end
diff --git a/Library/Formula/cminpack.rb b/Library/Formula/cminpack.rb
deleted file mode 100644
index f652e33fd..000000000
--- a/Library/Formula/cminpack.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Cminpack < Formula
-  homepage 'http://devernay.free.fr/hacks/cminpack/cminpack.html'
-  url 'http://devernay.free.fr/hacks/cminpack/cminpack-1.3.0.tar.gz'
-  sha1 '8bf19ce37b486707c402a046c33d823c9e359410'
-
-  depends_on 'cmake' => :build
-
-  def install
-    system "cmake", ".", *std_cmake_args
-    system "make install"
-  end
-end
diff --git a/Library/Formula/colpack.rb b/Library/Formula/colpack.rb
deleted file mode 100644
index b21a2d1e5..000000000
--- a/Library/Formula/colpack.rb
+++ /dev/null
@@ -1,12 +0,0 @@
-require 'formula'
-
-class Colpack < Formula
-  homepage 'http://www.cscapes.org/coloringpage/software.htm'
-  url 'http://cscapes.cs.purdue.edu/download/ColPack/ColPack-1.0.9.tar.gz'
-  sha1 'c963424c3e97a7bc3756d3feb742418e89721e48'
-
-  def install
-    system './configure', "--prefix=#{prefix}", '--disable-dependency-tracking'
-    system "make install"
-  end
-end
diff --git a/Library/Formula/flann.rb b/Library/Formula/flann.rb
deleted file mode 100644
index dc0503109..000000000
--- a/Library/Formula/flann.rb
+++ /dev/null
@@ -1,39 +0,0 @@
-require 'formula'
-
-class Flann < Formula
-  homepage 'http://www.cs.ubc.ca/~mariusm/index.php/FLANN/FLANN'
-  url 'http://people.cs.ubc.ca/~mariusm/uploads/FLANN/flann-1.8.2-src.zip'
-  sha1 '62ace1c41365dfc8ceabde1381febc5c8b71ad98'
-
-  option 'enable-python', 'Enable python bindings'
-  option 'enable-matlab', 'Enable matlab/octave bindings'
-  option 'with-examples', 'Build and install example binaries'
-
-  depends_on 'cmake' => :build
-  depends_on 'hdf5'
-
-  depends_on 'octave' if build.include? 'enable-matlab'
-  depends_on 'numpy' => :python if build.include? 'enable-python'
-
-  def install
-    args = std_cmake_args
-    if build.include? 'enable-matlab'
-      args << '-DBUILD_MATLAB_BINDINGS:BOOL=ON'
-    else
-      args << '-DBUILD_MATLAB_BINDINGS:BOOL=OFF'
-    end
-
-    if build.include? 'enable-python'
-      args << '-DBUILD_PYTHON_BINDINGS:BOOL=ON'
-    else
-      args << '-DBUILD_PYTHON_BINDINGS:BOOL=OFF'
-    end
-
-    inreplace 'CMakeLists.txt', 'add_subdirectory( examples )', '' unless build.include? 'with-examples'
-
-    mkdir 'build' do
-      system 'cmake', '..', *args
-      system 'make install'
-    end
-  end
-end
diff --git a/Library/Formula/glpk.rb b/Library/Formula/glpk.rb
deleted file mode 100644
index c89a7b848..000000000
--- a/Library/Formula/glpk.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Glpk < Formula
-  homepage 'http://www.gnu.org/software/glpk/'
-  url 'http://ftpmirror.gnu.org/glpk/glpk-4.48.tar.gz'
-  mirror 'http://ftp.gnu.org/gnu/glpk/glpk-4.48.tar.gz'
-  sha1 'e00c92faa38fd5d865fa27206abbb06680bab7bb'
-
-  def install
-    system "./configure", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/igraph.rb b/Library/Formula/igraph.rb
deleted file mode 100644
index f03b8d484..000000000
--- a/Library/Formula/igraph.rb
+++ /dev/null
@@ -1,21 +0,0 @@
-require 'formula'
-
-class Igraph < Formula
-  homepage 'http://igraph.sourceforge.net'
-  url 'http://downloads.sourceforge.net/sourceforge/igraph/igraph-0.6.5.tar.gz'
-  sha1 'f1605c5592e8bf3c97473f7781e77b6608448f78'
-
-  option :universal
-
-  # GMP is optional, and doesn't have a universal build
-  depends_on 'gmp' => :optional unless build.universal?
-
-  def install
-    ENV.universal_binary if build.universal?
-
-    system "./configure", "--disable-debug",
-                          "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/insighttoolkit.rb b/Library/Formula/insighttoolkit.rb
deleted file mode 100644
index c83c0e12c..000000000
--- a/Library/Formula/insighttoolkit.rb
+++ /dev/null
@@ -1,29 +0,0 @@
-require 'formula'
-
-class Insighttoolkit < Formula
-  homepage 'http://www.itk.org'
-  url 'http://sourceforge.net/projects/itk/files/itk/4.3/InsightToolkit-4.3.1.tar.gz'
-  sha1 '85375a316dd39f7f70dee5a2bd022f768db28eeb'
-
-  head 'git://itk.org/ITK.git'
-
-  option 'examples', 'Compile and install various examples'
-  option 'with-opencv-bridge', 'Include OpenCV bridge'
-
-  depends_on 'cmake' => :build
-
-  def install
-    args = std_cmake_args + %W[
-      -DBUILD_TESTING=OFF
-      -DBUILD_SHARED_LIBS=ON
-    ]
-    args << ".."
-    args << '-DBUILD_EXAMPLES=' + ((build.include? 'examples') ? 'ON' : 'OFF')
-    args << '-DModule_ITKVideoBridgeOpenCV=' + ((build.include? 'with-opencv-bridge') ? 'ON' : 'OFF')
-
-    mkdir 'itk-build' do
-      system "cmake", *args
-      system "make install"
-    end
-  end
-end
diff --git a/Library/Formula/mafft.rb b/Library/Formula/mafft.rb
deleted file mode 100644
index c16dd6e52..000000000
--- a/Library/Formula/mafft.rb
+++ /dev/null
@@ -1,35 +0,0 @@
-require 'formula'
-
-class Mafft < Formula
-  homepage 'http://mafft.cbrc.jp/alignment/software/index.html'
-  url 'http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.717-with-extensions-src.tgz'
-  sha1 '18d82340918949bbcdce659d4a09421ce06d67b1'
-
-  fails_with :clang do
-    build 421
-    cause <<-EOS.undent
-      Clang does not allow default arguments in out-of-line definitions of
-      class template members.
-      EOS
-  end
-
-  def install
-    cd 'core' do
-      system "make", "CC=#{ENV.cc}",
-                     "CFLAGS=#{ENV.cflags}",
-                     "PREFIX=#{prefix}",
-                     "MANDIR=#{man1}",
-                     "install"
-    end
-
-    cd 'extensions' do
-      system "make", "CC=#{ENV.cc}",
-                     "CXX=#{ENV.cxx}",
-                     "CXXFLAGS=#{ENV.cxxflags}",
-                     "CFLAGS=#{ENV.cflags}",
-                     "PREFIX=#{prefix}",
-                     "MANDIR=#{man1}",
-                     "install"
-    end
-  end
-end
diff --git a/Library/Formula/mallet.rb b/Library/Formula/mallet.rb
deleted file mode 100644
index 43ef6d28d..000000000
--- a/Library/Formula/mallet.rb
+++ /dev/null
@@ -1,28 +0,0 @@
-require 'formula'
-
-class Mallet < Formula
-  homepage 'http://mallet.cs.umass.edu/'
-  url 'http://mallet.cs.umass.edu/dist/mallet-2.0.7.tar.gz'
-  sha1 '45f6ad87ad7605d9f009be5f47b0bbf2ca47d89e'
-
-  # Creates a wrapper to set the classpath before executing
-  # the utility.
-  def startup_script(name)
-    <<-EOS.undent
-      #!/bin/sh
-      CLASSPATH=$CLASSPATH:#{libexec}/class:#{libexec}/lib/mallet-deps.jar "#{libexec}/bin/#{name}" "$@"
-    EOS
-  end
-
-  def install
-    rm Dir['bin/*.{bat,dll,exe}'] # Remove all windows files
-    prefix.install_metafiles
-    libexec.install Dir['*']
-    cd libexec+'bin' do
-      Dir['*'].each do |file|
-        fn = File.basename(file)
-        (bin+fn).write startup_script(fn)
-      end
-    end
-  end
-end
diff --git a/Library/Formula/mathgl.rb b/Library/Formula/mathgl.rb
deleted file mode 100644
index e670d5a3c..000000000
--- a/Library/Formula/mathgl.rb
+++ /dev/null
@@ -1,56 +0,0 @@
-require 'formula'
-
-class Mathgl < Formula
-  homepage 'http://mathgl.sourceforge.net/'
-  url 'http://downloads.sourceforge.net/mathgl/mathgl-2.1.2.tar.gz'
-  sha1 'bd3e797f8616c1f8afd0955fc9b87a2605cbf5ff'
-
-  option 'fltk',   'Build the fltk widget and mglview using X11'
-  option 'qt4',    'Build the Qt widget, the udav gui, and mglview using Qt4'
-  option 'wx',     'Build the wxWidget widget'
-  option 'gif',    'Build support for GIF'
-  option 'hdf5',   'Build support for hdf5'
-
-  depends_on 'cmake'   => :build
-  depends_on 'gsl'     => :recommended
-  depends_on 'jpeg'    => :recommended
-  depends_on 'libharu' => :recommended
-  depends_on :libpng   => :recommended
-  depends_on 'hdf5'   if build.include? 'hdf5'
-  depends_on 'fltk'   if build.include? 'fltk'
-  depends_on 'qt'     if build.include? 'qt4'
-  depends_on 'wxmac'  if build.include? 'wx'
-  depends_on 'giflib' if build.include? 'gif'
-  depends_on :x11 if build.include? 'fltk'
-
-  def install
-    args = std_cmake_args + %w[
-      -Denable-glut=ON
-      -Denable-gsl=ON
-      -Denable-jpeg=ON
-      -Denable-pthread=ON
-      -Denable-pdf=ON
-      -Denable-python=OFF
-      -Denable-octave=OFF
-    ]
-
-    args << '-Denable-qt=ON'      if build.include? 'qt4'
-    args << '-Denable-gif=ON'     if build.include? 'gif'
-    args << '-Denable-hdf5_18=ON' if build.include? 'hdf5'
-    args << '-Denable-fltk=ON'    if build.include? 'fltk'
-    args << '-Denable-wx=ON'      if build.include? 'wx'
-    args << '..'
-    rm 'ChangeLog' if File.exist? 'ChangeLog' # rm this problematic symlink.
-    mkdir 'brewery' do
-      system 'cmake', *args
-      system 'make install'
-      cd 'examples' do
-        bin.install Dir['mgl*_example']
-      end
-    end
-  end
-
-  test do
-    system "#{bin}/mgl_example"
-  end
-end
diff --git a/Library/Formula/mathomatic.rb b/Library/Formula/mathomatic.rb
deleted file mode 100644
index db6a24103..000000000
--- a/Library/Formula/mathomatic.rb
+++ /dev/null
@@ -1,17 +0,0 @@
-require 'formula'
-
-class Mathomatic < Formula
-  homepage 'http://www.mathomatic.org/'
-  url 'http://mathomatic.org/mathomatic-16.0.5.tar.bz2'
-  sha1 'aaaf4df4aa3dc9ea748211278e657c2195858c24'
-
-  def install
-    ENV['prefix'] = prefix
-    system "make READLINE=1"
-    system "make m4install"
-    cd 'primes' do
-      system 'make'
-      system 'make install'
-    end
-  end
-end
diff --git a/Library/Formula/maxima.rb b/Library/Formula/maxima.rb
deleted file mode 100644
index d93adb6b8..000000000
--- a/Library/Formula/maxima.rb
+++ /dev/null
@@ -1,53 +0,0 @@
-require 'formula'
-
-class Maxima < Formula
-  homepage 'http://maxima.sourceforge.net/'
-  url 'http://sourceforge.net/projects/maxima/files/Maxima-source/5.28.0-source/maxima-5.28.0.tar.gz'
-  sha1 '52d7dad4681711a6ead73b72835b177107363b9c'
-
-  depends_on 'gettext'
-  depends_on 'sbcl'
-  depends_on 'gnuplot'
-  depends_on 'rlwrap'
-
-  # required for maxima help(), describe(), "?" and "??" lisp functionality
-  skip_clean 'share/info'
-
-  def patches
-    # fixes 3468021: imaxima.el uses incorrect tmp directory on OS X:
-    # https://sourceforge.net/tracker/?func=detail&aid=3468021&group_id=4933&atid=104933
-    DATA
-  end
-
-  def install
-    ENV.deparallelize
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}",
-                          "--enable-sbcl",
-                          "--enable-gettext"
-    # Per build instructions
-    ENV['LANG'] = 'C'
-    system 'make'
-    system 'make check'
-    system 'make install'
-  end
-
-  def test
-    system "#{bin}/maxima", "--batch-string='run_testsuite(); quit();'"
-  end
-end
-
-__END__
-diff --git a/interfaces/emacs/imaxima/imaxima.el b/interfaces/emacs/imaxima/imaxima.el
-index e3feaa6..3a52a0b 100644
---- a/interfaces/emacs/imaxima/imaxima.el
-+++ b/interfaces/emacs/imaxima/imaxima.el
-@@ -296,6 +296,8 @@ nil means no scaling at all, t allows any scaling."
- 	 (temp-directory))
- 	((eql system-type 'cygwin)
- 	 "/tmp/")
-+	((eql system-type 'darwin)
-+	 "/tmp/")
- 	(t temporary-file-directory))
-   "*Directory used for temporary TeX and image files."
-   :type '(directory)
diff --git a/Library/Formula/mcl.rb b/Library/Formula/mcl.rb
deleted file mode 100644
index 5c56284cd..000000000
--- a/Library/Formula/mcl.rb
+++ /dev/null
@@ -1,21 +0,0 @@
-require 'formula'
-
-class Mcl < Formula
-  homepage 'http://micans.org/mcl'
-  url 'http://micans.org/mcl/src/mcl-12-135.tar.gz'
-  version '12-135'
-  sha1 '27e7bc08fe5f0d3361bbc98d343c9d045712e406'
-
-  def install
-    # Force the compiler to run in C89 mode because one of the source
-    # files uses "restrict" as a variable name and this is a restricted
-    # keyword in C99
-    ENV.append_to_cflags '-std=c89'
-
-    bin.mkpath
-    system "./configure", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}",
-                          "--enable-blast"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/metis.rb b/Library/Formula/metis.rb
deleted file mode 100644
index 4943459b4..000000000
--- a/Library/Formula/metis.rb
+++ /dev/null
@@ -1,14 +0,0 @@
-require 'formula'
-
-class Metis < Formula
-  homepage 'http://glaros.dtc.umn.edu/gkhome/views/metis'
-  url 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.0.2.tar.gz'
-  sha1 'b5a278fa06c581e068a8296d158576a4b750f983'
-
-  depends_on 'cmake' => :build
-
-  def install
-    system "make", "config", "prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/mpsolve.rb b/Library/Formula/mpsolve.rb
deleted file mode 100644
index db51974ea..000000000
--- a/Library/Formula/mpsolve.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Mpsolve < Formula
-  homepage 'http://www.dm.unipi.it/cluster-pages/mpsolve/index.htm'
-  url 'http://www.dm.unipi.it/cluster-pages/mpsolve/mpsolve.tgz'
-  sha1 '7b445f835325c62928deb99155b7ca9e646e6f97'
-  version '2.2'
-
-  depends_on 'gmp'
-
-  def install
-    system 'make'
-    bin.install 'unisolve'
-  end
-end
diff --git a/Library/Formula/nauty.rb b/Library/Formula/nauty.rb
deleted file mode 100644
index d8f073efe..000000000
--- a/Library/Formula/nauty.rb
+++ /dev/null
@@ -1,29 +0,0 @@
-require 'formula'
-
-class Nauty < Formula
-  homepage 'http://cs.anu.edu.au/~bdm/nauty/'
-  url 'http://cs.anu.edu.au/~bdm/nauty/nauty24r2.tar.gz'
-  version '24r2'
-  sha1 '3f012beb399a9340f77d0104bf1c9bf1100e8286'
-
-  option 'run-tests', "Runs the included test programs"
-
-  def install
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make all"
-    system "make checks" if build.include? 'run-tests'
-
-    bin.install %w{ NRswitchg addedgeg amtog biplabg catg complg copyg countg
-      deledgeg directg dreadnaut dretog genbg geng genrang gentourng labelg
-      listg multig newedgeg pickg planarg shortg showg }
-
-    prefix.install 'nug.pdf'
-  end
-
-  def caveats; <<-EOS.undent
-    User guide was saved locally to:
-      #{prefix}/nug.pdf
-    EOS
-  end
-end
diff --git a/Library/Formula/octave.rb b/Library/Formula/octave.rb
deleted file mode 100644
index 368bf6286..000000000
--- a/Library/Formula/octave.rb
+++ /dev/null
@@ -1,106 +0,0 @@
-require 'formula'
-
-# Leading underscore because this method is defined differently
-# in compat, and anything that loads this file would end up with
-# this definition instead!
-def _snow_leopard_64?
-  # 64 bit builds on 10.6 require some special handling.
-  MacOS.version == :snow_leopard and MacOS.prefer_64_bit?
-end
-
-class Octave < Formula
-  homepage 'http://www.gnu.org/software/octave/index.html'
-  url 'http://ftpmirror.gnu.org/octave/octave-3.6.4.tar.bz2'
-  mirror 'http://ftp.gnu.org/gnu/octave/octave-3.6.4.tar.bz2'
-  sha1 '3cc9366b6dbbd336eaf90fe70ad16e63705d82c4'
-
-  option 'without-fltk', 'Compile without fltk (disables native graphics)'
-  option 'test', 'Run tests before installing'
-
-  depends_on 'pkg-config' => :build
-  depends_on 'gnu-sed' => :build
-  depends_on 'texinfo' => :build     # OS X's makeinfo won't work for this
-
-  depends_on :x11
-  depends_on 'fftw'
-  # When building 64-bit binaries on Snow Leopard, there are naming issues with
-  # the dot product functions in the BLAS library provided by Apple's
-  # Accelerate framework. See the following thread for the gory details:
-  #
-  #   http://www.macresearch.org/lapackblas-fortran-106
-  #
-  # We can work around the issues using dotwrp.
-  depends_on 'dotwrp' if _snow_leopard_64?
-  # octave refuses to work with BSD readline, so it's either this or --disable-readline
-  depends_on 'readline'
-  depends_on 'curl' if MacOS.version == :leopard # Leopard's libcurl is too old
-
-  # additional features
-  depends_on 'suite-sparse'
-  depends_on 'glpk'
-  depends_on 'graphicsmagick' => :recommended
-  depends_on 'hdf5'
-  depends_on 'pcre'
-  depends_on 'qhull'
-  depends_on 'qrupdate'
-
-  if build.include? 'without-fltk'
-    # required for plotting if we don't have native graphics
-    depends_on 'gnuplot'
-  else
-    depends_on 'fltk'
-  end
-
-  def install
-    ENV.fortran
-
-    # yes, compiling octave takes a long time, but using -O2 gives negligible savings
-    # build time with -O2: user 58m5.295s   sys 7m29.064s
-    # build time with -O3: user 58m58.054s  sys 7m52.221s
-    ENV.m64 if MacOS.prefer_64_bit?
-    ENV.append_to_cflags "-D_REENTRANT"
-
-    args = [
-      "--disable-dependency-tracking",
-      "--prefix=#{prefix}",
-      # Cant use `-framework Accelerate` because `mkoctfile`, the tool used to
-      # compile extension packages, can't parse `-framework` flags.
-      "--with-blas=#{'-ldotwrp ' if _snow_leopard_64?}-Wl,-framework -Wl,Accelerate",
-      # SuiteSparse-4.x.x fix, see http://savannah.gnu.org/bugs/?37031
-      "--with-umfpack=-lumfpack -lsuitesparseconfig",
-    ]
-    args << "--without-framework-carbon" if MacOS.version >= :lion
-    # avoid spurious 'invalid assignment to cs-list' erorrs on 32 bit installs:
-    args << 'CXXFLAGS=-O0' unless MacOS.prefer_64_bit?
-
-    system "./configure", *args
-    system "make all"
-    system "make check 2>&1 | tee make-check.log" if build.include? 'test'
-    system "make install"
-
-    prefix.install ["test/fntests.log", "make-check.log"] if build.include? 'test'
-  end
-
-  def caveats
-    native_caveats = <<-EOS.undent
-      Octave supports "native" plotting using OpenGL and FLTK. You can activate
-      it for all future figures using the Octave command
-
-          graphics_toolkit ("fltk")
-
-      or for a specific figure handle h using
-
-          graphics_toolkit (h, "fltk")
-
-      Otherwise, gnuplot is still used by default, if available.
-    EOS
-
-    gnuplot_caveats = <<-EOS.undent
-      When plotting with gnuplot, you should set "GNUTERM=x11" before running octave;
-      if you are using Aquaterm, use "GNUTERM=aqua".
-    EOS
-
-    s = gnuplot_caveats
-    s = native_caveats + s unless build.include? 'without-fltk'
-  end
-end
diff --git a/Library/Formula/opencv.rb b/Library/Formula/opencv.rb
deleted file mode 100644
index 63b0a32c3..000000000
--- a/Library/Formula/opencv.rb
+++ /dev/null
@@ -1,126 +0,0 @@
-require 'formula'
-
-def which_python
-  "python" + `python -c 'import sys;print(sys.version[:3])'`.strip
-end
-
-def site_package_dir
-  "lib/#{which_python}/site-packages"
-end
-
-class Opencv < Formula
-  homepage 'http://opencv.org/'
-  url 'http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/2.4.4/OpenCV-2.4.4a.tar.bz2'
-  sha1 '6e518c0274a8392c0c98d18ef0ef754b9c596aca'
-
-  env :std # to find python
-
-  option '32-bit'
-  option 'with-qt',  'Build the Qt4 backend to HighGUI'
-  option 'with-tbb', 'Enable parallel code in OpenCV using Intel TBB'
-  option 'with-opencl', 'Enable gpu code in OpenCV using OpenCL'
-
-  depends_on 'cmake' => :build
-  depends_on 'pkg-config' => :build
-  depends_on 'numpy' => :python
-
-  depends_on 'eigen'   => :optional
-  depends_on 'libtiff' => :optional
-  depends_on 'jasper'  => :optional
-  depends_on 'tbb'     => :optional
-  depends_on 'qt'      => :optional
-  depends_on :libpng
-
-  # Can also depend on ffmpeg, but this pulls in a lot of extra stuff that
-  # you don't need unless you're doing video analysis, and some of it isn't
-  # in Homebrew anyway. Will depend on openexr if it's installed.
-
-  # Fix non-ASCII characters breaking in Java 1.7
-  # https://github.com/Itseez/opencv/pull/718
-  def patches; DATA; end
-
-  def install
-    args = std_cmake_args + %w[
-      -DCMAKE_OSX_DEPLOYMENT_TARGET=
-      -DWITH_CUDA=OFF
-      -DBUILD_ZLIB=OFF
-      -DBUILD_TIFF=OFF
-      -DBUILD_PNG=OFF
-      -DBUILD_JPEG=OFF
-      -DBUILD_JASPER=OFF
-      -DBUILD_TESTS=OFF
-      -DBUILD_PERF_TESTS=OFF
-    ]
-    if build.build_32_bit?
-      args << "-DCMAKE_OSX_ARCHITECTURES=i386"
-      args << "-DOPENCV_EXTRA_C_FLAGS='-arch i386 -m32'"
-      args << "-DOPENCV_EXTRA_CXX_FLAGS='-arch i386 -m32'"
-    end
-    args << '-DWITH_QT=ON' if build.with? 'qt'
-    args << '-DWITH_TBB=ON' if build.with? 'tbb'
-    args << '-DWITH_OPENCL=ON' if build.with? 'opencl'
-
-    # The CMake `FindPythonLibs` Module is dumber than a bag of hammers when
-    # more than one python installation is available---for example, it clings
-    # to the Header folder of the system Python Framework like a drowning
-    # sailor.
-    #
-    # This code was cribbed from the VTK formula and uses the output to
-    # `python-config` to do the job FindPythonLibs should be doing in the first
-    # place.
-    python_prefix = `python-config --prefix`.strip
-    # Python is actually a library. The libpythonX.Y.dylib points to this lib, too.
-    if File.exist? "#{python_prefix}/Python"
-      # Python was compiled with --framework:
-      args << "-DPYTHON_LIBRARY='#{python_prefix}/Python'"
-      if !MacOS::CLT.installed? and python_prefix.start_with? '/System/Library'
-        # For Xcode-only systems, the headers of system's python are inside of Xcode
-        args << "-DPYTHON_INCLUDE_DIR='#{MacOS.sdk_path}/System/Library/Frameworks/Python.framework/Versions/2.7/Headers'"
-      else
-        args << "-DPYTHON_INCLUDE_DIR='#{python_prefix}/Headers'"
-      end
-    else
-      python_lib = "#{python_prefix}/lib/lib#{which_python}"
-      if File.exists? "#{python_lib}.a"
-        args << "-DPYTHON_LIBRARY='#{python_lib}.a'"
-      else
-        args << "-DPYTHON_LIBRARY='#{python_lib}.dylib'"
-      end
-      args << "-DPYTHON_INCLUDE_DIR='#{python_prefix}/include/#{which_python}'"
-    end
-    args << "-DPYTHON_PACKAGES_PATH='#{lib}/#{which_python}/site-packages'"
-
-    args << '..'
-    mkdir 'macbuild' do
-      system 'cmake', *args
-      system "make"
-      system "make install"
-    end
-  end
-
-  def caveats; <<-EOS.undent
-    The OpenCV Python module will not work until you edit your PYTHONPATH like so:
-      export PYTHONPATH="#{HOMEBREW_PREFIX}/#{site_package_dir}:$PYTHONPATH"
-
-    To make this permanent, put it in your shell's profile (e.g. ~/.profile).
-    EOS
-  end
-end
-
-__END__
-diff --git a/modules/java/build.xml.in b/modules/java/build.xml.in
-index 98ba2e3..c1c1854 100644
---- a/modules/java/build.xml.in
-+++ b/modules/java/build.xml.in
-@@ -8,8 +8,9 @@
-     <!-- http://stackoverflow.com/questions/3584968/ant-how-to-compile-jar-that-includes-source-attachment -->
-     <javac sourcepath="" srcdir="src" destdir="src" debug="on" includeantruntime="false" >
-       <include name="**/*.java"/>
-+      <compilerarg line="-encoding utf-8"/>
-     </javac>
- 
-     <jar basedir="src" destfile="bin/@JAR_NAME@"/>
-   </target>
--</project>
-\ No newline at end of file
-+</project>
diff --git a/Library/Formula/openimageio.rb b/Library/Formula/openimageio.rb
deleted file mode 100644
index 5c1b55aff..000000000
--- a/Library/Formula/openimageio.rb
+++ /dev/null
@@ -1,143 +0,0 @@
-require 'formula'
-
-class J2kp4files < Formula
-  url 'http://pkgs.fedoraproject.org/repo/pkgs/openjpeg/j2kp4files_v1_5.zip/27780ed3254e6eb763ebd718a8ccc340/j2kp4files_v1_5.zip'
-  sha1 'a90cad94abbe764918175db72b49df6d2f63704b'
-end
-
-class Tiffpic < Formula
-  url 'ftp://ftp.remotesensing.org/pub/libtiff/pics-3.8.0.tar.gz'
-  sha1 'f50e14335fd98f73c6a235d3ff4d83cf4767ab37'
-end
-
-class Bmpsuite < Formula
-  url 'http://entropymine.com/jason/bmpsuite/bmpsuite.zip'
-  sha1 '2e43ec4d8e6f628f71a554c327433914000db7ba'
-  version '1.0.0'
-end
-
-class Tgautils < Formula
-  url 'http://makseq.com/materials/lib/Code/FileFormats/BitMap/TARGA/TGAUTILS.ZIP'
-  sha1 '0902c51e7b00ae70a460250f60d6adc41c8095df'
-  version '1.0.0'
-end
-
-class OpenexrImages < Formula
-  url 'http://download.savannah.nongnu.org/releases/openexr/openexr-images-1.5.0.tar.gz'
-  sha1 '22bb1a3d37841a88647045353f732ceac652fd3f'
-end
-
-class OiioImages < Formula
-  url 'https://github.com/OpenImageIO/oiio-images/tarball/9bf43561f5'
-  sha1 '8f12a86098120fd10ceb294a0d3aa1c95a0d3f80'
-  version '1.0.0'
-end
-
-
-class Openimageio < Formula
-  homepage 'http://openimageio.org'
-  url 'https://github.com/OpenImageIO/oiio/archive/Release-1.1.8.tar.gz'
-  sha1 '14ce1bb9067e70717de3f8d72c56342fa378a1e6'
-
-  head 'https://github.com/OpenImageIO/oiio.git'
-
-  option 'with-tests',  'Dowload 95MB of test images and verify Oiio (~2 min)'
-
-  depends_on 'cmake' => :build
-  depends_on 'pkg-config' => :build
-  depends_on 'opencolorio'
-  depends_on 'ilmbase'
-  depends_on 'openexr'
-  depends_on 'boost'
-  depends_on 'libtiff'
-  depends_on 'jpeg'
-  depends_on 'openjpeg'
-  depends_on 'cfitsio'
-  depends_on 'hdf5' => 'enable-cxx'
-  depends_on 'field3d'
-  depends_on 'webp'
-  depends_on 'glew'
-  depends_on 'qt'
-
-  def install
-    # Oiio is designed to have its testsuite images extracted one directory
-    # above the source.  That's not a safe place for HB.  Do the opposite,
-    # and move the entire source down into a subdirectory if --with-tests.
-    if build.include? 'with-tests' then
-      (buildpath+'localpub').install Dir['*']
-      chdir 'localpub'
-    end
-
-    j2k = Formula.factory('openjpeg').linked_keg.realpath
-    ENV.append 'MY_CMAKE_FLAGS', "-Wno-dev"   # stops a warning.
-    ENV.append 'MY_CMAKE_FLAGS', "-DOPENJPEG_INCLUDE_DIR=#{j2k}/include/openjpeg-1.5"
-    args = ["USE_TBB=1", "EMBEDPLUGINS=1"]
-
-
-    python_prefix = `python-config --prefix`.strip
-    # Python is actually a library. The libpythonX.Y.dylib points to this lib, too.
-    if File.exist? "#{python_prefix}/Python"
-      # Python was compiled with --framework:
-      ENV.append 'MY_CMAKE_FLAGS', "-DPYTHON_LIBRARY='#{python_prefix}/Python'"
-      ENV.append 'MY_CMAKE_FLAGS', "-DPYTHON_INCLUDE_DIR='#{python_prefix}/Headers'"
-    else
-      python_version = `python-config --libs`.match('-lpython(\d+\.\d+)').captures.at(0)
-      python_lib = "#{python_prefix}/lib/libpython#{python_version}"
-      ENV.append 'MY_CMAKE_FLAGS', "-DPYTHON_INCLUDE_DIR='#{python_prefix}/include/python#{python_version}'"
-      if File.exists? "#{python_lib}.a"
-        ENV.append 'MY_CMAKE_FLAGS', "-DPYTHON_LIBRARY='#{python_lib}.a'"
-      else
-        ENV.append 'MY_CMAKE_FLAGS', "-DPYTHON_LIBRARY='#{python_lib}.dylib'"
-      end
-    end
-
-    # Download standardized test images if the user throws --with-tests.
-    # 90% of the images are in tarballs, so they are cached normally.
-    # The webp and fits images are loose.  Curl them each install.
-    if build.include? 'with-tests' then
-      d = buildpath
-      mkdir d+'webp-images' do
-        curl "http://www.gstatic.com/webp/gallery/[1-5].webp", "-O"
-      end
-      mkdir d+'fits-images'
-      mkdir d+'fits-images/pg93' do
-        curl "http://www.cv.nrao.edu/fits/data/tests/pg93/tst000[1-3].fits", "-O"
-        curl "http://www.cv.nrao.edu/fits/data/tests/pg93/tst000[5-9].fits", "-O"
-        curl "http://www.cv.nrao.edu/fits/data/tests/pg93/tst0013.fits", "-O"
-      end
-      mkdir d+'fits-images/ftt4b' do
-        curl "http://www.cv.nrao.edu/fits/data/tests/ftt4b/file00[1-3].fits", "-O"
-        curl "http://www.cv.nrao.edu/fits/data/tests/ftt4b/file0{09,12}.fits", "-O"
-      end
-      J2kp4files.new.brew { (d+'j2kp4files_v1_5').install Dir['J2KP4files/*'] }
-      Tiffpic.new.brew { (d+'libtiffpic').install Dir['*'] }
-      Bmpsuite.new.brew { (d+'bmpsuite').install Dir['*'] }
-      Tgautils.new.brew { (d+'TGAUTILS').install Dir['*'] }
-      OpenexrImages.new.brew { (d+'openexr-images-1.5.0').install Dir['*'] }
-      OiioImages.new('oiioimages').brew { (d+'oiio-images').install Dir['*'] }
-    end
-
-    # make is a shell wrapper for cmake crafted by the devs (who have Lion).
-    system "make", *args
-    system "make test" if build.include? 'with-tests'
-    # There is no working make install in 1.1.6, devel or HEAD.
-    Dir.chdir 'dist/macosx' do
-      (lib + which_python ).install 'lib/python/site-packages'
-      prefix.install %w[ bin include ]
-      lib.install    Dir[ 'lib/lib*' ]
-      doc.install    'share/doc/openimageio/openimageio.pdf'
-      prefix.install Dir['share/doc/openimageio/*']
-    end
-  end
-
-  def caveats; <<-EOS.undent
-    If OpenImageIO is brewed using non-homebrew Python, then you need to amend
-    your PYTHONPATH like so:
-      export PYTHONPATH=#{HOMEBREW_PREFIX}/lib/#{which_python}/site-packages:$PYTHONPATH
-    EOS
-  end
-
-  def which_python
-    "python" + `python -c 'import sys;print(sys.version[:3])'`.strip
-  end
-end
diff --git a/Library/Formula/parmetis.rb b/Library/Formula/parmetis.rb
deleted file mode 100644
index 624b3346e..000000000
--- a/Library/Formula/parmetis.rb
+++ /dev/null
@@ -1,15 +0,0 @@
-require 'formula'
-
-class Parmetis < Formula
-  homepage 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
-  url 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.2.tar.gz'
-  sha1 '1699453f0bd2ffed34e5a755dec92048d797476d'
-
-  depends_on 'cmake' => :build
-  depends_on MPIDependency.new(:cc)
-
-  def install
-    system "make", "config", "prefix=#{prefix}"
-    system 'make install'
-  end
-end
diff --git a/Library/Formula/qhull.rb b/Library/Formula/qhull.rb
deleted file mode 100644
index 184e0eea1..000000000
--- a/Library/Formula/qhull.rb
+++ /dev/null
@@ -1,54 +0,0 @@
-require 'formula'
-
-class Qhull < Formula
-  homepage 'http://www.qhull.org/'
-  url 'http://www.qhull.org/download/qhull-2012.1-src.tgz'
-  sha1 '60f61580e1d6fbbd28e6df2ff625c98d15b5fbc6'
-
-  depends_on 'cmake' => :build
-
-  def patches
-    # Patch originally from MacPorts - cosmetic edits to CMakeLists.txt:
-    #
-    #  * The VERSION property is no longer set on the command line tools.
-    #    Setting this property causes CMake to install `binname-version` along
-    #    with a symlink `binname` that points to `binname-version`. This is
-    #    pointless for something that is managed by a package manager.
-    # https://trac.macports.org/export/83287/trunk/dports/math/qhull/files/patch-CMakeLists.txt.diff'}
-    DATA
-  end
-
-  def install
-    system "cmake", ".", *std_cmake_args
-    system "make install"
-  end
-end
-
-__END__
---- a/CMakeLists.txt	2012-02-21 19:38:47.000000000 -0800
-+++ b/CMakeLists.txt	2012-06-18 09:33:28.000000000 -0700
-@@ -312,13 +312,10 @@
- # ---------------------------------------
- 
- add_library(${qhull_STATIC} STATIC ${libqhull_SOURCES})
--set_target_properties(${qhull_STATIC} PROPERTIES
--    VERSION ${qhull_VERSION})
- 
- add_library(${qhull_STATICP} STATIC ${libqhull_SOURCES})
- set_target_properties(${qhull_STATICP} PROPERTIES
--    COMPILE_DEFINITIONS "qh_QHpointer"
--    VERSION ${qhull_VERSION})
-+    COMPILE_DEFINITIONS "qh_QHpointer")
- 
- if(UNIX)
-     target_link_libraries(${qhull_STATIC} m)
-@@ -331,8 +328,7 @@
- 
- add_library(${qhull_CPP} STATIC ${libqhullcpp_SOURCES})
- set_target_properties(${qhull_CPP} PROPERTIES
--    COMPILE_DEFINITIONS "qh_QHpointer"
--    VERSION ${qhull_VERSION})
-+    COMPILE_DEFINITIONS "qh_QHpointer")
- 
- # ---------------------------------------
- # Define qhull executables linked to qhullstatic library
diff --git a/Library/Formula/radx.rb b/Library/Formula/radx.rb
deleted file mode 100644
index 6160dfaaf..000000000
--- a/Library/Formula/radx.rb
+++ /dev/null
@@ -1,27 +0,0 @@
-require 'formula'
-
-class Radx < Formula
-  homepage 'http://www.ral.ucar.edu/projects/titan/docs/radial_formats/radx.html'
-  url 'ftp://ftp.rap.ucar.edu/pub/titan/radx/Radx-20121120.src.tgz'
-  version '20121120'
-  sha1 '2c0ffa04c0f6b942fb2de1ec35256f857b5d2d63'
-
-  depends_on 'hdf5'
-  depends_on 'udunits'
-  depends_on 'netcdf' => 'enable-cxx-compat'
-  depends_on 'fftw'
-
-  fails_with :clang do
-    build 421
-    cause "DsMdvx/msg_add.cc:516:11: error: '_printVsectWayPtsBuf' is a protected member of 'Mdvx'"
-  end
-
-  def install
-    system "./configure", "--disable-dependency-tracking", "--prefix=#{prefix}"
-    system "make install"
-  end
-
-  def test
-    system "#{bin}/RadxPrint", "-h"
-  end
-end
diff --git a/Library/Formula/scotch.rb b/Library/Formula/scotch.rb
deleted file mode 100644
index 146880998..000000000
--- a/Library/Formula/scotch.rb
+++ /dev/null
@@ -1,27 +0,0 @@
-require 'formula'
-
-class Scotch < Formula
-  homepage 'https://gforge.inria.fr/projects/scotch'
-  url 'https://gforge.inria.fr/frs/download.php/31831/scotch_6.0.0.tar.gz'
-  sha1 'eb32d846bb14449245b08c81e740231f7883fea6'
-
-  depends_on MPIDependency.new(:cc)
-
-  def install
-    cd 'src' do
-      ln_s 'Make.inc/Makefile.inc.i686_mac_darwin8', 'Makefile.inc'
-
-      inreplace 'Makefile.inc' do |s|
-        s.change_make_var! 'CCS', ENV['CC']
-        s.change_make_var! 'CCP', ENV['MPICC']
-        s.change_make_var! 'CCD', ENV['MPICC']
-        # OS X doesn't implement pthread_barriers required by Scotch
-        s.slice! '-DCOMMON_PTHREAD'
-        s.slice! '-DSCOTCH_PTHREAD'
-      end
-      system 'make', 'scotch','VERBOSE=ON'
-      system 'make', 'ptscotch','VERBOSE=ON'
-      system 'make', 'install', "prefix=#{prefix}"
-    end
-  end
-end
diff --git a/Library/Formula/suite-sparse.rb b/Library/Formula/suite-sparse.rb
deleted file mode 100644
index 3c133f6f7..000000000
--- a/Library/Formula/suite-sparse.rb
+++ /dev/null
@@ -1,51 +0,0 @@
-require 'formula'
-
-class SuiteSparse < Formula
-  homepage 'http://www.cise.ufl.edu/research/sparse/SuiteSparse'
-  url 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-4.1.0.tar.gz'
-  sha1 '4f0bd70a87c89ed734558ece724a1bf99616f27b'
-
-  option "without-tbb", "Do not link with tbb (Threading Building Block)"
-  option "with-metis", "Compile in metis libraries"
-  option "with-openblas", "Use openblas instead of Apple's Accelerate.framework"
-
-  depends_on "tbb" unless build.include? "without-tbb"
-  # Metis is optional for now because of
-  # cholmod_metis.c:164:21: error: use of undeclared identifier 'idxtype'
-  depends_on "metis" if build.include? "with-metis"
-  depends_on "homebrew/science/openblas" if build.include? "with-openblas"
-
-  def install
-    # SuiteSparse doesn't like to build in parallel
-    ENV.j1
-
-    inreplace 'SuiteSparse_config/SuiteSparse_config.mk' do |s|
-      if build.include? 'with-openblas'
-        s.change_make_var! "BLAS", "-lopenblas"
-        s.change_make_var! "LAPACK", "$(BLAS)"
-      else
-        s.change_make_var! "BLAS", "-Wl,-framework -Wl,Accelerate"
-        s.change_make_var! "LAPACK", "$(BLAS)"
-      end
-
-      unless build.include? "without-tbb"
-        s.change_make_var! "SPQR_CONFIG", "-DHAVE_TBB"
-        s.change_make_var! "TBB", "-ltbb"
-      end
-
-      if build.include? 'with-metis'
-        s.remove_make_var! "METIS_PATH"
-        s.change_make_var! "METIS", Formula.factory("metis").lib + "libmetis.a"
-      end
-
-      s.change_make_var! "INSTALL_LIB", lib
-      s.change_make_var! "INSTALL_INCLUDE", include
-    end
-
-    system "make library"
-
-    lib.mkpath
-    include.mkpath
-    system "make install"
-  end
-end
diff --git a/Library/Formula/symphony.rb b/Library/Formula/symphony.rb
deleted file mode 100644
index 35f797f5e..000000000
--- a/Library/Formula/symphony.rb
+++ /dev/null
@@ -1,38 +0,0 @@
-require 'formula'
-
-class Symphony < Formula
-  homepage 'http://www.coin-or.org/projects/SYMPHONY.xml'
-  url 'http://www.coin-or.org/download/source/SYMPHONY/SYMPHONY-5.3.3.tgz'
-  sha1 'afc38ee5655b52fc3fa0a5854b5cc5a7f31618cc'
-
-  option "enable-openmp", "Enable openmp support"
-  option "with-gmpl", "GNU Modeling Language support via GLPK"
-
-  def install
-    args = ["--disable-debug", "--disable-dependency-tracking",
-            "--enable-shared=no", # can't get shared libs to work
-            "--enable-static-executable",
-            "--prefix=#{prefix}"]
-
-    if build.include? "with-gmpl"
-      # Symphony uses a patched version of GLPK for reading MPL files.
-      # Use a private version rather than require the Homebrew version of GLPK.
-      cd 'ThirdParty/Glpk' do
-        system "./get.Glpk"
-      end
-
-      ENV.append "CPPFLAGS", "-I#{buildpath}/ThirdParty/Glpk/glpk/src"
-      ENV.append "CDEFS", "-DUSE_GLPMPL"
-      args << "--with-gmpl"
-    end
-
-    if build.include? "enable-openmp"
-      inreplace 'SYMPHONY/config', /^SYM_COMPILE_IN_LP = TRUE/, "SYM_COMPILE_IN_LP = FALSE"
-      args << "--enable-openmp"
-    end
-
-    system "./configure",  *args
-    system "make"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/triangle.rb b/Library/Formula/triangle.rb
deleted file mode 100644
index 3c9754d9c..000000000
--- a/Library/Formula/triangle.rb
+++ /dev/null
@@ -1,34 +0,0 @@
-require 'formula'
-
-class Triangle < Formula
-  homepage 'http://www.cs.cmu.edu/~quake/triangle.html'
-  url 'http://www.netlib.org/voronoi/triangle.zip'
-  sha1 '63d11e0b5bf097eb946a4da4ee18ddf279e16fc4'
-  version '1.6'
-
-  depends_on :x11
-
-  def install
-    inreplace 'makefile' do |s|
-      s.gsub! '-DLINUX', ''
-      s.remove_make_var! 'CC'
-    end
-
-    system 'make'
-    system 'make', 'trilibrary'
-    system 'ar', 'r', 'libtriangle.a', 'triangle.o'
-
-    bin.install %w(triangle showme)
-    lib.install 'libtriangle.a'
-    include.install 'triangle.h'
-    doc.install %w(README A.poly tricall.c)
-  end
-
-  def caveats; <<-EOS.undent
-      Triangle is distributed under a license that places restrictions on how
-      the code or library may be used in commercial products.  See the README
-      file for more info:
-          #{prefix}/README
-    EOS
-  end
-end
diff --git a/Library/Formula/unafold.rb b/Library/Formula/unafold.rb
deleted file mode 100644
index 688a8925e..000000000
--- a/Library/Formula/unafold.rb
+++ /dev/null
@@ -1,17 +0,0 @@
-require 'formula'
-
-class Unafold < Formula
-  homepage 'http://mfold.rna.albany.edu/'
-  url 'http://mfold.rna.albany.edu/cgi-bin/UNAFold-download.cgi?unafold-3.8.tar.gz'
-  sha1 'b4f0296af9809ecb9f067f5adf17249315a50b7d'
-
-  depends_on 'gd'
-  depends_on 'gnuplot'
-
-  def install
-    system "./configure", "--disable-debug", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/vcftools.rb b/Library/Formula/vcftools.rb
deleted file mode 100644
index ce73b408d..000000000
--- a/Library/Formula/vcftools.rb
+++ /dev/null
@@ -1,22 +0,0 @@
-require 'formula'
-
-class Vcftools < Formula
-  homepage 'http://vcftools.sourceforge.net/index.html'
-  url 'http://downloads.sourceforge.net/project/vcftools/vcftools_0.1.10.tar.gz'
-  sha1 'a41cf3b13b574fde60e4d713f083b53e223ace55'
-
-  def install
-    system "make", "install", "PREFIX=#{prefix}", "CPP=#{ENV.cxx}"
-  end
-
-  def caveats; <<-EOS.undent
-    To use the Perl modules, make sure Vcf.pm, VcfStats.pm, and FaSlice.pm
-    are included in your PERL5LIB environment variable:
-      export PERL5LIB=#{HOMEBREW_PREFIX}/lib/perl5/site_perl:${PERL5LIB}
-    EOS
-  end
-
-  def test
-    system "#{bin}/vcftools"
-  end
-end
diff --git a/Library/Formula/vips.rb b/Library/Formula/vips.rb
deleted file mode 100644
index ccbffb1e8..000000000
--- a/Library/Formula/vips.rb
+++ /dev/null
@@ -1,32 +0,0 @@
-require 'formula'
-
-class Vips < Formula
-  homepage 'http://www.vips.ecs.soton.ac.uk/'
-  url 'http://www.vips.ecs.soton.ac.uk/supported/7.32/vips-7.32.1.tar.gz'
-  sha1 'f07cb324c9695129d2de0c140943865dcb99268f'
-
-  depends_on 'pkg-config' => :build
-  depends_on :libpng
-  depends_on :fontconfig
-  depends_on 'gettext'
-  depends_on 'glib'
-  # Removed the optional flag to jpeg library as a temporary workaround since it fails to build
-  # Already reported on project here https://github.com/jcupitt/libvips/issues/57
-  depends_on 'jpeg'
-  depends_on 'openslide' => :optional
-  depends_on 'libtiff' => :optional
-  depends_on 'imagemagick' => :optional
-  depends_on 'fftw' => :optional
-  depends_on 'little-cms' => :optional
-  depends_on 'pango' => :optional
-  depends_on 'libexif' => :optional
-  depends_on 'liboil' => :optional
-  depends_on 'openexr' => :optional
-  depends_on 'cfitsio' => :optional
-
-  def install
-    system "./configure", "--disable-dependency-tracking",
-                          "--prefix=#{prefix}"
-    system "make install"
-  end
-end
diff --git a/Library/Formula/vtk.rb b/Library/Formula/vtk.rb
deleted file mode 100644
index 073e90f15..000000000
--- a/Library/Formula/vtk.rb
+++ /dev/null
@@ -1,144 +0,0 @@
-require 'formula'
-
-class Vtk < Formula
-  homepage 'http://www.vtk.org'
-  url 'http://www.vtk.org/files/release/5.10/vtk-5.10.1.tar.gz'
-  sha1 'deb834f46b3f7fc3e122ddff45e2354d69d2adc3'
-
-  depends_on 'cmake' => :build
-  depends_on :x11 if build.include? 'x11'
-  depends_on 'qt' if build.include? 'qt'
-
-  if build.include? 'pyqt' and build.include? 'python'
-    depends_on  'sip'
-    depends_on  'pyqt'
-  end
-
-  option 'examples',  'Compile and install various examples'
-  option 'python',    'Enable python wrapping of VTK classes'
-  option 'pyqt',      'Make python wrapped classes available to SIP/PyQt'
-  option 'qt',        'Enable Qt4 extension via the Homebrew qt formula'
-  option 'qt-extern', 'Enable Qt4 extension via non-Homebrew external Qt4'
-  option 'tcl',       'Enable Tcl wrapping of VTK classes'
-  option 'x11',       'Enable X11 extension rather than OSX native Aqua'
-
-  def patches
-    # Fix bug in Wrapping/Python/setup_install_paths.py: http://vtk.org/Bug/view.php?id=13699
-    DATA
-  end
-
-  def install
-    args = std_cmake_args + %W[
-      -DVTK_REQUIRED_OBJCXX_FLAGS=''
-      -DVTK_USE_CARBON=OFF
-      -DBUILD_TESTING=OFF
-      -DBUILD_SHARED_LIBS=ON
-      -DCMAKE_INSTALL_RPATH:STRING='#{lib}/vtk-5.10'
-      -DCMAKE_INSTALL_NAME_DIR:STRING='#{lib}/vtk-5.10'
-    ]
-
-    args << '-DBUILD_EXAMPLES=' + ((build.include? 'examples') ? 'ON' : 'OFF')
-
-    if build.include? 'python'
-      args << '-DVTK_WRAP_PYTHON=ON'
-
-      # Cmake picks up the system's python dylib, even if we have a brewed one.
-      python_prefix = `python-config --prefix`.strip
-      args << "-DPYTHON_LIBRARY='#{python_prefix}/Python'"
-
-      # Install to lib and let installer symlink to global python site-packages.
-      # The path in lib needs to exist first and be listed in PYTHONPATH.
-      pydir = lib/which_python/'site-packages'
-      pydir.mkpath
-      ENV['PYTHONPATH'] = pydir
-      args << "-DVTK_PYTHON_SETUP_ARGS:STRING='--prefix=#{prefix} --install-lib=#{pydir} --single-version-externally-managed --record=installed-files.txt'"
-
-      # For Xcode-only systems, the headers of system's python are inside of Xcode
-      if !MacOS::CLT.installed? and python_prefix.start_with? '/System/Library'
-        args << "-DPYTHON_INCLUDE_DIR='#{MacOS.sdk_path}/System/Library/Frameworks/Python.framework/Versions/2.7/Headers'"
-      end
-
-      if build.include? 'pyqt'
-        args << '-DVTK_WRAP_PYTHON_SIP=ON'
-        args << "-DSIP_PYQT_DIR='#{HOMEBREW_PREFIX}/share/sip'"
-      end
-    end
-
-    if build.include? 'qt' or build.include? 'qt-extern'
-      args << '-DVTK_USE_GUISUPPORT=ON'
-      args << '-DVTK_USE_QT=ON'
-      args << '-DVTK_USE_QVTK=ON'
-    end
-
-    args << '-DVTK_WRAP_TCL=ON' if build.include? 'tcl'
-
-    # Cocoa for everything except x11
-    if build.include? 'x11'
-      args << '-DVTK_USE_COCOA=OFF'
-      args << '-DVTK_USE_X=ON'
-    else
-      args << '-DVTK_USE_COCOA=ON'
-    end
-
-    unless MacOS::CLT.installed?
-      # We are facing an Xcode-only installation, and we have to keep
-      # vtk from using its internal Tk headers (that differ from OSX's).
-      args << "-DTK_INCLUDE_PATH:PATH=#{MacOS.sdk_path}/System/Library/Frameworks/Tk.framework/Headers"
-      args << "-DTK_INTERNAL_PATH:PATH=#{MacOS.sdk_path}/System/Library/Frameworks/Tk.framework/Headers/tk-private"
-    end
-
-    args << ".."
-
-    mkdir 'build' do
-      system 'cmake', *args
-      system 'make'
-      system 'make install'
-    end
-
-    (share+'vtk').install 'Examples' if build.include? 'examples'
-  end
-
-  def caveats
-    s = ''
-    vtk = Tab.for_formula 'vtk'
-    if build.include? 'python' or vtk.include? 'python'
-      s += <<-EOS.undent
-        For non-homebrew Python, you need to amend your PYTHONPATH like so:
-        export PYTHONPATH=#{HOMEBREW_PREFIX}/lib/#{which_python}/site-packages:$PYTHONPATH
-
-        Even without the --pyqt option, you can display native VTK render windows
-        from python. Alternatively, you can integrate the RenderWindowInteractor
-        in PyQt, PySide, Tk or Wx at runtime. Look at
-            import vtk.qt4; help(vtk.qt4) or import vtk.wx; help(vtk.wx)
-
-      EOS
-    end
-    if build.include? 'examples' or vtk.include? 'examples'
-      s += <<-EOS.undent
-
-        The scripting examples are stored in #{HOMEBREW_PREFIX}/share/vtk
-
-      EOS
-    end
-    return s.empty? ? nil : s
-  end
-
-  def which_python
-    "python" + `python -c 'import sys;print(sys.version[:3])'`.strip
-  end
-end
-
-__END__
-diff --git a/Wrapping/Python/setup_install_paths.py b/Wrapping/Python/setup_install_paths.py
-index 00f48c8..014b906 100755
---- a/Wrapping/Python/setup_install_paths.py
-+++ b/Wrapping/Python/setup_install_paths.py
-@@ -35,7 +35,7 @@ def get_install_path(command, *args):
-                 option, value = string.split(arg,"=")
-                 options[option] = value
-             except ValueError:
--                options[option] = 1
-+                options[arg] = 1
-
-     # check for the prefix and exec_prefix
-     try: