jblas.rb

require 'formula'

class Jblas < Formula
  homepage 'http://mikiobraun.github.io/jblas'
  url 'http://mikiobraun.github.io/jblas/jars/jblas-1.2.3.jar'
  sha1 '3c0d35c4e6b8d7ea7bbcbf109fd1863e54f9d061'

  def install
    (share / "java").install "jblas-#{version}.jar" => "jblas.jar"
  end
end

shogun.rb

require "formula"

class Shogun < Formula
  homepage "http://www.shogun-toolbox.org"
  url "http://shogun-toolbox.org/archives/shogun/releases/3.2/sources/shogun-3.2.0.tar.bz2"
  sha1 "442e212a19d0297b4df45a4dfe7deb6312441e54"
  head "https://github.com/shogun-toolbox/shogun.git", :branch => "develop"

  #option "without-check", "Skip build-time tests (not recommended)"
  option "with-check", "Perform build-time tests (there are failures!)"
  option "without-svm-light", "Disable SVM-light module, which is GPLv3 and makes all of shogun GPLv3"
  option "with-java", "Enable Java modular interface (requires JDK)"

  depends_on "pkg-config" => :build
  depends_on "arpack"
  depends_on "json-c"

  depends_on "readline"   => :recommended
  depends_on "lzo"        => :recommended
  depends_on "xz"         => :recommended  # provides lzma

  # To enable system Ruby, you must have permission to install gems. See
  # https://github.com/Homebrew/homebrew/blob/master/share/doc/homebrew/Gems%2C-Eggs-and-Perl-Modules.md#with-systems-ruby
  # Other versions of Ruby might work but they must be compiled with clang.
  option "with-ruby", "Enable Ruby modular interface (requires narray gem)"

  depends_on :java           if build.with? "java"
  depends_on "jblas"         if build.with? "java"
  depends_on "eigen"      => :recommended
  depends_on "glpk"       => :recommended
  depends_on "hdf5"       => :recommended
  depends_on "lua"        => :recommended
  depends_on "nlopt"      => :recommended
  depends_on "snappy"     => :recommended

  depends_on :python      => ["numpy", "matplotlib", :recommended]
  depends_on "swig"          if build.with? :python

  depends_on "colpack"    => :optional  # Broken.
  depends_on "octave"     => :optional  # Broken.
  depends_on "r"          => :optional  # Broken.

  def onoff(s, cond)
    s + ((cond) ? "ON" : "OFF")
  end

  stable do
    # See http://comments.gmane.org/gmane.comp.ai.machine-learning.shogun/4471
    patch :DATA
  end

  def install
    if build.with? "r"
      onoe "Compilation of the Shogun/R interface fails!"
      onoe "See https://github.com/shogun-toolbox/shogun/issues/2395"
      exit 1
    end

    if build.with? "octave"
      onoe "Compilation of the Shogun/Octave interface fails!"
      onoe "See https://github.com/shogun-toolbox/shogun/issues/2396"
      exit 1
    end

    # Fail if ColPack is installed.
    colpack_opts = Tab.for_formula(Formula["colpack"])
    if colpack_opts.time != nil
      onoe "Shogun will pick up your ColPack install and compilation will fail!"
      onoe "Please `brew uninstall colpack` before proceeding."
      onoe "See https://github.com/shogun-toolbox/shogun/issues/1804"
      exit 1
    end

    ENV.cxx11
    cmake_args = std_cmake_args
    cmake_args += ["-DBUNDLE_COLPACK=OFF"]  # Will fail if ColPack is installed!
    if build.with? "colpack"
      cmake_args += ["-DColpack_Include_Dir=#{Formula['colpack'].opt_include}",
                    "-DColpack_Library_Dir=#{Formula['colpack'].opt_lib}",
                    "-DColpack_Libraries=#{Formula['colpack'].opt_lib}/libColPack.dylib"]
    end
    cmake_args += ["-DArpack_Include_Dir=#{Formula['arpack'].opt_include}",
                   "-DArpack_Lib=#{Formula['arpack'].opt_lib}/libarpack.dylib",
                   "-DArpack_Path=#{Formula['arpack'].opt_prefix}"]
    cmake_args <<  "-DBUNDLE_JSON=OFF"

    if build.with? "eigen"
      cmake_args += ["-DBUNDLE_EIGEN=OFF",
                     "-DEigen_Include_Dir=#{Formula['eigen'].opt_include}"]
    end
    if build.with? "nlopt"
      cmake_args += ["-DBUNDLE_NLOPT=OFF",
                     "-DNLOPT_Include_Dir=#{Formula['nlopt'].opt_include}",
                     "-DNLOPT_Library=#{Formula['nlopt'].opt_lib}/libnlopt_cxx.dylib"]
    end
    if build.with? "glpk"
      cmake_args += ["-DGLPK_Include_Dir=#{Formula['glpk'].opt_include}",
                     "-DGLPK_Library=#{Formula['glpk'].opt_lib}/libglpk.dylib"]
    end
    if build.with? "snappy"
      cmake_args += ["-DSnappy_Include_Dir=#{Formula['snappy'].opt_include}",
                     "-DSnappy_Libraries=#{Formula['snappy'].opt_lib}/libsnappy.dylib"]
    end

    cmake_args << onoff("-DJavaModular=",    (build.with? "java"))
    cmake_args << onoff("-DPythonModular=",  (build.with? :python))
    cmake_args << onoff("-DOctaveModular=",  (build.with? "octave"))
    cmake_args << onoff("-DRModular=",       (build.with? "r"))
    cmake_args << onoff("-DRubyModular=",    (build.with? "ruby"))
    cmake_args << onoff("-DLuaModular=",     (build.with? "lua"))
    cmake_args << onoff("-DUSE_SVMLIGHT=",   (build.with? "svm-light"))
    cmake_args << onoff("-DENABLE_TESTING=", (build.with? "check"))

    cmake_args << "-DPYTHON_LIBRARY=#{%x(python-config --prefix).chomp}/lib/libpython2.7.dylib" if build.with? :python

    mkdir "build" do
      system "cmake", "..", *cmake_args
      system "make"
      system "make", "install"
      system "ctest", "-R", "unit" if build.with? "check"
    end
  end
end

__END__
diff --git a/src/shogun/evaluation/ContingencyTableEvaluation.cpp b/src/shogun/evaluation/ContingencyTableEvaluation.cpp
index 6a40d8f..e478112 100644
--- a/src/shogun/evaluation/ContingencyTableEvaluation.cpp
+++ b/src/shogun/evaluation/ContingencyTableEvaluation.cpp
@@ -52,7 +52,7 @@ float64_t CContingencyTableEvaluation::evaluate(CLabels* predicted, CLabels* gro
  return 42;
 }
 
-inline EEvaluationDirection CContingencyTableEvaluation::get_evaluation_direction() const
+EEvaluationDirection CContingencyTableEvaluation::get_evaluation_direction() const
 {
  switch (m_type)
  {