<commit_before>require 'formula'

class Cufflinks < Formula
  url 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.3.0.tar.gz'
  homepage 'http://cufflinks.cbcb.umd.edu/'
  sha1 'fa93a7a33f0649793ec1d185cb7043fd0dc2018b'

  depends_on 'boost'
  depends_on 'samtools'

  fails_with :clang do
    build 421
  end

  def install
    ENV.deparallelize
    system "./configure", "--disable-debug", "--disable-dependency-tracking",
                          "--prefix=#{prefix}"
    system "make install"
  end
end<commit_msg>cufflinks 2.0.2<commit_after>require 'formula'

class Cufflinks < Formula
  homepage 'http://cufflinks.cbcb.umd.edu/'
  url 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.0.2.tar.gz'
  sha1 '91954b4945c49ca133b39bffadf51bdf9ec2ff26'

  depends_on 'boost'    => :build
  depends_on 'samtools' => :build
  depends_on 'eigen'    => :build

  fails_with :clang do
    build 421
  end

  def install
    ENV['EIGEN_CPPFLAGS'] = '-I'+Formula.factory('eigen').include/'eigen3'
    ENV.append 'LDFLAGS', '-lboost_system-mt'
    cd 'src' do
      # Fixes 120 files redefining `foreach` that break building with boost
      # See http://seqanswers.com/forums/showthread.php?t=16637
      `for x in *.cpp *.h; do sed 's/foreach/for_each/' $x > x; mv x $x; done`
      inreplace 'common.h', 'for_each.hpp', 'foreach.hpp'
    end
    system "./configure", "--disable-debug", "--disable-dependency-tracking",
                          "--prefix=#{prefix}",
                          "--mandir=#{man}"
    system 'make'
    ENV.j1
    system 'make install'
  end
end
{'fraction_non_alphanumeric': 0.14231499051233396, 'fraction_numerical': 0.04680581910183428, 'mean_word_length': 2.8120481927710843, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3567297', 'n_tokens_mistral': 624, 'n_tokens_neox': 574, 'n_words': 115}