<commit_before>class Nonpareil < Formula
  desc "Estimates coverage in metagenomic datasets."
  homepage "http://enve-omics.ce.gatech.edu/nonpareil"

  # doi "10.1093/bioinformatics/btt584"
  # tag "bioinformatics"
  url "https://github.com/lmrodriguezr/nonpareil/archive/v3.1.1.tar.gz"
  sha256 "a29fb3a8d81cce78b3d6bb9b135af1bad0af1a2263a0ca215fee71890a1f1f5d"
  head "https://github.com/lmrodriguezr/nonpareil.git"

  bottle do
    cellar :any_skip_relocation
    sha256 "79ba3db2b4c7a817bb3d91aeef1a47bc32d78c461d2ae49534474e486e686a43" => :high_sierra
    sha256 "9da40351040a7c1259539ac37fe1d509282f9932967d029aeae0905ca66f0734" => :sierra
    sha256 "cc8904e3f870bf130609f3e53f469f1c2fbd8407d64fe202134323a950cbaf2f" => :el_capitan
  end

  depends_on "r"
  depends_on :mpi => [:cxx, :optional]

  def install
    r_library = lib/"R"/r_major_minor
    r_library.mkpath
    inreplace "Makefile", "CMD INSTALL", "CMD INSTALL --library=#{r_library}"
    system "make", "nonpareil"<commit_msg>nonpareil: update 3.1.1 bottle for Linuxbrew.<commit_after>class Nonpareil < Formula
  desc "Estimates coverage in metagenomic datasets."
  homepage "http://enve-omics.ce.gatech.edu/nonpareil"

  # doi "10.1093/bioinformatics/btt584"
  # tag "bioinformatics"
  url "https://github.com/lmrodriguezr/nonpareil/archive/v3.1.1.tar.gz"
  sha256 "a29fb3a8d81cce78b3d6bb9b135af1bad0af1a2263a0ca215fee71890a1f1f5d"
  head "https://github.com/lmrodriguezr/nonpareil.git"

  bottle do
    cellar :any_skip_relocation
    sha256 "79ba3db2b4c7a817bb3d91aeef1a47bc32d78c461d2ae49534474e486e686a43" => :high_sierra
    sha256 "9da40351040a7c1259539ac37fe1d509282f9932967d029aeae0905ca66f0734" => :sierra
    sha256 "cc8904e3f870bf130609f3e53f469f1c2fbd8407d64fe202134323a950cbaf2f" => :el_capitan
    sha256 "7b6edc1db05e82532fbd20166d1d7236bb4e353ee75dae7cb70a8e9b6d8d5fc3" => :x86_64_linux
  end

  depends_on "r"
  depends_on :mpi => [:cxx, :optional]

  def install
    r_library = lib/"R"/r_major_minor
    r_library.mkpath
    inreplace "Makefile", "CMD INSTALL", "CMD INSTALL --library=#{r_library}"
    system "make", "nonpareil"
{'fraction_non_alphanumeric': 0.10051911278905144, 'fraction_numerical': 0.19395941481831053, 'mean_word_length': 5.443768996960486, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 12, 'https://': 4, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2583520', 'n_tokens_mistral': 1155, 'n_tokens_neox': 945, 'n_words': 119}