old_contents: import rpy2.robjects as robjects
  import os
  import subprocess
  import sys
  
  def main():
  #    cmd = 'python ../setup.py install'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'wget "http://dl.bintray.com/boostorg/release/1.64.0/source/boost_1_64_0.tar.bz2"'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'tar --bzip2 -xf boost_1_64_0.tar.bz2'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'cd boost_1_64_0'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = './bootstrap.sh'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = './b2 install'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'cd ..'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'sudo mv boost_1_64_0 /usr/local/'
  #    subprocess.call(cmd, shell=True)
  
      robjects.r('''install.packages( 'multicore_0.2.tar.gz' , repos=NULL , dependencies = TRUE)''')
      robjects.r('''install.packages( 'caTools')''')
      robjects.r('''install.packages( 'bitops')''')
      robjects.r('''install.packages( 'snow')''')
      robjects.r('''install.packages( 'snowfall')''')
      robjects.r('''source("https://bioconductor.org/biocLite.R")''')
      robjects.r('''biocLite("Rsamtools",suppressUpdata=TRUE)''')
      robjects.r('''install.packages( 'oppa/spp/spp_1.14.tar.gz' )''')
  #    robjects.r('''install.packages( 'spp.tar.gz' )''')
  
  
  
  if __name__ == '__main__':
      main()
  
new_contents: import rpy2.robjects as robjects
  import os
  import subprocess
  import sys
  
  def main():
  #    cmd = 'python ../setup.py install'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'wget "http://dl.bintray.com/boostorg/release/1.64.0/source/boost_1_64_0.tar.bz2"'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'tar --bzip2 -xf boost_1_64_0.tar.bz2'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'cd boost_1_64_0'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = './bootstrap.sh'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = './b2 install'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'cd ..'
  #    subprocess.call(cmd, shell=True)
  
  #    cmd = 'sudo mv boost_1_64_0 /usr/local/'
  #    subprocess.call(cmd, shell=True)
  
      robjects.r('''install.packages( 'multicore_0.2.tar.gz' , repos=NULL , dependencies = TRUE)''')
      robjects.r('''install.packages( 'caTools')''')
      robjects.r('''install.packages( 'bitops')''')
      robjects.r('''install.packages( 'snow')''')
      robjects.r('''install.packages( 'snowfall')''')
      robjects.r('''source("https://bioconductor.org/biocLite.R")''')
      robjects.r('''biocLite("Rsamtools",suppressUpdata=TRUE)''')
      robjects.r('''install.packages( 'oppa/spp/spp_1.14.tar.gz' )''')
  #    robjects.r('''install.packages( 'spp.tar.gz' )''')
  
  #    cmd = 'sudo apt-get install bamtools'
  #    subprocess.call(cmd, shell=True)
      
  #    cmd = 'sudo apt-get install samtools'
  #    subprocess.call(cmd, shell=True)
      
  
  if __name__ == '__main__':
      main()
  
subject: Update dependencies.py