[Biopython-dev] setuptools breaking biopython-1.62b installation

Michiel de Hoon mjldehoon at yahoo.com
Wed Jul 24 07:31:08 UTC 2013

Dear all,

When trying to install Biopython on a new MacBook, I get the following error message when I run "python setup.py build":

tkx330:biopython-1.62b mdehoon$ python setup.py build
Traceback (most recent call last):
  File "setup.py", line 109, in <module>
    from setuptools import setup, Command
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.45-py2.7.egg/setuptools/__init__.py", line 2, in <module>
    from setuptools.extension import Extension, Library
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.45-py2.7.egg/pkg_resources.py", line 1211, in get_metadata
    return self._get(self._fn(self.egg_info,name))
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.45-py2.7.egg/pkg_resources.py", line 1326, in _get
    stream = open(path, 'rb')
IOError: [Errno 13] Permission denied: '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/python_dateutil-2.1-py2.7.egg/EGG-INFO/top_level.txt'

This looks like a simple problem with file permissions, and I hope can be solved easily.
Still, it is quite discouraging to first-time users of Biopython.
Do we actually need setuptools?
Looking at setup.py, it seems that distutils is sufficient for our needs.
If so, let's remove the dependency on setuptools.


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