[Biopython-dev] [Biopython - Bug #3384] Installation fails with pip-3.2

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Fri Sep 14 08:46:08 UTC 2012

Issue #3384 has been updated by Peter Cock.

Does the standard install mechanism work on your machine? i.e.

python3.2 setup.py build
python3.2 setup.py test
sudo python3.2 setup.py install

If you want to investigate the pip error, there is a possible workaround developed by NumPy (who also use 2to3 in a similar way to us), see http://projects.scipy.org/numpy/ticket/1857

Bug #3384: Installation fails with pip-3.2

Author: Roy Crihfield
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 

Linux 3.5.3-1-ARCH x86_64 GNU/Linux
Python 3.2.3
Bio.__version__ == '1.60'

Installation fails with with pip 1.2:

$ sudo pip-3.2 install biopython


Converting build/py3.2/Doc/examples/fasta_dictionary.py

Converting build/py3.2/Doc/examples/nmr/simplepredict.py

Python 2to3 processing done.

running egg_info

error: error in 'egg_base' option: 'pip-egg-info' does not exist or is not a directory


Command python setup.py egg_info failed with error code 1 in /tmp/pip-build/biopython

Exception information:
Traceback (most recent call last):
  File "/usr/lib/python3.2/site-packages/pip-1.2-py3.2.egg/pip/basecommand.py", line 106, in main
    status = self.run(options, args)
  File "/usr/lib/python3.2/site-packages/pip-1.2-py3.2.egg/pip/commands/install.py", line 256, in run
    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
  File "/usr/lib/python3.2/site-packages/pip-1.2-py3.2.egg/pip/req.py", line 1042, in prepare_files
  File "/usr/lib/python3.2/site-packages/pip-1.2-py3.2.egg/pip/req.py", line 236, in run_egg_info
    command_desc='python setup.py egg_info')
  File "/usr/lib/python3.2/site-packages/pip-1.2-py3.2.egg/pip/util.py", line 612, in call_subprocess
    % (command_desc, proc.returncode, cwd))
pip.exceptions.InstallationError: Command python setup.py egg_info failed with error code 1 in /tmp/pip-build/biopython

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