[Biopython-dev] Fwd: [Biopython - Bug #3187] pip install biopython

[Peter Cock]

Hi Brad (et al),

It looks like automatic emails from Redmine to the biopython-dev list
are not working properly... anyway, could you take a look at Bug 3187?

https://redmine.open-bio.org/issues/3187

I suspect this is related to PIP issue 8, i.e. PIP doesn't like our
setup.py file.

https://github.com/pypa/pip/issues/8

Thanks,

Peter


---------- Forwarded message ----------
From:  <redmine at redmine.open-bio.org>
Date: Mon, Mar 28, 2011 at 1:35 PM
Subject: [Biopython - Bug #3187] pip install biopython
To: casbon at gmail.com
Cc: p.j.a.cock at googlemail.com


Issue #3187 has been updated by James Casbon.

File pip.log added

It's pretty much the same as the output I posted, but I have attached.

________________________________

Bug #3187: pip install biopython

Author: James Casbon
Status: New
Priority: Normal
Assignee:
Category: Main Distribution
Target version:
URL:

james at flapjack:/tmp$ virtualenv bp-pip
New python executable in bp-pip/bin/python
Installing setuptools............done.
james at flapjack:/tmp$ source /tmp/bp-pip/bin/activate
(bp-pip)james at flapjack:/tmp$ pip install biopython
Downloading/unpacking biopython
  Downloading biopython-1.56.tar.gz (6.9Mb): 6.9Mb downloaded
  Running setup.py egg_info for package biopython

    warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
    warning: no previously-included files found matching 'Tests/Graphics/*.eps'
    warning: no previously-included files found matching 'Tests/Graphics/*.svg'
    warning: no previously-included files found matching 'Tests/Graphics/*.png'
    warning: no previously-included files matching '*' found under
directory 'Tests/UnitTests'
    warning: no previously-included files matching '.cvsignore' found
under directory '*'
    warning: no previously-included files matching '.gitignore' found
under directory '*'
    warning: no previously-included files matching '*.pyc' found under
directory '*'
Installing collected packages: biopython
  Running setup.py install for biopython
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
       or: -c --help [cmd1 cmd2 ...]
       or: -c --help-commands
       or: -c cmd --help

    error: option --single-version-externally-managed not recognized
    Complete output from command /private/tmp/bp-pip/bin/python -c
"import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7:
    usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]

   or: -c --help [cmd1 cmd2 ...]

   or: -c --help-commands

   or: -c cmd --help

error: option --single-version-externally-managed not recognized

----------------------------------------
Command /private/tmp/bp-pip/bin/python -c "import setuptools;
__file__='/private/tmp/bp-pip/build/biopython/setup.py';
execfile('/private/tmp/bp-pip/build/biopython/setup.py')" install
--single-version-externally-managed --record
/var/folders/Gn/GneSaDeKGaGpZXx+hcopdU+++TI/-Tmp-/pip-slq1Hy-record/install-record.txt
--install-headers /private/tmp/bp-pip/bin/../include/site/python2.7
failed with error code 1
Storing complete log in /Users/james/.pip/pip.log

________________________________

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