[Neuroimaging] nibabel / pkg_resources /setuptools question

[Satrajit Ghosh]

hi karl,

if you are using conda through miniconda/anaconda, you may consider adding
conda-forge channels.

conda config --add channels conda-forge

conda install nibabel # or nipype or dipy

or any one of these packages: https://conda-forge.github.io/feedstocks.html

it is a community supported package repository for conda.

i agree with matthew that it would be good not to mix apt-get and anaconda.

cheers,

satra

On Fri, Jul 29, 2016 at 12:37 PM, Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> On Fri, Jul 29, 2016 at 5:24 PM, Karl Helmer <helmer at nmr.mgh.harvard.edu>
> wrote:
> > Hi Everyone,
> >
> >    I've just started to get the error message below when I "import
> > nibabel" in a piece of code. I've just updated my anaconda, but was
> > getting the error before then, and also used apt-get to get the latest
> > python-nipype (that apt-get has anyway). I'm using Lubuntu:
> > DISTRIB_DESCRIPTION="Ubuntu 14.04.4 LTS"
> > and this is what it installed:
> > "Preparing to unpack .../python-nibabel_2.0.2-1~nd14.04+1_all.deb ...
> > Unpacking python-nibabel (2.0.2-1~nd14.04+1) ..."
> > ...
> > Setting up python-nibabel (2.0.2-1~nd14.04+1) ...
> >
> > It looks like it's not nibabel it's unhappy with, it's the setuptools
> > version or maybe the interaction between the two?  Has anyone seen this
> > and have a fix?
> >
> > thanks,
> > Karl
> > ---------------------------------------------------------
> >
> > Traceback (most recent call last):
> >   File "edited_histograms.py", line 24, in <module>
> >     import nibabel as nib
> >   File
> > "/home/karl/anaconda/lib/python2.7/site-packages/nibabel/__init__.py",
> > line 45, in <module>
> >     from .loadsave import load, save
> >   File
> > "/home/karl/anaconda/lib/python2.7/site-packages/nibabel/loadsave.py",
> > line 21, in <module>
> >     from .minc2 import Minc2Image
> >   File
> "/home/karl/anaconda/lib/python2.7/site-packages/nibabel/minc2.py",
> > line 30, in <module>
> >     from .optpkg import optional_package
> >   File
> > "/home/karl/anaconda/lib/python2.7/site-packages/nibabel/optpkg.py",
> > line 4, in <module>
> >     import nose
> >   File
> "/home/karl/anaconda/lib/python2.7/site-packages/nose/__init__.py",
> > line 1, in <module>
> >     from nose.core import collector, main, run, run_exit, runmodule
> >   File "/home/karl/anaconda/lib/python2.7/site-packages/nose/core.py",
> > line 11, in <module>
> >     from nose.config import Config, all_config_files
> >   File "/home/karl/anaconda/lib/python2.7/site-packages/nose/config.py",
> > line 9, in <module>
> >     from nose.plugins.manager import NoPlugins
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/nose/plugins/__init__.py",
> > line 185, in <module>
> >     from nose.plugins.manager import *
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/nose/plugins/manager.py",
> > line 418, in <module>
> >     import pkg_resources
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/pkg_resources.py",
> > line 2729, in <module>
> >     add_activation_listener(lambda dist: dist.activate())
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/pkg_resources.py",
> > line 700, in subscribe
> >     callback(dist)
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/pkg_resources.py",
> > line 2729, in <lambda>
> >     add_activation_listener(lambda dist: dist.activate())
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/pkg_resources.py",
> > line 2229, in activate
> >     self.insert_on(path)
> >   File
> >
> "/home/karl/anaconda/lib/python2.7/site-packages/distribute-0.6.17-py2.7.egg/pkg_resources.py",
> > line 2330, in insert_on
> >     "with distribute. Found one at %s" % str(self.location))
> > ValueError: A 0.7-series setuptools cannot be installed with distribute.
> > Found one at
> >
> /home/karl/anaconda/lib/python2.7/site-packages/setuptools-20.7.0-py2.7.egg
>
> That's a frightening mix of apt-get, neurodebian and anaconda!
>
> Have you also been using easy_install by any chance?  I see that your
> setuptools and distribute packages are in .egg directories.
>
> If it were me, I would start by clearing out the easy_install
> installs, as these can make a real mess of your imports - does
> https://matthew-brett.github.io/pydagogue/un_easy_install.html help?
> (you need to look in your anaconda directory rather than the system
> directories, I suspect).
>
> Do you need anaconda for anything specific, not covered by
> neurodebian?  I suspect your life would be simpler if you could use
> either `apt-get` or `conda` and not both.
>
> Cheers,
>
> Matthew
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/neuroimaging/attachments/20160729/f615280f/attachment.html>