[Neuroimaging] nibabel / pkg_resources /setuptools question

[Karl Helmer]

Thanks for the suggestion Matthew.  I cleaned out all of the .egg packages
and reinstalled from pip.  Once I did that for setuptools, all was well
again.

regards,
Karl



> 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
>
>
>


-- 
Karl Helmer, PhD
Athinoula A Martinos Center
for Biomedical Imaging
Massachusetts General Hospital
149 - 13th St Room 2301
Charlestown, MA 02129
(p) 617.726.8636
(f) 617.726.7422
helmer at nmr.mgh.harvard.edu





The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.