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Can't run nosetest #3711

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jeffreyrosenbluth opened this issue May 30, 2013 · 39 comments

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@jeffreyrosenbluth
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commented May 30, 2013

Trying to contribute but get the following error when trying to run nosetests with "nosetests pandas". I get the same error on both OSX 10.8.3 and Linux Ubuntu:

ERROR: Failure: ImportError (No module named dateutil.parser)

Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 390, in loadTestsFromName
addr.filename, addr.module)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 39, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 86, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/reedrosenbluth/pandas/pandas/init.py", line 6, in
from . import hashtable, tslib, lib
File "tslib.pyx", line 31, in init pandas.tslib (pandas/tslib.c:48137)
ImportError: No module named dateutil.parser


Ran 1 test in 0.001s

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commented May 30, 2013

do you have dateutil installed? anytime you see ImportError it means that the Python interpreter cannot find the module it's been asked to import. most of the time that means you don't have it installed or it cannot be found in sys.path, although on occasion an ImportError might be thrown when there's a syntax error leading to very annoying bugs. in this case it's probably the former.

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commented May 30, 2013

Yes, It seems like the problem has to do with hashtable

ERROR: Failure: ImportError (cannot import name hashtable)

Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/nose/loader.py", line 413, in
loadTestsFromName
addr.filename, addr.module)
File "/Library/Python/2.7/site-packages/nose/importer.py", line 47, in
importFromPath
return self.importFromDir(dir_path, fqname)
File "/Library/Python/2.7/site-packages/nose/importer.py", line 94, in
importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/Users/jeffreyrosenbluth/pandas/pandas/init.py", line 6, in

from . import hashtable, tslib, lib
ImportError: cannot import name hashtable


Ran 1 test in 0.003s

On Wed, May 29, 2013 at 8:12 PM, Phillip Cloud notifications@github.comwrote:

do you have dateutil installed?


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commented May 30, 2013

oh that traceback is brutal. try to make sure you 1) put in monospaced font (you can still type github flavored markdown from email) and 2) separate it from prose. i only get hashtable import errors when i'm ignoring the linters and i've edited some code and made a syntax error. obligatory question: what version are you running?

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commented May 30, 2013

The thing is, I'm getting this error without even making any changes to the
code???

On Wed, May 29, 2013 at 8:39 PM, Phillip Cloud notifications@github.comwrote:

oh that traceback is brutal. try to make sure you 1) put in monospaced
font and 2) separate it from prose. i only get hashtable import errors when
i'm ignoring the linters and i've edited some code and made a syntax error


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commented May 30, 2013

on linux, did you build?

python setup.py build_ext --inplace

where you cloned it?

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commented May 30, 2013

yes

On Wed, May 29, 2013 at 8:50 PM, jreback notifications@github.com wrote:

on linux, did you build?

python setup.py build_ext --inplace

where you cloned it?


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commented May 30, 2013

python
import pandas

do anything?

(if that works), then the following should too

make sure you are in the same dir that you built in, call it pandas

nosetests pandas/tests_test_frame.py

do anything?

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commented May 30, 2013

should be pandas/tests/test_frame.py

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commented May 30, 2013

oh! i think i know what it is: i get this error when i blindly use the command line history to (re)install pandas after a merge/rebase/change and i end up doing python setup.py install after i've already done python setup.py develop or vice versa. i don't know what the fix is here so i just uninstall pandas and reinstall and that fixes

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commented May 30, 2013

@jeffreyrosenbluth u might want to do something like

pip uninstall --yes pandas
while [ $? -eq 0 ]; do
    pip uninstall --yes pandas
done

to remove all the versions of pandas that you have installed. you probably shouldn't use this if you aren't in a virtualenv

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commented May 30, 2013

Python 2.7.3 (v2.7.3:70274d53c1dd, Apr 9 2012, 20:52:43)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

import pandas
cannot import name hashtable
Traceback (most recent call last):
File "", line 1, in
File "pandas/init.py", line 6, in
from . import hashtable, tslib, lib
ImportError: cannot import name hashtable

On Wed, May 29, 2013 at 8:56 PM, jreback notifications@github.com wrote:

python
import pandas

do anything?

(if that works), then the following should too

make sure you are in the same dir that you built in, call it pandas

nosetests pandas/tests_test_frame.py

do anything?


Reply to this email directly or view it on GitHubhttps://github.com//issues/3711#issuecomment-18655681
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commented May 30, 2013

Is hashtable built? Do

find . -name '*hashtable*'

in the pandas directory and look for files with the so extension.

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commented May 30, 2013

yes it's there and buitl

On Thu, May 30, 2013 at 9:33 AM, Phillip Cloud notifications@github.comwrote:

Is hashtable built? Do

find . -name 'hashtable'

in the pandas directory and look for files with the so extension.


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commented May 30, 2013

and you're sure you only have one version of pandas installed?

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commented May 30, 2013

I have a production build installed, but in the directory I'm working I am
trying to build from the source via: python setup.py build_ext --inplace. I
get lots of warnings about deprecated API in numpy 1.7.

On Thu, May 30, 2013 at 10:49 AM, Phillip Cloud notifications@github.comwrote:

and you're sure you only have one version of pandas installed?


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commented May 30, 2013

the numpy warnings aren't a big deal. can u uninstall your production build and/or setup a virtualenv with no site packages allowed? that way you can isolate the issue more easily

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commented May 30, 2013

Sure, I'll set up a virtualenv and give it a go.
thanks, i'll let you know what happens

On Thu, May 30, 2013 at 10:58 AM, Phillip Cloud notifications@github.comwrote:

the numpy warnings aren't a big deal. can u uninstall your production
build and/or setup a virtualenv with no site packages allowed? that way you
can isolate the issue more easily


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commented Jun 4, 2013

Any progress here?

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commented Jun 4, 2013

Sorry, I haven't had a chance to try the virualenv idea yet, I've been
swamped on another project. Hopefully, I'll get to it in a day or two.

j.

On Tue, Jun 4, 2013 at 11:25 AM, Phillip Cloud notifications@github.comwrote:

Any progress here?


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commented Jun 7, 2013

Finally got a chance to try again under a virtual env and had same problem.
Here is what I'm doing.

  1. I create a virtualenv.
  2. In the virtualenv I pip install Cython and numpy.
  3. Then I try: python setup.py build_ext --inplace
  4. Finally I enter: nosetests pandas and I get back:
======================================================================
ERROR: Failure: ValueError (numpy.dtype has the wrong size, try recompiling)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/nose/loader.py", line 413, in
loadTestsFromName
    addr.filename, addr.module)
  File "/Library/Python/2.7/site-packages/nose/importer.py", line 47, in
importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Library/Python/2.7/site-packages/nose/importer.py", line 94, in
importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/jeffreyrosenbluth/pandas_env/pandas/pandas/__init__.py",
line 6, in <module>
    from . import hashtable, tslib, lib
  File "numpy.pxd", line 157, in init pandas.hashtable
(pandas/hashtable.c:19547)
ValueError: numpy.dtype has the wrong size, try recompiling

----------------------------------------------------------------------
Ran 1 test in 0.001s

FAILED (errors=1)
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commented Jun 7, 2013

you have another version numpy installed somewhere (that's why you're getting the dtype size error). looks like ur on a mac, but i can reproduce this on an ubuntu machine if i do

mkvirtualenv pandas
sudo apt-get build-dep scipy
workon pandas
pip install cython
pip install numpy
git clone git://github.com/pydata/pandas.git
cd pandas
python setup.py build_ext --inplace
nosetests pandas

since it will find the numpy that was installed by ubuntu. The fix here is to add --no-site-packages when you create your virtualenv.

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commented Jun 7, 2013

so if ur using virtualenvwrapper as i show above do mkvirtualenv --no-site-packages pandas

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commented Jun 8, 2013

I started from scratch and tried again as you recommended with
mkvirtualenv --no-site-packages pandas.
Then I workon pandas, create a pandas directory and git clone pandas.
I need to pip install numpy an cython or python setup.py --build_ext
pandas won't run. I still get the same numpy.dtype has wrong size
error. I'd really like to contribute, to pandas but I don't know what
else to try.

On Fri, Jun 7, 2013 at 12:21 PM, Phillip Cloud notifications@github.com wrote:

so if ur using virtualenvwrapper as i show above do mkvirtualenv
--no-site-packages pandas


Reply to this email directly or view it on GitHub.

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commented Jun 8, 2013

By the way, I tried the same procedure on my ubuntu setup and I get
the same exact error???

On Fri, Jun 7, 2013 at 10:40 PM, Jeffrey Rosenbluth
jeffrey.rosenbluth@gmail.com wrote:

I started from scratch and tried again as you recommended with
mkvirtualenv --no-site-packages pandas.
Then I workon pandas, create a pandas directory and git clone pandas.
I need to pip install numpy an cython or python setup.py --build_ext
pandas won't run. I still get the same numpy.dtype has wrong size
error. I'd really like to contribute, to pandas but I don't know what
else to try.

On Fri, Jun 7, 2013 at 12:21 PM, Phillip Cloud notifications@github.com wrote:

so if ur using virtualenvwrapper as i show above do mkvirtualenv
--no-site-packages pandas


Reply to this email directly or view it on GitHub.

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commented Jun 8, 2013

ok. i'm going to try the following on an ubuntu 64-bit precise (12.04 i think)

# install the build dependencies
mkvirtualenv pandas
workon pandas
pip install cython
pip install numpy
pip install python-dateutil
pip install pytz
git clone git://github.com/pydata/pandas.git
cd pandas
python setup.py build_ext --inplace
nosetests pandas
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commented Jun 8, 2013

@jeffreyrosenbluth i can repro your very first error (the one at the top) if i forget to install python-dateutil. as for the numpy dtype error there must be another numpy or cython somewhere that hasn't been compiled with the same compiler as you're trying to use for pandas, e.g., a binary package installed from homebrew/apt-get/macports. make sure you've also installed pytz or else you'll get a bunch of test errors/failures

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commented Jun 8, 2013

I don't see how thats possible if i'm installing numpy fresh in the virtual
env?

On Sat, Jun 8, 2013 at 12:42 AM, Phillip Cloud notifications@github.comwrote:

@jeffreyrosenbluth https://github.com/jeffreyrosenbluth i can repro
your very first error (the one at the top) if i forget to install
python-dateutil. as for the numpy dtype error there must be another
numpy or cython somewhere that hasn't been compiled with the same compiler
as you're trying to use for pandas, e.g., a binary package installed from
homebrew/apt-get/macports. make sure you've also installed pytz or else
you'll get a bunch of test errors/failures


Reply to this email directly or view it on GitHubhttps://github.com//issues/3711#issuecomment-19142987
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commented Jun 8, 2013

did u try the above? i don't actually have a separate machine sitting around with ubuntu i actually use something called vagrant which let's you set virtualbox or vmware bare systems (thanks @jreback). i use it mostly for testing. in this case it might be useful to see if you can get it running on that machine...i can walk you through setting one up if you want...

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commented Jun 8, 2013

thanks, I have to go out for a few hours. If you around when we get back we
can give it a shot.

On Sat, Jun 8, 2013 at 9:16 AM, Phillip Cloud notifications@github.comwrote:

did u try the above? i don't actually have a separate machine sitting
around with ubuntu i actually use something called vagranthttp://www.vagrantup.comwhich let's you set virtualbox or vmware bare systems (thanks
@jreback https://github.com/jreback). i use it mostly for testing. in
this case it might be useful to see if you can get it running on that
machine...i can walk you through setting one up if you want...


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commented Jul 10, 2013

resolved?

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commented Jul 10, 2013

i'm not sure what else to try here....

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commented Jul 10, 2013

No, I was never able to get it to work.
I have tried it on both osx and linux with not luck.
I must be doing something wrong.

On Wed, Jul 10, 2013 at 9:23 AM, jreback notifications@github.com wrote:

resolved?


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commented Jul 10, 2013

there must be another version of numpy somewhere. there's no way that i know of to get those dtype/multiarray import errors.

when you do locate numpy (assuming you haven't installed a virtualenv) what comes out?

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commented Jul 10, 2013

/src/scipy/scipy/io/matlab/numpy_rephrasing.h
/src/scipy/scipy/sparse/sparsetools/numpy.i
/src/scipy/scipy/weave/numpy_scalar_spec.py
/src/scipy/scipy/weave/tests/test_numpy_scalar_spec.py

On Wed, Jul 10, 2013 at 9:46 AM, Phillip Cloud notifications@github.comwrote:

there must be another version of numpy somewhere. there's no way that i
know of to get those dtype/multiarray import errors.

when you do locate numpy (assuming you haven't installed a virtualenv)
what comes out?


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commented Jul 10, 2013

actually i'm mistaken is all over, see attached

On Wed, Jul 10, 2013 at 9:46 AM, Phillip Cloud notifications@github.comwrote:

there must be another version of numpy somewhere. there's no way that i
know of to get those dtype/multiarray import errors.

when you do locate numpy (assuming you haven't installed a virtualenv)
what comes out?


Reply to this email directly or view it on GitHubhttps://github.com//issues/3711#issuecomment-20742882
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/Applications/PyCharm.app/plugins/pycharm-numpy
/Applications/PyCharm.app/plugins/pycharm-numpy/lib
/Applications/PyCharm.app/plugins/pycharm-numpy/lib/pycharm-numpy.jar
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/multiarray_api.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/__ufunc_api.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/arrayobject.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/arrayscalars.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/multiarray_api.txt
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/noprefix.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/npy_interrupt.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/numpyconfig.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/old_defines.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/oldnumeric.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/ufunc_api.txt
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/core/include/numpy/ufuncobject.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils
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/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/tests/f2py_f90_ext/include
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/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/tests/swig_ext/src
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/distutils/tests/swig_ext/src/zoo.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/f2py
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/f2py/src
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/f2py/src/fortranobject.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/numarray
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/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/numarray/numpy/arraybase.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.5/Extras/lib/python/numpy/numarray/numpy/cfunc.h
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commented Jul 10, 2013

i think therein lies the issue, leave what you must but see if you can get rid of some of the extra numpy installs .e.g, don't unintsll the version that comes with the devtools probably

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commented Jul 20, 2013

@jeffreyrosenbluth have you gotten to the bottom of this?

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commented Jul 22, 2013

haven't had a chance to root out stray numpy instances.
I should have some time this week.
I want to see how many instance i have on my linux machine, it might be
easier to clean up.

thanks for staying on top of it.
jeff

On Sat, Jul 20, 2013 at 7:44 PM, Phillip Cloud notifications@github.comwrote:

@jeffreyrosenbluth https://github.com/jeffreyrosenbluth have you gotten
to the bottom of this?


Reply to this email directly or view it on GitHubhttps://github.com//issues/3711#issuecomment-21302452
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commented Sep 5, 2013

I hit this error also, not really sure the cause, however, I was able to resolve by develop install of pandas repo. Never did seem to resolve via pip uninstall. If I find out more, I'll make sure and post here!

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