[SciPy-User] Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

[Virgil Stokes]

On 23-Jul-2012 08:50, Scott Sinclair wrote:
> On 22 July 2012 11:20, Virgil Stokes <vs at it.uu.se> wrote:
>> On 22-Jul-2012 09:14, Scott Sinclair wrote:
>>
>> On Jul 21, 2012 1:19 PM, "Virgil Stokes" <vs at it.uu.se> wrote:
>>> I installed SciPy 0.11.0rc1 on an Ubuntu 12.04 (64-bit) platform with what
>>> seemed to be no problems.
>>> However, when I ran Spyder it still was using SciPy 0.10.1. I then tried
>>> to
>>> uninstall SciPy completely using
>>>
>>>    >pip uninstall SciPy
>>>
>>> which again seemed to be ok. But, now I was unable to execute Spyder! I
>>> tried
>>> several times to uninstall and reinstall Spyder but I am stuck with no
>>> possibility to run Spyder. I get no error; but, clicking in this
>>> application in
>>> Ubuntu 12.04 seems to be ignored.
>> I tried some more things; but, first here is what I get when I try to run
>> Spyder from a command line:
>>
>> root at virgil-laptop:/usr/local/bin# spyder
>> Traceback (most recent call last):
>>    File "/usr/local/bin/spyder", line 2, in <module>
>>      from spyderlib import spyder
>>    File "/usr/local/lib/python2.7/dist-packages/spyderlib/spyder.py", line
>> 91, in <module>
>>      from spyderlib.utils.environ import WinUserEnvDialog
>>    File "/usr/local/lib/python2.7/dist-packages/spyderlib/utils/environ.py",
>> line 17, in <module>
>>      from spyderlib.widgets.dicteditor import DictEditor
>>    File
>> "/usr/local/lib/python2.7/dist-packages/spyderlib/widgets/dicteditor.py",
>> line 31, in <module>
>>      from spyderlib.config import get_icon, get_font
>>    File "/usr/local/lib/python2.7/dist-packages/spyderlib/config.py", line
>> 27, in <module>
>>      from spyderlib.utils import iofuncs, codeanalysis
>>    File "/usr/local/lib/python2.7/dist-packages/spyderlib/utils/iofuncs.py",
>> line 33, in <module>
>>      import scipy.io as spio
>>    File "/usr/local/lib/python2.7/dist-packages/scipy/io/__init__.py", line
>> 83, in <module>
>>      from matlab import loadmat, savemat, byteordercodes
>>    File "/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/__init__.py",
>> line 11, in <module>
>>      from mio import loadmat, savemat
>>    File "/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio.py", line
>> 15, in <module>
>>      from mio4 import MatFile4Reader, MatFile4Writer
>>    File "/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py",
>> line 9, in <module>
>>      import scipy.sparse/usr/local/lib/python2.7/dist-packages/scipy
>>    File "/usr/local/lib/python2.7/dist-packages/scipy/sparse/__init__.py",
>> line 182, in <module>
>>      from csgraph import *
>> AttributeError: 'module' object has no attribute 'csgraph_to_masked'
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> It's not a good idea to be running as root. The recommended practice
> is to run terminal sessions as your regular user and use `sudo` if you
> need temporary privileges to access system directories etc.
>
> It looks like your scipy install in
> /usr/local/lib/python2.7/dist-packages/scipy/ was broken when you
> tried to install the release candidate. The minimum you'll need to do
> is remove the broken scipy install and reinstall it. I suggest the
> following (as your regular user):
>
> # Remove broken scipy install
> virgil at virgil-laptop:~$ sudo rm -rf
> /usr/local/lib/python2.7/dist-packages/scipy/
> virgil at virgil-laptop:~$ sudo rm -rf
> /usr/local/lib/python2.7/dist-packages/scipy-*.egg*
>
> # Do a fresh install
> # Either
> virgil at virgil-laptop:~$ sudo pip install scipy
> # or avoid mucking in your system directories
> virgil at virgil-laptop:~$ pip install --user scipy
>
> # Install python-nose using your package manager or do
> virgil at virgil-laptop:~$ pip install --user nose
>
> # and test your scipy
> virgil at virgil-laptop:~$ python -c "import scipy; scipy.test()"
>
> If you're lucky the scipy test suite will complete without any errors
> and Spyder will work at this point. If you still have problems with
> scipy let us know, if your spyder install doesn't work you'll need to
> trouble-shoot it over on the spyder list
> (https://groups.google.com/forum/?fromgroups#!forum/spyderlib).
>
> Good luck!
>
> Cheers,
> Scott
> _______________________________________________
> SciPy-User mailing list
> SciPy-User at scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user
Ok Scott,
Your instructions were good --- I now have Spyder working with scipy 0.10.1. 
However, when I ran the scipy.test(), I received the following final outputs:

  Ran 5103 tests in in 47.160s

  OK (KNOWNFAIL=13, SKIP=24)

Is the the expected results for a working scipy 0.10.1?

Thanks very much for your help Scott,
Have a good day!