Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

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Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Virgil Stokes
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.

Any suggestions as to how to recover Spyder and how to get SciPy running again
would be appreciated.


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Re: Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Scott Sinclair-4

On Jul 21, 2012 1:19 PM, "Virgil Stokes" <[hidden email]> 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.
>
> Any suggestions as to how to recover Spyder and how to get SciPy running again
> would be appreciated.

I don't know about Spyder (I don't use it and you haven't given much information about how you tried to un/reinstall it). I suspect it was via the package manager?

Did you run pip uninstall with sudo?

What happens when you run:

python -c "import scipy; print scipy.__version__; print scipy"

at the command line?

If you get an import error for scipy try reinstalling python-scipy from the package manager.

Cheers,
Scott


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Re: Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Virgil Stokes
On 22-Jul-2012 09:14, Scott Sinclair wrote:

On Jul 21, 2012 1:19 PM, "Virgil Stokes" <[hidden email]> 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.
>
> Any suggestions as to how to recover Spyder and how to get SciPy running again
> would be appreciated.

I don't know about Spyder (I don't use it and you haven't given much information about how you tried to un/reinstall it). I suspect it was via the package manager?

Yes, the first time that I installed it was via the package manager, and it worked as expected.

Did you run pip uninstall with sudo?

I tried both with pip and via the package manager. When this didn't work I also removed all references to Spyder.

What happens when you run:

python -c "import scipy; print scipy.__version__; print scipy"

at the command line?

root@virgil-laptop:/home/virgil# python -c "import scipy;print scipy.__version__;print scipy"
0.10.1
<module 'scipy' from '/usr/local/lib/python2.7/dist-packages/scipy/__init__.pyc'>

If you get an import error for scipy try reinstalling python-scipy from the package manager.

Cheers,
Scott

Ok thanks Scott for your assistance with this problem.

Note, I have tried several different methods to uninstall/install Spyder (e.g. package manager and pip) but I still never get the Spyder splash window :-(

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Re: Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Virgil Stokes
In reply to this post by Scott Sinclair-4
On 22-Jul-2012 09:14, Scott Sinclair wrote:

On Jul 21, 2012 1:19 PM, "Virgil Stokes" <[hidden email]> 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.
>
> Any suggestions as to how to recover Spyder and how to get SciPy running again
> would be appreciated.

I don't know about Spyder (I don't use it and you haven't given much information about how you tried to un/reinstall it). I suspect it was via the package manager?

Did you run pip uninstall with sudo?

What happens when you run:

python -c "import scipy; print scipy.__version__; print scipy"

at the command line?

If you get an import error for scipy try reinstalling python-scipy from the package manager.

Cheers,
Scott



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Ok Scott,
I tried some more things; but, first here is what I get when I try to run Spyder from a command line:

root@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
  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'
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

I installed scipy-0.10.1 and then tried to run Spyder --- the following crash report was generated:

The crashed program seems to use third-party or local libraries:

/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_coo.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csc.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/_shortest_path.so
/usr/local/lib/python2.7/dist-packages/numpy/linalg/lapack_lite.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/_tools.so
/usr/local/lib/python2.7/dist-packages/numpy/random/mtrand.so
/usr/local/lib/python2.7/dist-packages/numpy/core/scalarmath.so
/usr/local/lib/python2.7/dist-packages/numpy/core/multiarray.so
/usr/local/lib/python2.7/dist-packages/numpy/lib/_compiled_base.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/_min_spanning_tree.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_bsr.so
/usr/local/lib/python2.7/dist-packages/numpy/core/_dotblas.so
/usr/local/lib/python2.7/dist-packages/numpy/core/umath.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csgraph.so
/usr/local/lib/python2.7/dist-packages/numpy/fft/fftpack_lite.so
/usr/local/lib/python2.7/dist-packages/numpy/core/_sort.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_csr.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/csgraph/_traversal.so
/usr/local/lib/python2.7/dist-packages/scipy/sparse/sparsetools/_dia.so

It is highly recommended to check if the problem persists without those first.

Do you want to continue the report process anyway?
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Interestingly, a search for csgraph in the file system gives nothing.

Do you have any suggestions as to how to fix Spyder-SciPy?





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Re: Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Scott Sinclair-4
On 22 July 2012 11:20, Virgil Stokes <[hidden email]> wrote:

> On 22-Jul-2012 09:14, Scott Sinclair wrote:
>
> On Jul 21, 2012 1:19 PM, "Virgil Stokes" <[hidden email]> 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@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@virgil-laptop:~$ sudo rm -rf
/usr/local/lib/python2.7/dist-packages/scipy/
virgil@virgil-laptop:~$ sudo rm -rf
/usr/local/lib/python2.7/dist-packages/scipy-*.egg*

# Do a fresh install
# Either
virgil@virgil-laptop:~$ sudo pip install scipy
# or avoid mucking in your system directories
virgil@virgil-laptop:~$ pip install --user scipy

# Install python-nose using your package manager or do
virgil@virgil-laptop:~$ pip install --user nose

# and test your scipy
virgil@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
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Re: 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 <[hidden email]> wrote:
>> On 22-Jul-2012 09:14, Scott Sinclair wrote:
>>
>> On Jul 21, 2012 1:19 PM, "Virgil Stokes" <[hidden email]> 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@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@virgil-laptop:~$ sudo rm -rf
> /usr/local/lib/python2.7/dist-packages/scipy/
> virgil@virgil-laptop:~$ sudo rm -rf
> /usr/local/lib/python2.7/dist-packages/scipy-*.egg*
>
> # Do a fresh install
> # Either
> virgil@virgil-laptop:~$ sudo pip install scipy
> # or avoid mucking in your system directories
> virgil@virgil-laptop:~$ pip install --user scipy
>
> # Install python-nose using your package manager or do
> virgil@virgil-laptop:~$ pip install --user nose
>
> # and test your scipy
> virgil@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
> [hidden email]
> 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!
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Re: Spyder-Ubuntu 12.04 problem with SciPy 0.11.0rc1

Scott Sinclair-4
On 23 July 2012 09:57, Virgil Stokes <[hidden email]> wrote:
> Your instructions were good --- I now have Spyder working with scipy 0.10.1.

Glad to hear that.

> 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?

Yes. The 'OK' informs you that the tests were completed successfully.
Don't worry about the KNOWNFAILS.

Cheers,
Scott
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