Re: [Matplotlib-users] installed python-scipy causing errors with numpy

[Eric F. <ef...@ha...>]

On 02/18/2012 11:54 AM, Michael Rawlins wrote:
>
>
> ------------------------------------------------------------------------
> *From:* Eric Firing <ef...@ha...>
> *To:* Michael Rawlins <raw...@ya...>
> *Cc:* "mat...@li..."
> <mat...@li...>
> *Sent:* Saturday, February 18, 2012 3:57 PM
> *Subject:* Re: [Matplotlib-users] installed python-scipy causing errors
> with numpy
>
> On 02/18/2012 10:49 AM, Michael Rawlins wrote:
>  >
>  >
>  > ------------------------------------------------------------------------
>  > *From:* Eric Firing <ef...@ha... <mailto:ef...@ha...>>
>  > *To:* mat...@li...
> <mailto:mat...@li...>
>  > *Sent:* Saturday, February 18, 2012 12:26 PM
>  > *Subject:* Re: [Matplotlib-users] installed python-scipy causing errors
>  > with numpy
>  >
>  > On 02/18/2012 07:17 AM, Michael Rawlins wrote:
>  > >
>  > > A couple weeks ago I installed version 1.2 from sources, as described
>  > here:
>  > >
>  > > http://matplotlib.sourceforge.net/users/installing.html
>  > >
>  > > I'm running Ubuntu 10.04 LTS. Everything was working fine. Looks like
>  > > numpy version 1.3 in place. A few minutes ago I installed python-scipy
>  > > from the Ubuntu Synaptic package manager. Getting this any time I run a
>  > > program:
>  > >
>  > > >python colorbar_testing.py <http://colorbar_testing.py>
> <http://colorbar_testing.py>
>  > > Traceback (most recent call last):
>  > > File "colorbar_testing.py", line 5, in <module>
>  > > from matplotlib import pyplot, mpl
>  > > File "/usr/local/lib/python2.6/dist-packages/matplotlib/__init__.py",
>  > > line 173, in <module>
>  > > __version__numpy__, numpy.__version__))
>  > > ImportError: numpy 1.4 or later is required; you have 1.3.0
>  > >
>  > >
>  > > Version control with python, matplotlib, numpy, etc problematic when
>  > > compiled from source? Shall I reinstall everything again, including
>  > > python-scipy? What order? Thanks.
>  >
>  > You need to remove your numpy and scipy packages and install both of
>  > these from source (just use the most recent releases), and then rebuild
>  > matplotlib. Numpy has to be installed before building either scipy or
>  > mpl, but mpl and scipy are independent of each other so either can be
>  > built once a suitable numpy is there.
>  >
>  > Eric
>  >
>  >
>  >
>  > Thanks Eric. One things escapes me. Are scipy and python redundant?
>  > Should both be installed?
>  >
>  > I'd installed numpy and matplotlib from source. Working right now on
>  > locating and remove all traces of those programs before re-installing.
>  > Can python 2.6 that I installed through Synapic Package manager stay in
>  > place. Perhaps I should remove it too just to be sure everything works
>  > right?
>
> No! The python 2.6 package is perfectly fine. Try to remove that, and
> you are likely to hose your whole system. It sounds like your only
> problem was that you had the numpy package installed, and it was being
> found instead of the one installed from source.
>
> Eric
>
>
> I don't understand what you mean when you say "...you had the numpy
> package installed,.." Are you saying a version of numpy came along with
> scipy, and that was the one "being found"? Also, to run programs which

No, scipy builds on numpy but does not include it.


> need scipy.stats I'll have to again install scipy. When I did that using
> Synaptic it broke my system. In summary, I don't understand what caused

Installing the scipy package will pull in numpy as its dependency, so if 
you need a newer version of numpy, as you do for mpl, then you also need 
to remove any packages that depend on it and install them from source.

> the problem. Shall I install scipy from source?

Yes, after completely removing the numpy package and installing numpy 
from source.

>
> The version of numpy I installed last month from source is 1.61. I've
> just found a couple files:
>
> /usr/bin/numpy-1.6.1/doc/release/1.3.0-notes.rst

This looks wrong.  Did you untar the tarball in /usr/bin?  Don't.  Untar 
it in some non-system location, maybe a subdirectory of your home 
directory, and then

cd numpy
python setup.py build
sudo python setup.py install

which should install in /usr/local/lib/python2.6/dist-packages.  Same 
drill for scipy and matplotlib.

The idea is that synaptic packages get installed in the /usr tree, and 
anything you install from source gets installed in the /usr/local tree, 
so they don't get mixed up.


> /usr/lib/python2.6/dist-packages/numpy-1.3.0.egg-info.

Not good. This is from the ubuntu package.

>
> I'll assume those numbers 1.3.0 are not an issue.

I wouldn't assume that.  Things seem rather scrambled up.

Eric

>
> Mike
>