On Mon, Dec 28, 2009 at 2:30 PM, Gökhan Sever <gokhansever@gmail.com> wrote:
On Mon, Dec 28, 2009 at 12:15 PM, Gökhan Sever <gokhansever@gmail.com>wrote:
On Mon, Dec 28, 2009 at 11:16 AM, Gökhan Sever <gokhansever@gmail.com>wrote:
On Mon, Dec 28, 2009 at 11:07 AM, Robert Kern <robert.kern@gmail.com>wrote:
On Mon, Dec 28, 2009 at 11:00, Gökhan Sever <gokhansever@gmail.com> wrote:
One interesting thing I have noticed while installing the numpy from the source is that numpy dependent libraries must be re-installed and this must be a clean re-install. For instance I can't import some matplotlib and scipy modules without making a fresh installation for these packages. My attempts result with a runtime error.
Please, please, always copy-and-paste the traceback when reporting an error. I know you aren't formally reporting a bug here, but it always helps.
Could someone clarify this point? Is this due to API change in the numpy core?
Cython/Pyrex code does a runtime check on the struct sizes of types. We have carefully added a member to the PyArrayDescr struct; i.e. it shouldn't cause any actual problems, but Cython does the check anyways. This affects a few modules in scipy, but shouldn't have affected anything in matplotlib. The traceback may help us identify the issue you are seeing.
It is too late for the tracebacks. I have already removed the problematic packages and did clean installs. However, next time I will be more careful while reporting such issues. If it helps, in both matplotlib (via ipython -pylab) and scipy.stats import cases the runtime errors was raised due to numpy.core.multiarray module import.
--
Robert Kern
"I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth." -- Umberto Eco _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
-- Gökhan
Here is another interesting point to consider. To reproduce the runtime error I mentioned previously I downgraded numpy (from the latest check-out installation) following these steps:
svn co http://svn.scipy.org/svn/numpy/branches/1.3.x/ numpy cd numpy python setup.py install Writing /usr/lib/python2.6/site-packages/numpy-1.3.1.dev8031-py2.6.egg-info
I[2]: import matplotlib.pyplot as plt Segmentation fault
I[3]: from scipy import stats Segmentation fault
I have installed matplotlib and scipy using the latest numpy dev version. A little later I will downgrade matplotlib and scipy to their previous stable versions, and compile them using numpy 1.3.x. Afterwards I will update numpy and test to see if I can re-produce the runtime error to provide the tracebacks. First let me know if any tracebacks needed for these segfaults or are these known failures?
================================================================================ Platform : Linux-2.6.29.6-217.2.3.fc11.i686.PAE-i686-with-fedora-11-Leonidas Python : ('CPython', 'tags/r26', '66714')
================================================================================
-- Gökhan
Since no one has replied, I tried to reproduce the runtime error but ended up with different errors. Read more for the details:
svn co http://svn.scipy.org/svn/scipy/tags/0.7.1/ scipy python setup.py install Writing /usr/lib/python2.6/site-packages/scipy-0.7.1-py2.6.egg-info
svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/tags/v0_99_0/matpl... python setup.py install Writing /usr/lib/python2.6/site-packages/matplotlib-0.99.0-py2.6.egg-info
install them using
import numpy numpy.__version__ '1.3.1.dev8031'
scipy import is fine but matplotlib fails with a different import error. I wonder if the buildbots test the source and releases for against different numpy versions or it is just might system acting weird.
from scipy import stats
import matplotlib.pyplot as plt Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/pyplot.py", line 6, in <module> from matplotlib.figure import Figure, figaspect File "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/figure.py", line 17, in <module> import artist File "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/artist.py", line 5, in <module> from transforms import Bbox, IdentityTransform, TransformedBbox, TransformedPath File "/home/gsever/Desktop/python-repo/matplotlib/lib/matplotlib/transforms.py", line 34, in <module> from matplotlib._path import affine_transform ImportError: No module named _path
Anyways, back to the main point. First remove the numpy 1.3.x:
[root@ccn site-packages]# rm -rf numpy [root@ccn site-packages]# rm -rf numpy-1.3.1.dev8031-py2.6.egg-info
and install from the latest trunk:
svn co http://svn.scipy.org/svn/numpy/trunk numpy python setup.py install Writing /usr/lib/python2.6/site-packages/numpy-1.5.0.dev8032-py2.6.egg-info
This time scipy asserts:
from scipy import stats
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.6/site-packages/scipy/stats/__init__.py", line 7, in <module> from stats import * File "/usr/lib/python2.6/site-packages/scipy/stats/stats.py", line 203, in <module> from morestats import find_repeats #is only reference to scipy.stats File "/usr/lib/python2.6/site-packages/scipy/stats/morestats.py", line 7, in <module> import distributions File "/usr/lib/python2.6/site-packages/scipy/stats/distributions.py", line 27, in <module> import vonmises_cython File "numpy.pxd", line 30, in scipy.stats.vonmises_cython (scipy/stats/vonmises_cython.c:2939) ValueError: numpy.dtype does not appear to be the correct type object
That is the cython problem. I think they fixed it, but I don't know if that is in the recent release. Chuck