On Mon, Dec 28, 2009 at 12:15 PM, Gökhan Sever <gokhanse...@gmail.com>wrote:
> > > On Mon, Dec 28, 2009 at 11:16 AM, Gökhan Sever <gokhanse...@gmail.com>wrote: > >> >> >> On Mon, Dec 28, 2009 at 11:07 AM, Robert Kern <robert.k...@gmail.com>wrote: >> >>> On Mon, Dec 28, 2009 at 11:00, Gökhan Sever <gokhanse...@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/matplotlib 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: [r...@ccn site-packages]# rm -rf numpy [r...@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 import matplotlib.pyplot as plt yields same as previous import attempt. I must have caught an old issue. -- Gökhan
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