[Biopython-dev] test_SVDSuperimposer.py

[Peter Cock]

On Mon, Sep 8, 2008 at 1:11 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Try if the eigenvalues function in Numerical Python works. If it hangs, you'll know the problem is in Numerical Python.

Good thinking - it does indeed hang on the machine in question,

$ python
Python 2.5 (r25:51908, Nov 23 2006, 18:40:28)
[GCC 4.1.1 20061011 (Red Hat 4.1.1-30)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Numeric, LinearAlgebra
>>> Numeric.__version__
'24.2'
>>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]])
>>> LinearAlgebra.eigenvalues(data)
[hangs here]

This works fine on another Linux box,

$ python
Python 2.4.3 (#1, Jun 27 2006, 16:32:39)
[GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Numeric, LinearAlgebra
>>> Numeric.__version__
'24.2'
>>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]])
>>> LinearAlgebra.eigenvalues(data)
array([  1.61168440e+01,  -1.11684397e+00,  -1.30367773e-15])

And this example also works on the Mac:

$ python
Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53)
[GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import Numeric, LinearAlgebra
>>> Numeric.__version__
'24.2'
>>> data = Numeric.array([[1,2,3],[4,5,6],[7,8,9]])
>>> LinearAlgebra.eigenvalues(data)
array([  1.61168440e+01,  -1.11684397e+00,  -1.30367773e-15])

So we can probably rule out a problem with Biopython in
test_SVDSuperimposer.py which is good, but I should probably try and
work out what is wrong with Numeric on this particular machine...

Thanks for your advice,

Peter