[Biopython-dev] Re: [BioPython] Patch to fix testing failures in biopython-1.30

[Michiel Jan Laurens de Hoon]

Bill Barnard wrote:
> Finally, the Tests/test_SVDSuperimposer.py test does not appear to
> run correctly. The function itself appears to be broken, as it runs
> for upwards of two hours on my machine (1.8 GHz Athlon XP 2500+) with
> no output. I moved the test to a new Tests/broken directory.
> 
>> Thanks for your patch, Bill. The failed test_SVDSuperimposer may be
>> due to an incorrect compilation of the Lapack libraries on your
>> computer. For example, the default compilation of numerical python on
>> Cygwin and possibly Linux results in a broken Lapack, in which some
>> linear algebra functions hang forever. The SVD code in Biopython uses
>> these functions, so that may be the reason that the test didn't
>> finish.
Bill checked this and it turned out that the failed test was indeed due 
to Lapack problems in Numerical Python. So no need to move the 
test_SVDSuperimposer.py to Tests/broken.

--Michiel.