[Biopython-dev] RE: please help

Michiel De Hoon mdehoon at c2b2.columbia.edu
Wed Feb 22 11:23:25 EST 2006

The reason that test_Cluster fails is that on 64-bits machines, the size of
an int is not equal to the size of a long. Numerical Python integer arrays
are of type long by default, and casting to int causes the data stored in the
arrays to be misinterpreted at the C-level. The fix is more or less
straightforward; I expect to have this fixed within a few days.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032

-----Original Message-----
From: Sarosh Fatakia [mailto:sarosh.fatakia at gmail.com]
Sent: Tue 2/21/2006 7:26 PM
To: Michiel De Hoon; biopython-dev at biopython.org
Subject: please help
Hi folks,
I have been trying all weekend to make the biopython functional. It seems
that more than one
module is non-functional in the 64 bit arch of my machine, viz:
Linux DK12AR4059LNX1 2.6.9-22.0.2.ELsmp #1 SMP Thu Jan 5 17:11:56 EST 2006
x86_64 x86_64 x86_64 GNU/Linux
and the OS is with
Red Hat Enterprise Linux WS release 4.
(Red Hat 3.4.3-9.EL4)
Is there a web page that describes stepwise all the dependant module
intallation which lead to a complete
biopython-1.41 installation.
The python version is: Python 2.3.4
With a partial installation I can only have a limited functionality. The
lone test that fails in the
biopython-1.41 is test_Cluster.py.
Hope you can please help,

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