[Biopython-dev] RE: problem in using biopython-1.41

Michiel De Hoon mdehoon at c2b2.columbia.edu
Sun Feb 19 12:15:57 EST 2006

Dear Sarosh,

>From the test results, it looks like all of Biopython is working correctly,
except for Bio.Cluster. So if you don't plan on using the clustering
algorithms in Bio.Cluster, you've got nothing to worry about.

I would like to find out though why Bio.Cluster is failing. It may have to do
with the fact that you're on a 64-bits machine; the code has not been tested
there. So I'd like to ask you the following:
a) Which version of Numerical Python are you using?
b) Can you run the following commands and send me the output of step 3:
    1) Install biopython with "python setup.py install"
    2) From the biopython-1.41/Tests directory, run "python -i
    3) From the python prompt, execaute "run_tests("Bio.Cluster")"
This will show you the exact output from the Bio.Cluster tests.

Thanks in advance,


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

-----Original Message-----
From: mailman-bounces at portal.open-bio.org on behalf of Sarosh Fatakia
Sent: Sat 2/18/2006 9:14 PM
To: biopython-dev-owner at biopython.org
Subject: problem in using biopython-1.41
Hi I tried sending my problem to
biopython developers. Hope you can please help,

---------- Forwarded message ----------
From: biopython-dev-owner at portal.open-bio.org <
biopython-dev-owner at portal.open-bio.org>
Date: Feb 18, 2006 7:15 PM
Subject: problem in using biopython-1.41
To: sarosh.fatakia at gmail.com

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---------- Forwarded message ----------
From: "Sarosh Fatakia" <sarosh.fatakia at gmail.com>
To: biopython-dev at biopython.org
Date: Sat, 18 Feb 2006 18:50:58 -0500
Subject: problem in using biopython-1.41
I installed biopython-1.41 on my unix box which is:
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

After following the preliminary steps in
I get an error message for the tests performed as:

python setup.py test  2>&1 |  tee python_setup.py-test.out.txt

The main error message is below and the full diagnostic info is attached as
a txt file.
I hope you can please help figure out the problem since I am a novice python
and want to get into biopython for using it as a research tool asap.

FAIL: test_Cluster
Traceback (most recent call last):
  File "run_tests.py", line 148, in runTest
  File "run_tests.py", line 185, in runSafeTest
  File "run_tests.py", line 285, in compare_output
    assert expected_line == output_line, \
Output  : 'Wrong clustering solution found.\n'
Expected: 'Correct clustering solution found.\n'

Ran 93 tests in 78.138s

Sarosh N. Fatakia

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