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

Tue Feb 21 10:50:13 EST 2006

Hi Sarosh,

Thanks for your reply. The problem may be the fact that you're using numarray
instead of Numerical Python. If I remember correctly, numarray has some
facilities to handle large arrays on 64-bits machines. Since Bio.Cluster is
created for Numerical Python, it doesn't know about the numarray-specific
stuff. So the simplest solution may be to install Numerical Python instead of
numarray.

>From your output of "python setup.py install", it appears that even the
compilation of Bio.Cluster failed -- if not all modules that need
compilation: I don't see any of the compiled modules in the install output.
So it looks like something terrible went wrong during "python setup.py
build". Did you get any error messages while running "python setup.py build"?

Finally, there's a typo when you execute 'run_tests("Bio.Cluster")': That
should be Bio.Cluster, not Bio_Cluster.

I think it's best to execute "python setup.py build" again and check if you
get any error messages. Once that works OK, you probably won't get any
testing errors any more. If you do, try again with Numerical Python instead
of numarray. The latest good version of Numerical Python is 24.2.

--Michiel.

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 10:01 AM
To: Michiel De Hoon
Cc: biopython-dev at biopython.org
Subject: Re: problem in using biopython-1.41

Hello Michiel,
Thanks for your response. Hope you can please help resolve the issue.
a) The numpy (numarray) version is:   numarray-1.5.1/
b) I am attaching the outputs you require. I hope there is sufficient info.
Please do let me know if more information is required.
Thanks once again,
best,
sarosh

On 2/19/06, Michiel De Hoon <mdehoon at c2b2.columbia.edu> wrote:
>
> 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
> test_Cluster.py"
>     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.
>
>
>
> 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,
> thanks
> sarosh
>
>
> ---------- 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
>
> You are not allowed to post to this mailing list, and your message has
> been automatically rejected.  If you think that your messages are
> being rejected in error, contact the mailing list owner at
> biopython-dev-owner at biopython.org.
>
>
>
>
> ---------- 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
> Greetings!
> 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
> http://bioinformatics.org/bradstuff/bp/tut/Tutorial001.html
> 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
> user,
> and want to get into biopython for using it as a research tool asap.
> Thanks
> Sarosh,
> NIDDK/NIH
>
>
> ======================================================================
> FAIL: test_Cluster
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "run_tests.py", line 148, in runTest
>     self.runSafeTest()
>   File "run_tests.py", line 185, in runSafeTest
>     expected_handle)
>   File "run_tests.py", line 285, in compare_output
>     assert expected_line == output_line, \
> AssertionError:
> Output  : 'Wrong clustering solution found.\n'
> Expected: 'Correct clustering solution found.\n'
>
> ----------------------------------------------------------------------
> Ran 93 tests in 78.138s
>
>
>
>
>
> --
> Sarosh N. Fatakia
>
http://budoe.bu.edu/~sfatakia/sarosh/sarosh.html<http://budoe.bu.edu/%7Esfata
kia/sarosh/sarosh.html>
>
>
>

--
Sarosh N. Fatakia
http://budoe.bu.edu/~sfatakia/sarosh/sarosh.html<http://budoe.bu.edu/%7Esfata
kia/sarosh/sarosh.html>