[Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri May 4 09:20:31 UTC 2007


------- Comment #13 from mdehoon at ims.u-tokyo.ac.jp  2007-05-04 05:20 EST -------

I found one Linux system on which test_Cluster.py hangs in the call to kmedoids
instead of the call to kcluster. It turned out that this was due to a
floating-point comparison in the kmedoids function. Since the same comparison
occurs in the kcluster function, this may very well be the reason
test_Cluster.py hangs on your platform in the call to kcluster. The comparison
involves two floating-point variables which are bit-wise identical to each
other. However, variable1 <= variable2 returns False.

Could you have a look at line 2071 in Bio/Cluster/cluster.c (Biopython release
1.43) and print out the two variables "total" and "previous"? (You may find
that test_Cluster.py no longer hangs when you add the printf statement; at
least that is what happened with the call to kmedoids). If total and previous
have the same value, but total>=previous returns False, then that would explain
why the call to kcluster hangs.

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