[Biopython-dev] [Bug 2589] New: Errors in running tests in 1.48

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2589

           Summary: Errors in running tests in 1.48
           Product: Biopython
           Version: 1.48
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


I downloaded BioPython 1.48 on x64 Linux fedora rawhide (kernel
2.6.27-0.329.rc6.git2.fc10.x86_64)
$python setup.py build
$python setup.py test

The test that fails is:

ERROR: test_MarkovModel
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 152, in runTest
    self.runSafeTest()
  File "run_tests.py", line 165, in runSafeTest
    cur_test = __import__(self.test_name)
  File "test_MarkovModel.py", line 61, in <module>
    p_emission=p_emission
  File
"/home/bsouthey/bioinfo/biopython-1.48/build/lib.linux-x86_64-2.5/Bio/MarkovModel.py",
line 199, in _baum_welch
    lpseudo_initial, lpseudo_transition, lpseudo_emission,)
  File
"/home/bsouthey/bioinfo/biopython-1.48/build/lib.linux-x86_64-2.5/Bio/MarkovModel.py",
line 255, in _baum_welch_one
    lp_initial[:] = lp_arcout_t[:,0]
ValueError: matrices are not aligned for copy

Also these two errors with no explanation because Fdist and SimCoal are not
included as required or optional software. Should be added to the list.
test_PopGen_FDist ... skipping. Fdist not found (not a problem if you do not
intend to use it). 
test_PopGen_SimCoal ... skipping. SimCoal not found (not a problem if you do
not intend to use it).

No explanation of what this is:
test_GFF ... skipping. Environment is not configured for this test (not
important if you do not plan to use Bio.GFF).

I know these ones because MySQL is not installed but this test should be
cleaner especially since this is involves optional software:
test_BioSQL ... skipping.
test_BioSQL_SeqIO ... skipping.


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