[Biopython-dev] Failed tests.

[Gavin E. Crooks]

I have just installed biopython using the latest code in CVS. A whole bunch of
tests fail. Are these my problem's, or biopython's?


Gavin Crooks
gec at compbio.berkeley.edu
http://threeplusone.com

=====================================================================
ERROR: test_KEGG
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Traceback (most recent call last):
  File "./run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "./test_KEGG.py", line 8, in ?
    from Bio.KEGG import Map
ImportError: cannot import name Map
======================================================================
ERROR: test_Pathway
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Traceback (most recent call last):
  File "./run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "./test_Pathway.py", line 10, in ?
    from Bio.Pathway import *
ImportError: No module named Pathway
======================================================================
ERROR: test_intelligenetics
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Traceback (most recent call last):
  File "./run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "./test_intelligenetics.py", line 29, in ?
    src_handle = open( datafile )
IOError: [Errno 2] No such file or directory: 'IntelliGenetics/TAT_mase_nuc.txt'======================================================================
ERROR: test_metatool
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Traceback (most recent call last):
  File "./run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "./test_metatool.py", line 29, in ?
    src_handle = open( datafile )
IOError: [Errno 2] No such file or directory: 'MetaTool/meta.out'
======================================================================
FAIL: test_GenBank
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Traceback (most recent call last):
  File "./run_tests.py", line 153, in runTest
    expected_handle)
  File "./run_tests.py", line 247, in compare_output
    assert expected_line == output_line, \
AssertionError:
Output  : "keys: ['L31939', 'AJ237582', 'X62281', 'AF297471', 'M81224', 'X55053']\n"
Expected: "keys: ['X55053', 'M81224', 'AF297471', 'X62281', 'L31939', 'AJ237582']\n"
======================================================================
FAIL: test_SubsMat
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Traceback (most recent call last):
  File "./run_tests.py", line 153, in runTest
    expected_handle)
  File "./run_tests.py", line 247, in compare_output
    assert expected_line == output_line, \
AssertionError:
Output  : 'M -0.0 0.4 0.7 0.8 1.0\n'
Expected: 'M 0.0 0.4 0.7 0.8 1.0\n'
----------------------------------------------------------------------
Ran 31 tests in 71.317s