[Biopython-dev] [Bug 2361] New: Test Suite Failures

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Sep 11 20:00:32 UTC 2007 

http://bugzilla.open-bio.org/show_bug.cgi?id=2361

           Summary: Test Suite Failures
           Product: Biopython
           Version: 1.43
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: sjf4 at u.washington.edu


Your test suite does not seem to function correctly (or your software).  I've
been trying to make several of the tests succeed for days, but have not been
able to.  I've tried many different versions of biopython and the related
modules on RHEL4 and RHEL5.  I finally thought to try the tests on Windows, and
many of the same tests fail there as well.

Many of the failing tests use the mxtexttools module, which you can only obtain
v3.0.0 of now, but the documentation refers to 2.0.x.

If the software works properly, but just the tests fail, I would appreciate you
updating the tests.  As a non-scientist, I have no way to test this software
before I pass it on to my users, so I rely upon test suites like these to
assure some level of functionality before handing it off.

The output of the failed tests is below.

======================================================================
ERROR: test_CodonUsage
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_CodonUsage.py", line 10,
in
 ?
    X.generate_index("./CodonUsage/HighlyExpressedGenes.txt")
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/SeqUtils/
CodonUsage.py", line 74, in generate_index
    self._count_codons(FastaFile)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/SeqUtils/
CodonUsage.py", line 117, in _count_codons
    cur_record = iterator.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__i
nit__.py", line 72, in next
    result = self._iterator.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterPa
rser.py", line 152, in iterateFile
    self.header_parser.parseString(rec)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 356, in parseString
    self._err_handler.fatalError(result)
  File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
l
ine 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 0

======================================================================
ERROR: test_Fasta2
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_Fasta2.py", line 44, in ?
    data = record_parser.parse( src_handle )
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__i
nit__.py", line 100, in parse
    return self.convert_lax(iterator.next())
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterPa
rser.py", line 152, in iterateFile
    self.header_parser.parseString(rec)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 356, in parseString
    self._err_handler.fatalError(result)
  File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
l
ine 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 0

======================================================================
ERROR: test_KEGG
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_KEGG.py", line 67, in ?
    t_KEGG_Enzyme(test_KEGG_Enzyme_files)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_KEGG.py", line 23, in
t_KEG
G_Enzyme
    record = records.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/KEGG/Enzy
me/__init__.py", line 225, in next
    data = self._reader.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Record
Reader.py", line 295, in next
    positions = _find_end_positions(lookahead, self.tagtable)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Record
Reader.py", line 239, in _find_end_positions
    raise ReaderError("invalid format starting with %s" % repr(text[:50]))
ReaderError: invalid format starting with ''

======================================================================
ERROR: test_align
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_align.py", line 129, in ?
    alignment = FastaAlign.parse_file(to_parse, 'PROTEIN')
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/Fas
taAlign.py", line 48, in parse_file
    cur_align = iterator.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Fasta/__i
nit__.py", line 72, in next
    result = self._iterator.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/IterPa
rser.py", line 152, in iterateFile
    self.header_parser.parseString(rec)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 356, in parseString
    self._err_handler.fatalError(result)
  File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
l
ine 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 0

======================================================================
ERROR: test_format_registry
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_format_registry.py", line
4
9, in ?
    parser.parseFile(_open('EDD_RAT.dat'))
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 452, in parseFile
    self._err_handler.fatalError(ParserRecordException(
  File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
l
ine 38, in fatalError
    raise exception
ParserRecordException: Traceback (most recent call last):
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 444, in parseFile
    record = reader.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Record
Reader.py", line 295, in next
    positions = _find_end_positions(lookahead, self.tagtable)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Record
Reader.py", line 239, in _find_end_positions
    raise ReaderError("invalid format starting with %s" % repr(text[:50]))
ReaderError: invalid format starting with ''


======================================================================
ERROR: test_geo
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 162, in runSafeTest
    cur_test = __import__(self.test_name)
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_geo.py", line 24, in ?
    record = records.next()
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Geo/__ini
t__.py", line 79, in next
    return self._parser.parse(File.StringHandle(data))
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Geo/__ini
t__.py", line 228, in parse
    self._scanner.feed(handle, self._consumer)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Bio/Geo/__ini
t__.py", line 126, in feed
    self._parser.parseFile(handle)
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 328, in parseFile
    self.parseString(fileobj.read())
  File
"/scratch/sjf4/temp/biopython-1.43/build/lib.linux-i686-2.4/Martel/Parser
.py", line 356, in parseString
    self._err_handler.fatalError(result)
  File "/nfs/gs/software/rhel5/python-2.4.4/lib/python2.4/xml/sax/handler.py",
l
ine 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 1427

======================================================================
FAIL: test_Fasta
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 186, in runSafeTest
    expected_handle)
  File "run_tests.py", line 286, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  : 'Basic operation of the Record Parser. ... ERROR\n'
Expected: 'Basic operation of the Record Parser. ... ok\n'

======================================================================
FAIL: test_GenBankFormat
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 166, in runSafeTest
    cur_test.run_tests([])
  File "/scratch/sjf4/temp/biopython-1.43/Tests/test_GenBankFormat.py", line
588
, in run_tests
    test_list.test()
  File "/scratch/sjf4/temp/biopython-1.43/Tests/martel_support.py", line 51, in 
test
    raise AssertionError, "cannot parse"
AssertionError: cannot parse

======================================================================
FAIL: test_NNGene
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 186, in runSafeTest
    expected_handle)
  File "run_tests.py", line 286, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  : 'Find all motifs in a set of sequences. ... ERROR\n'
Expected: 'Find all motifs in a set of sequences. ... ok\n'

======================================================================
FAIL: test_SCOP_Astral
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 149, in runTest
    self.runSafeTest()
  File "run_tests.py", line 186, in runSafeTest
    expected_handle)
  File "run_tests.py", line 286, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  : 'testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ...
ERROR\
n'
Expected: 'testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ... ok\n'

----------------------------------------------------------------------
Ran 91 tests in 99.339s

FAILED (failures=4, errors=6)


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