[Biopython-dev] upgrade to python 3.1.2

Wed Oct 27 11:19:13 EDT 2010

Hi Peter,

I did everything from scratch, get biopython with git, than tun those
two commands for
2to3 from README file and at the end I run run_tests.py from Tests folder.

I am sending you log file just to check am I on right track. I will
continue to investigate
errors.

One error is related to numpy module, so I will try to install numpy
for python 3.1.2

Anyway, two test FAIL, test_SeqIO_online and test_Wise

Kind regards

-- 
Dragoslav Zaric

Professional Programmer
MSc Astrophysics
-------------- next part --------------
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_convert ... ok
test_BioSQL ... /home/maiev/work/biopython/BioSQL/Loader.py:799: UserWarning: order location operators are not fully supported
  % feature.location_operator)
ok
test_BioSQL_SeqIO ... /home/maiev/work/biopython/BioSQL/Loader.py:799: UserWarning: bond location operators are not fully supported
  % feature.location_operator)
ok
test_CAPS ... ok
test_Clustalw ... /home/maiev/work/biopython/Bio/Clustalw/__init__.py:83: PendingDeprecationWarning: This function is obsolete, and any new code should call Bio.AlignIO instead.
  warnings.warn("This function is obsolete, and any new code should call Bio.AlignIO instead.", PendingDeprecationWarning)
ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use Bio.Clustalw.
test_Cluster ... skipping. If you want to use Bio.Cluster, install NumPy first and then reinstall Biopython
test_CodonTable ... ok
test_CodonUsage ... ok
test_Compass ... ok
test_Crystal ... ok
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
test_EmbossPrimer ... ok
test_Entrez ... ok
test_Enzyme ... ok
test_FSSP ... ok
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
test_GFF ... skipping. Environment is not configured for this test (not important if you do not plan to use Bio.GFF).
test_GFF2 ... skipping. Install MySQLdb if you want to use Bio.GFF.
test_GenBank ... ok
test_GenomeDiagram ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsBitmaps ... skipping. Install ReportLab if you want to use Bio.Graphics.
test_GraphicsChromosome ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsDistribution ... skipping. Install reportlab if you want to use Bio.Graphics.
test_GraphicsGeneral ... skipping. Install reportlab if you want to use Bio.Graphics.
test_HMMCasino ... ok
test_HMMGeneral ... ok
test_HotRand ... ok
test_IsoelectricPoint ... ok
test_KDTree ... skipping. Install NumPy if you want to use Bio.KDTree.
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LocationParser ... skipping. This deprecated module doesn't work on Python 3.
test_LogisticRegression ... skipping. Install NumPy if you want to use Bio.LogisticRegression.
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
test_MarkovModel ... skipping. Install NumPy if you want to use Bio.MarkovModel.
test_Medline ... ok
test_Motif ... ok
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
test_NCBIStandalone ... /home/maiev/work/biopython/Bio/Blast/NCBIStandalone.py:53: PendingDeprecationWarning: The plain text parser in this module still works at the time of writing, but is considered obsolete and updating it to cope with the latest versions of BLAST is not a priority for us.
  warnings.warn("The plain text parser in this module still works at the time of writing, but is considered obsolete and updating it to cope with the latest versions of BLAST is not a priority for us.", PendingDeprecationWarning)
/home/maiev/work/biopython/Bio/Blast/NCBIStandalone.py:1850: PendingDeprecationWarning: This function is obsolete, you are encouraged to the command line wrapper Bio.Blast.Applications.BlastpgpCommandline instead.
  warnings.warn("This function is obsolete, you are encouraged to the command line wrapper Bio.Blast.Applications.BlastpgpCommandline instead.", PendingDeprecationWarning)
/home/maiev/work/biopython/Bio/Blast/NCBIStandalone.py:1970: PendingDeprecationWarning: This function is obsolete, you are encouraged to the command line wrapper Bio.Blast.Applications.BlastrpsCommandline instead.
  warnings.warn("This function is obsolete, you are encouraged to the command line wrapper Bio.Blast.Applications.BlastrpsCommandline instead.", PendingDeprecationWarning)
ok
test_NCBITextParser ... ok
test_NCBIXML ... ok
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
test_NCBI_qblast ... ok
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_Nexus ... ok
test_PDB ... skipping. Install NumPy if you want to use Bio.PDB.
test_PDB_KDTree ... skipping. Install NumPy if you want to use Bio.PDB.
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_Phylo ... ok
test_PhyloXML ... ok
test_Phylo_depend ... skipping. Install NetworkX if you want to use Bio.Phylo._utils.
test_PopGen_FDist ... skipping. Install FDist if you want to use Bio.PopGen.FDist.
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
test_PopGen_GenePop_nodepend ... ok
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use Bio.PopGen.SimCoal.
test_PopGen_SimCoal_nodepend ... ok
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
test_ProtParam ... ok
test_Restriction ... ok
test_SCOP_Astral ... ok
test_SCOP_Cla ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SVDSuperimposer ... skipping. Install NumPy if you want to use Bio.SVDSuperimposer.
test_SeqIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ok
test_SeqIO_index ... skipping. Skipping since currently this is very slow on Python 3.
test_SeqIO_online ... FAIL
test_SeqRecord ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
test_UniGene ... ok
test_UniGene_obsolete ... ok
test_Wise ... FAIL
test_align ... ok
test_geo ... ok
test_kNN ... ERROR
test_lowess ... skipping. Install NumPy if you want to use Bio.Statistics.lowess.
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... skipping. This deprecated module doesn't work on Python 3.
test_prosite1 ... ok
test_prosite2 ... ok
test_prosite_patterns ... skipping. The (deprecated) Bio.Prosite module uses the Python library sgmllib which is not supported on Python 3
test_psw ... ok
test_seq ... ok
test_translate ... ok
test_trie ... skipping. Could not import Bio.trie, check C code was compiled.
Bio.Alphabet docstring test ... ok
Bio.Application docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Blast.Applications docstring test ... ok
Bio.Clustalw docstring test ... ok
Bio.Emboss.Applications docstring test ... ok
Bio.KEGG.Compound docstring test ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio.Motif docstring test ... ok
======================================================================
ERROR: test_nuccore_X52960 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(nuccore, X52960, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 85, in <lambda>
    method = lambda x : x.simple(d, f, e, l, c)
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 63, in simple
    record = SeqIO.read(handle, f)
  File "/home/maiev/work/biopython/Bio/SeqIO/__init__.py", line 585, in read
    first = next(iterator)
  File "/home/maiev/work/biopython/Bio/SeqIO/FastaIO.py", line 39, in FastaIterator
    if line[0] == ">":
IndexError: index out of range

======================================================================
ERROR: test_nucleotide_6273291 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(nucleotide, 6273291, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 85, in <lambda>
    method = lambda x : x.simple(d, f, e, l, c)
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 63, in simple
    record = SeqIO.read(handle, f)
  File "/home/maiev/work/biopython/Bio/SeqIO/__init__.py", line 585, in read
    first = next(iterator)
  File "/home/maiev/work/biopython/Bio/SeqIO/FastaIO.py", line 39, in FastaIterator
    if line[0] == ">":
IndexError: index out of range

======================================================================
ERROR: test_protein_16130152 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(protein, 16130152, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 85, in <lambda>
    method = lambda x : x.simple(d, f, e, l, c)
  File "/home/maiev/work/biopython/Tests/test_SeqIO_online.py", line 63, in simple
    record = SeqIO.read(handle, f)
  File "/home/maiev/work/biopython/Bio/SeqIO/__init__.py", line 585, in read
    first = next(iterator)
  File "/home/maiev/work/biopython/Bio/SeqIO/FastaIO.py", line 39, in FastaIterator
    if line[0] == ">":
IndexError: index out of range

======================================================================
FAIL: test_dnal (test_Wise.TestWiseDryRun)
Call dnal, and do a trivial check on its output.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_Wise.py", line 26, in test_dnal
    self.assertTrue(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
AssertionError: False is not True

======================================================================
FAIL: test_psw (test_Wise.TestWiseDryRun)
Call psw, and do a trivial check on its output.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_Wise.py", line 31, in test_psw
    self.assertTrue(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
AssertionError: False is not True

======================================================================
ERROR: test_kNN
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/maiev/work/biopython/Tests/test_kNN.py", line 12, in <module>
    import numpy
ImportError: No module named numpy

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "run_tests.py", line 289, in runTest
    suite = unittest.TestLoader().loadTestsFromName(name)
  File "/usr/local/lib/python3.1/unittest.py", line 1266, in loadTestsFromName
    module = __import__('.'.join(parts_copy))
  File "/home/maiev/work/biopython/Tests/test_kNN.py", line 15, in <module>
    raise MissingPythonDependencyError(
NameError: name 'MissingPythonDependencyError' is not defined
----------------------------------------------------------------------
Ran 140 tests in 478.298 seconds

FAILED (failures = 3)