[Biopython-dev] Running unit tests on non-English OS

Tue Jun 29 23:27:20 EDT 2010

Peter,
actually the problems with Entrez tools are Unicode related.
I suppose, that the test failures are related with  the current working dir
path: it contains a non-English word in it, thus it can not be represented
as an ascii string.
Also there are similar problems with Genbank to Sql tests.

Please, see the error-log attached.

On Tue, Jun 29, 2010 at 4:57 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Mon, Jun 28, 2010 at 6:55 PM, Konstantin Okonechnikov
> <k.okonechnikov at gmail.com> wrote:
> > Peter,
> > I have built and run the latest code from git on Russian Ubuntu 10.4.
>
> Thank you,
>
> > Entrez tests have failed.
>
> That can happen due to network problems. I'd like to see the error though.
>
> > Muscle, clustal and emboss tests have been skipped successfully.
>
> Good :)
>
> > The tests have been executed from build.py script and I am not sure how
> to
> > generate test report. Redirecting the script output to file didn't help.
>
> I normally just run "python setup.py test" from the source directory or
> "python run_tests.py" from the Tests subdirectory at the terminal, and
> copy and paste the interesting bits of the output.
>
> If you want to capture the test output to a file, you should probably
> redirect
> both stdout and stderr:
>
> python run_tests.py &> output.txt
>
> Regards,
>
> Peter
>

-- 
Best regards,
        Konstantin
-------------- next part --------------
running test
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_convert ... ok
test_BioSQL ... FAIL
test_BioSQL_SeqIO ... /home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/Loader.py:797: UserWarning: order location operators are not fully supported
  % feature.location_operator)
/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/Loader.py:797: UserWarning: bond location operators are not fully supported
  % feature.location_operator)
ok
test_CAPS ... ok
test_Clustalw ... ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use Bio.Clustalw.
test_Cluster ... ok
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 ... FAIL
test_Enzyme ... ok
test_FSSP ... ok
test_Fasta ... 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 ... ok
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LocationParser ... ok
test_LogisticRegression ... ok
test_MEME ... ok
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
test_MarkovModel ... ok
test_Medline ... ok
test_Motif ... ok
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
test_NCBIStandalone ... 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 ... ok
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 ... ok
test_SeqIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ok
test_SeqIO_index ... ok
test_SeqIO_online ... ok
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 ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_align ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite1 ... ok
test_prosite2 ... ok
test_prosite_patterns ... ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_seq ... ok
test_translate ... ok
test_trie ... ok
test_triefind ... ok
Bio.Application docstring test ... ok
Bio.Seq 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 ... FAIL
Bio.Wise.psw docstring test ... ok
Bio.Motif docstring test ... ok
Bio.Statistics.lowess docstring test ... ok
======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, NC_000932.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 423, in test_NC_000932
    self.loop(os.path.join(os.getcwd(), "GenBank", "NC_000932.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, NC_005816.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 419, in test_NC_005816
    self.loop(os.path.join(os.getcwd(), "GenBank", "NC_005816.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, NT_019265.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 427, in test_NT_019265
    self.loop(os.path.join(os.getcwd(), "GenBank", "NT_019265.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, arab1.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 447, in test_arab1
    self.loop(os.path.join(os.getcwd(), "GenBank", "arab1.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, cor6_6.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 443, in test_cor6_6
    self.loop(os.path.join(os.getcwd(), "GenBank", "cor6_6.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, noref.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 435, in test_no_ref
    self.loop(os.path.join(os.getcwd(), "GenBank", "noref.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, one_of.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 439, in test_one_of
    self.loop(os.path.join(os.getcwd(), "GenBank", "one_of.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL and back to a GenBank file, protein_refseq2.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 431, in test_protein_refseq2
    self.loop(os.path.join(os.getcwd(), "GenBank", "protein_refseq2.gb"), "gb")
  File "test_BioSQL.py", line 456, in loop
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, NC_000932.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 496, in test_NC_000932
    self.trans(os.path.join(os.getcwd(), "GenBank", "NC_000932.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, NC_005816.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 492, in test_NC_005816
    self.trans(os.path.join(os.getcwd(), "GenBank", "NC_005816.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, NT_019265.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 500, in test_NT_019265
    self.trans(os.path.join(os.getcwd(), "GenBank", "NT_019265.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, arab1.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 520, in test_arab1
    self.trans(os.path.join(os.getcwd(), "GenBank", "arab1.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, cor6_6.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 516, in test_cor6_6
    self.trans(os.path.join(os.getcwd(), "GenBank", "cor6_6.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, noref.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 508, in test_no_ref
    self.trans(os.path.join(os.getcwd(), "GenBank", "noref.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, one_of.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 512, in test_one_of
    self.trans(os.path.join(os.getcwd(), "GenBank", "one_of.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: GenBank file to BioSQL, then again to a new namespace, protein_refseq2.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_BioSQL.py", line 504, in test_protein_refseq2
    self.trans(os.path.join(os.getcwd(), "GenBank", "protein_refseq2.gb"), "gb")
  File "test_BioSQL.py", line 529, in trans
    db = server.new_database(db_name)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 142, in new_database
    self.adaptor.execute(sql, (db_name,authority, description))
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/BioSeqDatabase.py", line 336, in execute
    self.dbutils.execute(self.cursor, sql, args)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/BioSQL/DBUtils.py", line 45, in execute
    cursor.execute(sql.replace("%s", "?"), args or ())
ProgrammingError: You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings.

======================================================================
ERROR: Test parsing XML returned by EFetch, Journals database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3451, in test_journals
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, Nucleotide database (first test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3893, in test_nucleotide1
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, Protein database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 4045, in test_nucleotide2
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, OMIM database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3607, in test_omim
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, PubMed database (first test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3034, in test_pubmed1
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, PubMed database (second test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3237, in test_pubmed2
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EFetch, Taxonomy database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3784, in test_taxonomy
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML output returned by EGQuery (first test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2706, in test_egquery1
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML output returned by EGQuery (second test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2858, in test_egquery2
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing database list returned by EInfo
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 26, in test_list
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing database info returned by EInfo
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 72, in test_pubmed
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing cancerchromosomes links returned by ELink
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2690, in test_cancerchromosomes
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing medline indexed articles returned by ELink
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 1965, in test_medline
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing Nucleotide to Protein links returned by ELink
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 1239, in test_nucleotide
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed links returned by ELink (first test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 934, in test_pubmed1
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed links returned by ELink (second test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 1253, in test_pubmed2
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed link returned by ELink (third test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2404, in test_pubmed3
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed links returned by ELink (fourth test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2431, in test_pubmed4
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed links returned by ELink (fifth test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2499, in test_pubmed5
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing pubmed links returned by ELink (sixth test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 2669, in test_pubmed6
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EPost
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 535, in test_epost
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EPost with an invalid id (overflow tag)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 553, in test_invalid
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by EPost with incorrect arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 545, in test_wrong
    self.assertRaises(RuntimeError, Entrez.read, handle)
  File "/usr/lib/python2.6/unittest.py", line 336, in failUnlessRaises
    callableObj(*args, **kwargs)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from the Journals database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 322, in test_journals
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch when no items were found
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 502, in test_notfound
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from the Nucleotide database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 444, in test_nucleotide
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from PubMed Central
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 366, in test_pmc
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from the Protein database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 479, in test_protein
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from PubMed (first test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 107, in test_pubmed1
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from PubMed (second test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 136, in test_pubmed2
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESearch from PubMed (third test)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 289, in test_pubmed3
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML output returned by ESpell
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 3013, in test_espell
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the Journals database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 653, in test_journals
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the Nucleotide database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 766, in test_nucleotide
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the Protein database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 727, in test_protein
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from PubMed
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 576, in test_pubmed
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the Structure database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 805, in test_structure
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the Taxonomy database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 855, in test_taxonomy
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary from the UniSTS database
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 895, in test_unists
    record = Entrez.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
ERROR: Test parsing XML returned by ESummary with incorrect arguments
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez.py", line 921, in test_wrong
    self.assertRaises(RuntimeError, Entrez.read, handle)
  File "/usr/lib/python2.6/unittest.py", line 336, in failUnlessRaises
    callableObj(*args, **kwargs)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/__init__.py", line 262, in read
    record = handler.read(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 108, in read
    self.parser.ParseFile(handle)
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Entrez/Parser.py", line 348, in externalEntityRefHandler
    path = os.path.join(self.dtd_dir, filename)
  File "/usr/lib/python2.6/posixpath.py", line 70, in join
    path += '/' + b
UnicodeDecodeError: 'ascii' codec can't decode byte 0xd1 in position 11: ordinal not in range(128)

======================================================================
FAIL: Doctest: Bio.Wise._build_align_cmdline
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.6/doctest.py", line 2152, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for Bio.Wise._build_align_cmdline
  File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Wise/__init__.py", line 23, in _build_align_cmdline

----------------------------------------------------------------------
File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Wise/__init__.py", line 26, in Bio.Wise._build_align_cmdline
Failed example:
    _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/output", kbyte=100000)
Expected:
    'dnal -kbyte 100000 seq1.fna seq2.fna > /tmp/output'
Got:
    'dnal -kbyte 100000 -quiet seq1.fna seq2.fna > /tmp/output'
----------------------------------------------------------------------
File "/home/okko/??????/biopython/build/lib.linux-i686-2.6/Bio/Wise/__init__.py", line 28, in Bio.Wise._build_align_cmdline
Failed example:
    _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/output_aa")
Expected:
    'psw -kbyte 300000 seq1.faa seq2.faa > /tmp/output_aa'
Got:
    'psw -kbyte 300000 -quiet seq1.faa seq2.faa > /tmp/output_aa'

----------------------------------------------------------------------
Ran 144 tests in 192.676 seconds

FAILED (failures = 3)