Package manager version: 0.32.99.git
Distribution version: selfupdate-cvs Tue Mar 6 09:18:52 2012, 10.7, x86_64
Trees: local/main stable/main local/injected
Xcode: 4.3
Max. Fink build jobs: 4
I happened to be building in maintainer mode and found the following:
...
pushd Tests
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58
/sw/bin/python2.7 ./run_tests.py || exit 2
Python version: 2.7.2 (default, Feb 27 2012, 00:06:38)
[GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.45)]
Operating system: posix darwin
test_Ace ... ok
test_AlignIO ... ok
test_AlignIO_FastaIO ... ok
test_AlignIO_convert ... ok
test_BioSQL ...
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/BioSQL/Loader.py:799:
UserWarning: order location operators are not fully supported
% feature.location_operator)
ok
test_BioSQL_SeqIO ...
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/BioSQL/Loader.py:799:
UserWarning: bond location operators are not fully supported
% feature.location_operator)
ok
test_CAPS ... ok
test_Chi2 ... ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you
want to use it from Biopython.
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 ... ok
test_Enzyme ... ok
test_FSSP ...
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/Bio/Align/Generic.py:54:
BiopythonDeprecationWarning: With the introduction of the
MultipleSeqAlignment class in Bio.Align, this base class is deprecated
and is likely to be removed in a future release of Biopython.
warnings.warn("With the introduction of the MultipleSeqAlignment
class in Bio.Align, this base class is deprecated and is likely to be
removed in a future release of Biopython.",
Bio.BiopythonDeprecationWarning)
ok
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
test_GenBank ... ok
test_GenomeDiagram ... ok
test_GraphicsBitmaps ... ok
test_GraphicsChromosome ... ok
test_GraphicsDistribution ... ok
test_GraphicsGeneral ... ok
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 ...
/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/Bio/Parsers/__init__.py:11:
BiopythonDeprecationWarning: Bio.Parsers (including our copy of SPARK)
and the only part of Biopython which used it,
Bio.GenBank.LocationParser, are now deprecated and will be removed in
a future release of Biopython. If you want to continue to use any of
this code, please get in contact with the Biopython developers via the
mailing lists to avoid its permanent removal from Biopython.
"Biopython.", Bio.BiopythonDeprecationWarning)
ok
test_LogisticRegression ... 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_PAML_baseml ... ok
test_PAML_codeml ... ok
test_PAML_tools ... skipping. Install PAML if you want to use the
Bio.Phylo.PAML wrapper.
test_PAML_yn00 ... ok
test_PDB ... ok
test_PDB_KDTree ... 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_DFDist ... skipping. Install Dfdist, Ddatacal, pv2 and
cplot2 if you want to use DFDist with Bio.PopGen.FDist.
test_PopGen_FDist ... skipping. Install fdist2, datacal, pv and cplot
if you want to use FDist2 with 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_AbiIO ... ok
test_SeqIO_FastaIO ... ok
test_SeqIO_QualityIO ... ok
test_SeqIO_SeqXML ... ok
test_SeqIO_convert ... ok
test_SeqIO_features ... ok
test_SeqIO_index ... ok
test_SeqIO_online ... FAIL
test_SeqIO_write ... 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_Tutorial ... ok
test_UniGene ... ok
test_UniGene_obsolete ... ok
test_Uniprot ... ok
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_align ... ok
test_geo ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_prosite1 ... ok
test_prosite2 ... ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_seq ... ok
test_translate ... ok
test_trie ... ok
Bio.Alphabet docstring test ... 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.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Align docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.Align.Applications._Clustalw docstring test ... ok
Bio.Align.Applications._Mafft docstring test ... ok
Bio.Align.Applications._Muscle docstring test ... ok
Bio.Align.Applications._Probcons docstring test ... ok
Bio.Align.Applications._Prank docstring test ... ok
Bio.Align.Applications._TCoffee docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Blast.Applications 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
Bio.Statistics.lowess docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.Selection docstring test ... ok
======================================================================
ERROR: test_nuccore_X52960 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(nuccore, X52960, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 90, in <lambda>
method = lambda x : x.simple(d, f, e, l, c)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 68, in simple
record = SeqIO.read(handle, f)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/Bio/SeqIO/__init__.py",
line 617, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle
======================================================================
ERROR: test_nucleotide_6273291 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(nucleotide, 6273291, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 90, in <lambda>
method = lambda x : x.simple(d, f, e, l, c)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 68, in simple
record = SeqIO.read(handle, f)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/Bio/SeqIO/__init__.py",
line 617, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle
======================================================================
ERROR: test_protein_16130152 (test_SeqIO_online.EntrezTests)
Bio.Entrez.efetch(protein, 16130152, ...)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 90, in <lambda>
method = lambda x : x.simple(d, f, e, l, c)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_SeqIO_online.py",
line 68, in simple
record = SeqIO.read(handle, f)
File
"/sw/src/fink.build/biopython-py27-1.58-1/biopython-1.58/build/lib.macosx-10.7-x86_64-2.7/Bio/SeqIO/__init__.py",
line 617, in read
raise ValueError("No records found in handle")
ValueError: No records found in handle
----------------------------------------------------------------------
Ran 157 tests in 101.570 seconds
FAILED (failures = 1)
### execution of /tmp/fink.Jb37A failed, exit code 2
--
Alexander K. Hansen
akh AT finkproject DOT org
Fink User Liaison and Documenter
------------------------------------------------------------------------------
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