[Biopython] Biopython and Snow Leopard

[Kelly F Oakeson]

Peter,
I only ran the setup.py test, but here are the results:
$ python setup.py test
running test
test_Ace ... ok
test_AlignIO ... ok
test_BioSQL ... skipping. Enter your settings in Tests/setup_BioSQL.py  
(not important if you do not plan to use BioSQL).
test_BioSQL_SeqIO ... skipping. Enter your settings in Tests/ 
setup_BioSQL.py (not important if you do not plan to use BioSQL).
test_CAPS ... ok
test_Clustalw ... 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_EmbossPrimer ... ok
test_Entrez ... ok
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_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 ... ok
test_LogisticRegression ... skipping. Install NumPy if you want to use  
Bio.LogisticRegression.
test_MEME ... ok
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 ... ok
test_NCBITextParser ... ok
test_NCBIXML ... ok
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_unit ... skipping. Install NumPy if you want to use Bio.PDB.
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_PopGen_FDist ... skipping. Install FDist if you want to use  
Bio.PopGen.FDist.
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... 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_features ... ok
test_SeqIO_online ... 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 ... skipping. Install NumPy if you want to use Bio.kNN.
test_lowess ... skipping. Install NumPy if you want to use  
Bio.Statistics.lowess.
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... 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.Seq docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application 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
----------------------------------------------------------------------
Ran 124 tests in 62.858 seconds


On Sep 9, 2009, at 10:21 AM, Peter wrote:

> On Wed, Sep 9, 2009 at 5:16 PM, Kelly F  
> Oakeson<kelly.oakeson at utah.edu> wrote:
>> Peter,
>> It looks like I may have solved it! Taking the advice from the post  
>> on
>> http://mtrichardson.com/2009/09/fixing-jinja2-and-pycrypto-and-probably-others-on-snow-leopard/
>> I changed the makefile in /Library/Frameworks/Python.framework/
>> Versions/2.6/lib/python2.6/config/Makefile replacing all of the
>> occurrences of 10.4u with 10.6.
>> I then ran
>> $python setup.py build
>> $python setup.py test
>> $sudo python setup.py install
>>
>> Everything worked just fine without any gcc errors. This worked on
>> both my MacBook pro and MacPro both running the 64 bit kernel.
>
> That's great, but doesn't seem like a "proper" solution for us in
> the long run. Did you run the Biopython unit tests? It would be
> good to know they are all fine.
>
> Peter