[Biopython-dev] [Bug 2880] New: Two unit tests issues in 1.51b (t-coffee and mafft)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2880

           Summary: Two unit tests issues in 1.51b (t-coffee and mafft)
           Product: Biopython
           Version: 1.51b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


biopython-1.51b # 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 ... ok
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 ... /usr/lib/python2.6/site-packages/MySQLdb/__init__.py:34:
DeprecationWarning: the sets module is deprecated
  from sets import ImmutableSet
ok
test_Emboss ... ok
test_EmbossPrimer ... ok
test_Entrez ... ok
test_Enzyme ... ok
test_FSSP ... ok
test_Fasta ... ok
test_Fasta2 ... 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 ...
/var/tmp/portage/sci-biology/biopython-1.51b/work/biopython-1.51b/build/lib.linux-i686-2.6/Bio/Translate.py:23:
DeprecationWarning: Bio.Translate and Bio.Transcribe are deprecated, and will
be removed in a future release of Biopython. Please use the functions or object
methods defined in Bio.Seq instead (described in the tutorial). If you want to
continue to use this code, please get in contact with the Biopython developers
via the mailing lists to avoid its permanent removal from Biopython.
  DeprecationWarning)
ok
test_GenBank ... ok
test_GenomeDiagram ... 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 ... ok
test_LogisticRegression ... ok
test_MEME ... ok
test_Mafft_tool ... FAIL
test_MarkovModel ... ok
test_Medline ... ok
test_Motif ... ok
test_Muscle_tool ... ok
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 ... ok
test_PDB_unit ... ok
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 ... ok
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_features ... ok
test_SeqIO_online ... ok
test_SeqUtils ... ok
test_Seq_objs ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... 


Probably t-coffee is waiting for some data on its stdin.

root      2987  6482  1 11:36 pts/8    00:03:17 python setup.py test
root     20102  2987  0 11:45 pts/8    00:00:00 sh -c { t_coffee; } 2>&1
root     20121 20102  0 11:45 pts/8    00:00:00 t_coffee




Further note that test_Mafft_tool failed as well.

$ mafft
checking nawk
checking gawk
prog=/usr/bin/gawk

---------------------------------------------------------------------

   MAFFT v6.240 (2007/04/04)

        Copyright (c) 2006 Kazutaka Katoh
        NAR 30:3059-3066, NAR 33:511-518
        http://align.bmr.kyushu-u.ac.jp/mafft/software/
---------------------------------------------------------------------


Input file? (fasta format)
@ 
Input file? (fasta format)
@ quit
quit: No such file.


Input file? (fasta format)
@ exit
exit: No such file.


Input file? (fasta format)
@ 
Input file? (fasta format)
@ x
x: No such file.


Input file? (fasta format)
@ ^C
$


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