[Biopython-dev] [Bug 2880] New: Two unit tests issues in 1.51b (t-coffee and mafft)
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Fri Jul 17 13:12:09 UTC 2009
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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