[Reproducible-builds] Bug#824048: python-biopython: FTBFS: AssertionError: 10 != 1

Chris Lamb lamby at debian.org
Wed May 11 16:35:27 UTC 2016


Source: python-biopython
Version: 1.66+dfsg-2
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

python-biopython fails to build from source in unstable/amd64:

  [..]

                               cp -a Doc/Tutorial.tex /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/Tutorial /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/examples /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Tests /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build; \
                               cd /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
                               env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline
  test_Ace ... ok
  test_AlignIO ... ok
  test_AlignIO_ClustalIO ... ok
  test_AlignIO_EmbossIO ... ok
  test_AlignIO_FastaIO ... ok
  test_AlignIO_PhylipIO ... ok
  test_AlignIO_convert ... ok
  test_Application ... ok
  test_BWA_tool ... ok
  test_BioSQL_mysql_connector ... skipping. Install mysql.connector if you want to use mysql with BioSQL 
  test_BioSQL_sqlite3 ... ok
  test_CAPS ... ok
  test_CelFile ... ok
  test_Chi2 ... ok
  test_ClustalOmega_tool ... ok
  test_Clustalw_tool ... ok
  test_Cluster ... ok
  test_CodonTable ... ok
  test_CodonUsage ... ok
  test_ColorSpiral ... ok
  test_Compass ... ok
  test_Consensus ... ok
  test_Crystal ... ok
  test_DSSP_tool ... ok
  test_Dialign_tool ... ok
  test_DocSQL ... ok
  test_EMBL_unittest ... ok
  test_Emboss ... ok
  test_EmbossPrimer ... ok
  test_Entrez ... ok
  test_Entrez_online ... skipping. internet not available
  test_Enzyme ... ok
  test_FSSP ... ok
  test_Fasttree_tool ... 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_GenBank_unittest ... ok
  test_GenomeDiagram ... ok
  test_GraphicsBitmaps ... ok
  test_GraphicsChromosome ... ok
  test_GraphicsDistribution ... ok
  test_GraphicsGeneral ... ok
  test_HMMCasino ... ok
  test_HMMGeneral ... ok
  test_KDTree ... ok
  test_KEGG ... ok
  test_KEGG_online ... skipping. internet not available
  test_KGML_graphics ... ok
  test_KGML_graphics_online ... skipping. internet not available
  test_KGML_nographics ... ok
  test_KeyWList ... ok
  test_Location ... ok
  test_LogisticRegression ... ok
  test_MMCIF ... ok
  test_Mafft_tool ... ok
  test_MarkovModel ... ok
  test_Medline ... ok
  test_Motif ... ok
  test_Muscle_tool ... ok
  test_NCBITextParser ... ok
  test_NCBIXML ... ok
  test_NCBI_BLAST_tools ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py:280: UserWarning: NCBI BLAST+ deltablast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round)
    ",".join(sorted(missing))))
  /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py:280: UserWarning: NCBI BLAST+ psiblast and Biopython out sync. Please update Biopython, or report this issue if you are already using the latest version. (Extra args: ; Missing: -save_each_pssm,-save_pssm_after_last_round)
    ",".join(sorted(missing))))
  FAIL
  test_NCBI_qblast ... skipping. internet not available
  test_NNExclusiveOr ... ok
  test_NNGene ... ok
  test_NNGeneral ... ok
  test_Nexus ... ok
  test_PAML_baseml ... ok
  test_PAML_codeml ... ok
  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_CDAO ... ok
  test_Phylo_NeXML ... ok
  test_Phylo_depend ... /usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
    warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
  ok
  test_PopGen_FDist_nodepend ... ok
  test_PopGen_FastSimCoal ... skipping. Install fastsimcoal if you want to use Bio.PopGen.SimCoal.Controller.FastSimCoalController.
  test_PopGen_GenePop_nodepend ... ok
  test_PopGen_SimCoal_nodepend ... ok
  test_Prank_tool ... ok
  test_Probcons_tool ... ok
  test_ProtParam ... ok
  test_QCPSuperimposer ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/PDB/QCPSuperimposer/__init__.py:22: BiopythonExperimentalWarning: Bio.PDB.QCPSuperimposer is an experimental submodule which may undergo significant changes prior to its future official release.
    BiopythonExperimentalWarning)
  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_SCOP_online ... skipping. internet not available
  test_SVDSuperimposer ... ok
  test_SearchIO_blast_tab ... ok
  test_SearchIO_blast_tab_index ... ok
  test_SearchIO_blast_text ... ok
  test_SearchIO_blast_xml ... ok
  test_SearchIO_blast_xml_index ... ok
  test_SearchIO_blat_psl ... ok
  test_SearchIO_blat_psl_index ... ok
  test_SearchIO_exonerate ... ok
  test_SearchIO_exonerate_text_index ... ok
  test_SearchIO_exonerate_vulgar_index ... ok
  test_SearchIO_fasta_m10 ... ok
  test_SearchIO_fasta_m10_index ... ok
  test_SearchIO_hmmer2_text ... ok
  test_SearchIO_hmmer2_text_index ... ok
  test_SearchIO_hmmer3_domtab ... ok
  test_SearchIO_hmmer3_domtab_index ... ok
  test_SearchIO_hmmer3_tab ... ok
  test_SearchIO_hmmer3_tab_index ... ok
  test_SearchIO_hmmer3_text ... ok
  test_SearchIO_hmmer3_text_index ... ok
  test_SearchIO_model ... ok
  test_SearchIO_write ... ok
  test_SeqIO ... ok
  test_SeqIO_AbiIO ... ok
  test_SeqIO_FastaIO ... ok
  test_SeqIO_Insdc ... ok
  test_SeqIO_PdbIO ... ok
  test_SeqIO_QualityIO ... ok
  test_SeqIO_SeqXML ... ok
  test_SeqIO_convert ... ok
  test_SeqIO_features ... ok
  test_SeqIO_index ... ok
  test_SeqIO_online ... skipping. internet not available
  test_SeqIO_write ... ok
  test_SeqRecord ... ok
  test_SeqUtils ... ok
  test_Seq_objs ... ok
  test_SffIO ... ok
  test_SubsMat ... ok
  test_SwissProt ... ok
  test_TCoffee_tool ... ok
  test_TogoWS ... skipping. internet not available
  test_TreeConstruction ... ok
  test_Tutorial ... ok
  test_UniGene ... ok
  test_Uniprot ... ok
  test_Wise ... ok
  test_align ... ok
  test_bgzf ... ok
  test_codonalign ... ok
  test_geo ... ok
  test_kNN ... ok
  test_lowess ... ok
  test_motifs ... ok
  test_motifs_online ... skipping. internet not available
  test_pairwise2 ... ok
  test_prodoc ... ok
  test_prosite1 ... ok
  test_prosite2 ... ok
  test_psw ... ok
  test_py3k ... ok
  test_raxml_tool ... ok
  test_seq ... ok
  test_translate ... ok
  test_trie ... ok
  Bio.Align docstring test ... ok
  Bio.Align.Generic docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Align/Generic.py:55: 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
  Bio.Align.Applications._Clustalw docstring test ... ok
  Bio.Align.Applications._ClustalOmega docstring test ... ok
  Bio.Align.Applications._MSAProbs 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.Alphabet docstring test ... ok
  Bio.Application docstring test ... ok
  Bio.bgzf docstring test ... ok
  Bio.codonalign docstring test ... ok
  Bio.Blast.Applications docstring test ... ok
  Bio.Emboss.Applications docstring test ... ok
  Bio.GenBank docstring test ... ok
  Bio.KEGG.Compound docstring test ... ok
  Bio.KEGG.Enzyme docstring test ... ok
  Bio.NMR.xpktools docstring test ... ok
  Bio.Motif docstring test ... ok
  Bio.motifs docstring test ... ok
  Bio.motifs.applications._alignace docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications/_alignace.py:54: BiopythonDeprecationWarning: The AlignACE application wrapper is deprecated and
                        is likely to be removed in a future release of Biopython,
                        since an up to date version of the AlignACE software
                        cannot be obtained anymore. If you have a copy of
                        AlignACE 4, please consider contacting the Biopython
                        developers.
    developers.""", BiopythonDeprecationWarning)
  /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/motifs/applications/_alignace.py:122: BiopythonDeprecationWarning: The CompareACE application wrapper is deprecated and
                        is likely to be removed in a future release of Biopython,
                        since an up to date version of the AlignACE software
                        cannot be obtained anymore. If you have a copy of
                        AlignACE 4, please consider contacting the Biopython
                        developers.
    developers.""", BiopythonDeprecationWarning)
  ok
  Bio.motifs.applications._xxmotif docstring test ... ok
  Bio.pairwise2 docstring test ... ok
  Bio.Phylo.Applications._Raxml docstring test ... ok
  Bio.SearchIO docstring test ... ok
  Bio.SearchIO._model docstring test ... ok
  Bio.SearchIO._model.query docstring test ... ok
  Bio.SearchIO._model.hit docstring test ... ok
  Bio.SearchIO._model.hsp docstring test ... ok
  Bio.SearchIO.BlastIO docstring test ... ok
  Bio.SearchIO.HmmerIO docstring test ... ok
  Bio.SearchIO.FastaIO docstring test ... ok
  Bio.SearchIO.BlatIO docstring test ... ok
  Bio.SearchIO.ExonerateIO docstring test ... ok
  Bio.Seq docstring test ... ok
  Bio.SeqIO docstring test ... ok
  Bio.SeqIO.FastaIO 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.SeqFeature docstring test ... ok
  Bio.SeqRecord docstring test ... ok
  Bio.SeqUtils docstring test ... /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/SeqUtils/__init__.py:560: BiopythonDeprecationWarning: The quick_FASTA_reader has been deprecated and will be removed in a future release of Biopython. Please try function SimpleFastaParser from Bio.SeqIO.FastaIO instead.
    "instead.", BiopythonDeprecationWarning)
  ok
  Bio.SeqUtils.MeltingTemp docstring test ... ok
  Bio.Sequencing.Applications._Novoalign docstring test ... ok
  Bio.Sequencing.Applications._bwa docstring test ... ok
  Bio.Sequencing.Applications._samtools docstring test ... ok
  Bio.Wise docstring test ... ok
  Bio.Wise.psw docstring test ... ok
  Bio.Affy.CelFile docstring test ... ok
  Bio.Statistics.lowess docstring test ... ok
  Bio.PDB.Polypeptide docstring test ... ok
  Bio.PDB.Selection docstring test ... ok
  ======================================================================
  FAIL: test_blastp (test_NCBI_BLAST_tools.Pairwise)
  Pairwise BLASTP search
  ----------------------------------------------------------------------
  Traceback (most recent call last):
    File "/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_NCBI_BLAST_tools.py", line 103, in test_blastp
      self.assertEqual(10, stdoutdata.count("Query= "))
  AssertionError: 10 != 1
  
  ----------------------------------------------------------------------
  Ran 228 tests in 101.627 seconds
  
  FAILED (failures = 1)
  Skipping any tests requiring internet access
  Python version: 2.7.11+ (default, May  9 2016, 15:54:33) 
  [GCC 5.3.1 20160429]
  Operating system: posix linux2
  E: pybuild pybuild:274: test: plugin custom failed with: exit code=1: set -e; \
                               mkdir -p /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home; \
                               mkdir -p /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc/examples; \
                               cp -a Doc/Tutorial.tex /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/Tutorial /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Doc/examples /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Doc; \
                               cp -a Tests /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build; \
                               cd /home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/Tests; \
                               env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg/.pybuild/pythonX.Y_2.7/build/home python2.7 run_tests.py --offline
  dh_auto_test: pybuild --test -i python{version} -p 2.7 --test --system=custom --test-args=set -e; \
                               mkdir -p {build_dir}/home; \
                               mkdir -p {build_dir}/Doc/examples; \
                               cp -a Doc/Tutorial.tex {build_dir}/Doc; \
                               cp -a Doc/Tutorial {build_dir}/Doc; \
                               cp -a Doc/examples {build_dir}/Doc; \
                               cp -a Tests {build_dir}; \
                               cd {build_dir}/Tests; \
                               env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} run_tests.py --offline --dir . returned exit code 13
  debian/rules:69: recipe for target 'override_dh_auto_test' failed
  make[1]: *** [override_dh_auto_test] Error 25
  make[1]: Leaving directory '/home/lamby/temp/cdt.20160511172943.3m3eRDBdi6.python-biopython/python-biopython-1.66+dfsg'
  debian/rules:51: recipe for target 'build' failed
  make: *** [build] Error 2

  [..]

The full build log is attached.


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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