Your message dated Thu, 19 May 2016 16:29:20 +0000
with message-id <e1b3qp6-0002in...@franck.debian.org>
and subject line Bug#824048: fixed in python-biopython 1.66+dfsg-3
has caused the Debian Bug report #824048,
regarding python-biopython: FTBFS: AssertionError: 10 != 1
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
824048: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824048
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: python-biopython
Version: 1.66+dfsg-2
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@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
`. `'` la...@debian.org / chris-lamb.co.uk
`-
python-biopython.1.66+dfsg-2.unstable.amd64.log.txt.gz
Description: Binary data
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.66+dfsg-3
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 824...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated python-biopython package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 19 May 2016 16:48:15 +0200
Source: python-biopython
Binary: python-biopython python3-biopython python-biopython-doc
python-biopython-sql python3-biopython-sql
Architecture: source amd64 all
Version: 1.66+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
python-biopython - Python library for bioinformatics (implemented in Python 2)
python-biopython-doc - Documentation for the Biopython library
python-biopython-sql - Biopython support for the BioSQL database schema
(Python 2)
python3-biopython - Python library for bioinformatics (implemented in Python 3)
python3-biopython-sql - Biopython support for the BioSQL database schema
(Python 3)
Closes: 824048
Changes:
python-biopython (1.66+dfsg-3) unstable; urgency=medium
.
* Apply fix from upstream for test case dealing with new blastp output format
Closes: #824048
* cme fix dpkg-control
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python-biopython-dbgsym_1.66+dfsg-3_amd64.deb
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python-biopython-doc_1.66+dfsg-3_all.deb
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python3-biopython_1.66+dfsg-3_amd64.deb
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